0s autopkgtest [20:19:59]: starting date and time: 2025-11-15 20:19:59+0000 0s autopkgtest [20:19:59]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:19:59]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0lcb0jz_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:requests --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=requests/2.32.5+dfsg-1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-3.secgroup --name adt-resolute-amd64-python-skbio-20251115-201959-juju-7f2275-prod-proposed-migration-environment-15-32d410d2-3e71-433a-896c-b533b768f639 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-python-skbio-20251115-201959-juju-7f2275-prod-proposed-migration-environment-15-32d410d2-3e71-433a-896c-b533b768f639 from image adt/ubuntu-resolute-amd64-server-20251115.img (UUID defe59a7-3f6c-4c3e-b6a5-c1b00ec74db3)... 48s autopkgtest [20:20:47]: testbed dpkg architecture: amd64 48s autopkgtest [20:20:47]: testbed apt version: 3.1.11 49s autopkgtest [20:20:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s autopkgtest [20:20:48]: testbed release detected to be: None 49s autopkgtest [20:20:48]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 50s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [821 kB] 50s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 50s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [78.5 kB] 50s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 50s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [154 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [115 kB] 50s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3108 B] 50s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 50s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 50s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 50s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [272 kB] 50s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [581 kB] 50s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [17.0 kB] 50s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5984 B] 50s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.9 kB] 50s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [628 B] 52s Fetched 2251 kB in 1s (2999 kB/s) 52s Reading package lists... 53s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 54s Reading package lists... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s python3-requests python3-rpds-py 54s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 420 kB of archives. 54s After this operation, 843 kB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-rpds-py amd64 0.27.1-2ubuntu1 [366 kB] 54s dpkg-preconfigure: unable to re-open stdin: No such file or directory 54s Fetched 420 kB in 0s (0 B/s) 54s (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 ... 83371 files and directories currently installed.) 54s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 54s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 54s Preparing to unpack .../python3-rpds-py_0.27.1-2ubuntu1_amd64.deb ... 55s Unpacking python3-rpds-py (0.27.1-2ubuntu1) over (0.21.0-2ubuntu2) ... 55s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 55s Setting up python3-rpds-py (0.27.1-2ubuntu1) ... 55s autopkgtest [20:20:54]: upgrading testbed (apt dist-upgrade and autopurge) 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s autopkgtest [20:20:57]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 58s autopkgtest [20:20:57]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 60s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-skbio 0.6.2-4build2 (dsc) [2921 B] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-skbio 0.6.2-4build2 (tar) [2204 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-skbio 0.6.2-4build2 (diff) [12.0 kB] 60s gpgv: Signature made Tue Mar 4 14:51:35 2025 UTC 60s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 60s gpgv: Can't check signature: No public key 60s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.6.2-4build2.dsc: no acceptable signature found 60s autopkgtest [20:20:59]: testing package python-skbio version 0.6.2-4build2 60s autopkgtest [20:20:59]: build not needed 61s autopkgtest [20:21:00]: test pybuild-autopkgtest: preparing testbed 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Solving dependencies... 61s The following NEW packages will be installed: 61s architecture-properties autoconf automake autopoint autotools-dev blt 61s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 61s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 61s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 61s fonts-lyx fonts-mathjax fonts-open-sans g++ g++-15 g++-15-x86-64-linux-gnu 61s g++-x86-64-linux-gnu gcc gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu 61s gettext intltool-debian libaec0 libarchive-zip-perl libasan8 libblas3 61s libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev 61s libfile-stripnondeterminism-perl libfontconfig1 libgcc-15-dev libgfortran5 61s libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhwasan0 61s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 61s libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl 61s liblapack3 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libopenjp2-7 61s libpython3-all-dev libpython3-dev libpython3.13-dev libqhull-r8.0 61s libquadmath0 libraqm0 libsharpyuv0 libsimde-dev libssw-dev libssw0 61s libstdc++-15-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 61s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 61s libxss1 libzopfli1 m4 node-fortawesome-fontawesome-free po-debconf 61s pybuild-plugin-autopkgtest python-biom-format-doc python-matplotlib-data 61s python-numpy-doc python-pandas-doc python-scipy-doc python-skbio-doc 61s python3-accessible-pygments python3-alabaster python3-all python3-all-dev 61s python3-asttokens python3-biom-format python3-brotli python3-bs4 61s python3-cachecontrol python3-click python3-contourpy python3-cycler 61s python3-decorator python3-defusedxml python3-dev python3-doc 61s python3-docutils python3-executing python3-fonttools python3-fs python3-h5py 61s python3-h5py-serial python3-hdmedians python3-imagesize python3-iniconfig 61s python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lxml 61s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mpmath 61s python3-msgpack python3-natsort python3-numpy python3-numpy-dev 61s python3-numpydoc python3-pandas python3-pandas-lib python3-parso 61s python3-patsy python3-pil python3-pil.imagetk python3-platformdirs 61s python3-pluggy python3-prompt-toolkit python3-pure-eval 61s python3-pydata-sphinx-theme python3-pytest python3-pytz python3-roman 61s python3-scipy python3-skbio python3-sklearn python3-sklearn-lib 61s python3-snowballstemmer python3-soupsieve python3-sphinx 61s python3-sphinx-copybutton python3-sphinx-design python3-stack-data 61s python3-statsmodels python3-statsmodels-lib python3-sympy 61s python3-threadpoolctl python3-tk python3-traitlets python3-typeshed 61s python3-ufolib2 python3-wcwidth python3-zopfli python3.13-dev python3.13-doc 61s python3.13-tk python3.14-tk sgml-base sphinx-common tk8.6-blt2.5 61s unicode-data x11-common xml-core zlib1g-dev 61s 0 upgraded, 191 newly installed, 0 to remove and 0 not upgraded. 61s Need to get 251 MB of archives. 61s After this operation, 1418 MB of additional disk space will be used. 61s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 61s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 61s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 62s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 architecture-properties amd64 0.2.6 [2210 B] 62s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 62s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 62s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-2 [581 kB] 62s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 62s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 62s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 62s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 62s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 62s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 62s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 62s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 62s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 62s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 62s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 62s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 62s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 62s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1 [685 kB] 62s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 62s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-7ubuntu1 [12.9 MB] 63s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-7ubuntu1 [1026 B] 63s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 63s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 63s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-7ubuntu1 [47.4 kB] 63s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB] 63s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-7ubuntu1 [29.7 kB] 63s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-7ubuntu1 [3071 kB] 63s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-7ubuntu1 [1360 kB] 63s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-7ubuntu1 [2757 kB] 63s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-7ubuntu1 [1210 kB] 63s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-7ubuntu1 [1685 kB] 63s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-7ubuntu1 [153 kB] 63s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-7ubuntu1 [2864 kB] 63s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-7ubuntu1 [25.4 MB] 64s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-7ubuntu1 [524 kB] 64s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 64s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 64s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-7ubuntu1 [2573 kB] 64s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-7ubuntu1 [14.4 MB] 64s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-7ubuntu1 [23.7 kB] 64s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 64s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 64s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 64s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 cython3 amd64 3.1.6+dfsg-1ubuntu1 [3428 kB] 64s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.24.2ubuntu1 [95.7 kB] 64s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-7 [169 kB] 64s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 64s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 64s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [20.5 kB] 64s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1 [5090 B] 64s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 64s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 64s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 64s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 64s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 64s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.24.2ubuntu1 [896 kB] 64s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 6.20250414 [119 kB] 64s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 64s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 64s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 64s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 64s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 64s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-open-sans all 1.11-2 [635 kB] 64s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.4-2 [22.9 kB] 64s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 64s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libexpat1-dev amd64 2.7.3-1 [143 kB] 64s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 64s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 64s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.4-2 [5516 B] 64s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.5+repack-4 [1432 kB] 64s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [59.8 kB] 64s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 64s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 64s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 64s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 64s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 64s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 64s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 64s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 64s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 64s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 64s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 64s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.13-dev amd64 3.13.9-1 [5821 kB] 64s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3-dev amd64 3.13.7-1 [10.8 kB] 64s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3-all-dev amd64 3.13.7-1 [908 B] 64s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 64s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 64s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 64s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsimde-dev all 0.8.2-3 [469 kB] 64s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 64s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 libssw-dev amd64 1.1-15 [23.8 kB] 64s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 64s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 64s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 64s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 64s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 64s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 64s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 64s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-fortawesome-fontawesome-free all 6.7.2+ds1-1 [1653 kB] 64s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 6.20250414 [1746 B] 64s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-biom-format-doc all 2.1.16-1build3 [57.5 kB] 64s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 65s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 python-numpy-doc all 1:2.2.4+ds-1ubuntu1 [5769 kB] 65s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 65s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-pandas-doc all 2.3.3+dfsg-1ubuntu1 [14.1 MB] 65s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-skbio-doc all 0.6.2-4build2 [2342 kB] 65s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-accessible-pygments all 0.0.5-2 [790 kB] 65s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 65s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-dev amd64 3.13.9-1 [508 kB] 65s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dev amd64 3.13.7-1 [26.6 kB] 65s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all-dev amd64 3.13.7-1 [906 B] 65s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-asttokens all 3.0.0-2 [20.5 kB] 65s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py-serial amd64 3.13.0-1ubuntu1 [1184 kB] 65s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py all 3.13.0-1ubuntu1 [8230 B] 65s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 65s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 65s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 65s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 65s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 65s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 66s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biom-format amd64 2.1.16-1build3 [152 kB] 66s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 66s Get:129 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-soupsieve all 2.7-2 [33.6 kB] 66s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-bs4 all 4.13.4-3 [137 kB] 66s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-msgpack amd64 1.0.3-3build5 [114 kB] 66s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cachecontrol all 0.14.3-1 [18.7 kB] 66s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-2 [255 kB] 66s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 66s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-defusedxml all 0.7.1-3 [42.2 kB] 66s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-doc all 3.13.9-1 [14.3 MB] 66s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-doc all 3.13.7-1 [10.8 kB] 66s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman all 5.1-1 [10.6 kB] 66s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 66s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-executing all 2.2.0-0.2 [25.0 kB] 66s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 66s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 66s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 66s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 66s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 66s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 66s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 66s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 66s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 66s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 66s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-hdmedians amd64 0.14.2-6build2 [186 kB] 66s Get:152 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 66s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-1 [6840 B] 66s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-parso all 0.8.5-1 [68.0 kB] 66s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-4 [1554 kB] 66s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 66s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 66s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 66s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 66s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prompt-toolkit all 3.0.52-1 [258 kB] 66s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 66s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 66s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipython all 8.35.0-2 [575 kB] 66s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 66s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 66s Get:166 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 66s Get:167 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 66s Get:168 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 66s Get:169 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 66s Get:170 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-1 [8946 B] 66s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 66s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 67s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-natsort all 8.4.0-1 [34.1 kB] 67s Get:174 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-common all 8.2.3-1ubuntu2 [656 kB] 67s Get:175 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 67s Get:176 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 67s Get:177 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-sphinx all 8.2.3-1ubuntu2 [482 kB] 67s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-numpydoc all 1.9.0-1 [53.2 kB] 67s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-patsy all 1.0.2-1 [179 kB] 67s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 67s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pydata-sphinx-theme all 0.16.1+dfsg-3 [959 kB] 67s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 67s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-statsmodels-lib amd64 0.14.5+dfsg-1ubuntu1 [2615 kB] 67s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-statsmodels all 0.14.5+dfsg-1ubuntu1 [4970 kB] 67s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-skbio amd64 0.6.2-4build2 [1459 kB] 67s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn-lib amd64 1.7.2+dfsg-3ubuntu1 [6361 kB] 67s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 67s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn all 1.7.2+dfsg-3ubuntu1 [2616 kB] 67s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-copybutton all 0.5.2-3 [16.7 kB] 67s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-design all 0.6.1-2 [894 kB] 67s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-scipy-doc all 1.15.3-1ubuntu1 [26.6 kB] 67s Fetched 251 MB in 6s (44.0 MB/s) 67s Selecting previously unselected package python3-numpy-dev:amd64. 67s (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 ... 83372 files and directories currently installed.) 67s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 67s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 67s Selecting previously unselected package libblas3:amd64. 67s Preparing to unpack .../001-libblas3_3.12.1-7_amd64.deb ... 67s Unpacking libblas3:amd64 (3.12.1-7) ... 67s Selecting previously unselected package libgfortran5:amd64. 67s Preparing to unpack .../002-libgfortran5_15.2.0-7ubuntu1_amd64.deb ... 67s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ... 67s Selecting previously unselected package liblapack3:amd64. 67s Preparing to unpack .../003-liblapack3_3.12.1-7_amd64.deb ... 67s Unpacking liblapack3:amd64 (3.12.1-7) ... 67s Selecting previously unselected package python3-numpy. 68s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 68s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 68s Selecting previously unselected package architecture-properties:amd64. 68s Preparing to unpack .../005-architecture-properties_0.2.6_amd64.deb ... 68s Unpacking architecture-properties:amd64 (0.2.6) ... 68s Selecting previously unselected package m4. 68s Preparing to unpack .../006-m4_1.4.20-2_amd64.deb ... 68s Unpacking m4 (1.4.20-2) ... 68s Selecting previously unselected package autoconf. 68s Preparing to unpack .../007-autoconf_2.72-3.1ubuntu1_all.deb ... 68s Unpacking autoconf (2.72-3.1ubuntu1) ... 68s Selecting previously unselected package autotools-dev. 68s Preparing to unpack .../008-autotools-dev_20240727.1_all.deb ... 68s Unpacking autotools-dev (20240727.1) ... 68s Selecting previously unselected package automake. 68s Preparing to unpack .../009-automake_1%3a1.18.1-2_all.deb ... 68s Unpacking automake (1:1.18.1-2) ... 68s Selecting previously unselected package autopoint. 68s Preparing to unpack .../010-autopoint_0.23.2-1_all.deb ... 68s Unpacking autopoint (0.23.2-1) ... 68s Selecting previously unselected package libtcl8.6:amd64. 68s Preparing to unpack .../011-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 68s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 68s Selecting previously unselected package fonts-dejavu-mono. 68s Preparing to unpack .../012-fonts-dejavu-mono_2.37-8_all.deb ... 68s Unpacking fonts-dejavu-mono (2.37-8) ... 68s Selecting previously unselected package fonts-dejavu-core. 68s Preparing to unpack .../013-fonts-dejavu-core_2.37-8_all.deb ... 68s Unpacking fonts-dejavu-core (2.37-8) ... 68s Selecting previously unselected package fontconfig-config. 68s Preparing to unpack .../014-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 68s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 68s Selecting previously unselected package libfontconfig1:amd64. 68s Preparing to unpack .../015-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 68s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 68s Selecting previously unselected package libxrender1:amd64. 68s Preparing to unpack .../016-libxrender1_1%3a0.9.12-1_amd64.deb ... 68s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 68s Selecting previously unselected package libxft2:amd64. 68s Preparing to unpack .../017-libxft2_2.3.6-1build1_amd64.deb ... 68s Unpacking libxft2:amd64 (2.3.6-1build1) ... 68s Selecting previously unselected package x11-common. 68s Preparing to unpack .../018-x11-common_1%3a7.7+24ubuntu1_all.deb ... 68s Unpacking x11-common (1:7.7+24ubuntu1) ... 68s Selecting previously unselected package libxss1:amd64. 68s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_amd64.deb ... 68s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 68s Selecting previously unselected package libtk8.6:amd64. 68s Preparing to unpack .../020-libtk8.6_8.6.17-1_amd64.deb ... 68s Unpacking libtk8.6:amd64 (8.6.17-1) ... 68s Selecting previously unselected package tk8.6-blt2.5. 68s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 68s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 68s Selecting previously unselected package blt. 68s Preparing to unpack .../022-blt_2.5.3+dfsg-8_amd64.deb ... 68s Unpacking blt (2.5.3+dfsg-8) ... 68s Selecting previously unselected package libisl23:amd64. 68s Preparing to unpack .../023-libisl23_0.27-1_amd64.deb ... 68s Unpacking libisl23:amd64 (0.27-1) ... 68s Selecting previously unselected package libmpc3:amd64. 68s Preparing to unpack .../024-libmpc3_1.3.1-2_amd64.deb ... 68s Unpacking libmpc3:amd64 (1.3.1-2) ... 68s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 68s Preparing to unpack .../025-cpp-15-x86-64-linux-gnu_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package cpp-15. 68s Preparing to unpack .../026-cpp-15_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking cpp-15 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package cpp-x86-64-linux-gnu. 68s Preparing to unpack .../027-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 68s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 68s Selecting previously unselected package cpp. 68s Preparing to unpack .../028-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 68s Unpacking cpp (4:15.2.0-4ubuntu1) ... 68s Selecting previously unselected package libcc1-0:amd64. 68s Preparing to unpack .../029-libcc1-0_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libcc1-0:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libgomp1:amd64. 68s Preparing to unpack .../030-libgomp1_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libgomp1:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libitm1:amd64. 68s Preparing to unpack .../031-libitm1_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libitm1:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libasan8:amd64. 68s Preparing to unpack .../032-libasan8_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libasan8:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package liblsan0:amd64. 68s Preparing to unpack .../033-liblsan0_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking liblsan0:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libtsan2:amd64. 68s Preparing to unpack .../034-libtsan2_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libtsan2:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libubsan1:amd64. 68s Preparing to unpack .../035-libubsan1_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libubsan1:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libhwasan0:amd64. 68s Preparing to unpack .../036-libhwasan0_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libhwasan0:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libquadmath0:amd64. 68s Preparing to unpack .../037-libquadmath0_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libquadmath0:amd64 (15.2.0-7ubuntu1) ... 68s Selecting previously unselected package libgcc-15-dev:amd64. 68s Preparing to unpack .../038-libgcc-15-dev_15.2.0-7ubuntu1_amd64.deb ... 68s Unpacking libgcc-15-dev:amd64 (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 69s Preparing to unpack .../039-gcc-15-x86-64-linux-gnu_15.2.0-7ubuntu1_amd64.deb ... 69s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package gcc-15. 69s Preparing to unpack .../040-gcc-15_15.2.0-7ubuntu1_amd64.deb ... 69s Unpacking gcc-15 (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package gcc-x86-64-linux-gnu. 69s Preparing to unpack .../041-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 69s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 69s Selecting previously unselected package gcc. 69s Preparing to unpack .../042-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 69s Unpacking gcc (4:15.2.0-4ubuntu1) ... 69s Selecting previously unselected package libstdc++-15-dev:amd64. 69s Preparing to unpack .../043-libstdc++-15-dev_15.2.0-7ubuntu1_amd64.deb ... 69s Unpacking libstdc++-15-dev:amd64 (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package g++-15-x86-64-linux-gnu. 69s Preparing to unpack .../044-g++-15-x86-64-linux-gnu_15.2.0-7ubuntu1_amd64.deb ... 69s Unpacking g++-15-x86-64-linux-gnu (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package g++-15. 69s Preparing to unpack .../045-g++-15_15.2.0-7ubuntu1_amd64.deb ... 69s Unpacking g++-15 (15.2.0-7ubuntu1) ... 69s Selecting previously unselected package g++-x86-64-linux-gnu. 69s Preparing to unpack .../046-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 69s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 69s Selecting previously unselected package g++. 69s Preparing to unpack .../047-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 69s Unpacking g++ (4:15.2.0-4ubuntu1) ... 69s Selecting previously unselected package build-essential. 69s Preparing to unpack .../048-build-essential_12.12ubuntu1_amd64.deb ... 69s Unpacking build-essential (12.12ubuntu1) ... 69s Selecting previously unselected package cython3. 69s Preparing to unpack .../049-cython3_3.1.6+dfsg-1ubuntu1_amd64.deb ... 69s Unpacking cython3 (3.1.6+dfsg-1ubuntu1) ... 69s Selecting previously unselected package libdebhelper-perl. 69s Preparing to unpack .../050-libdebhelper-perl_13.24.2ubuntu1_all.deb ... 69s Unpacking libdebhelper-perl (13.24.2ubuntu1) ... 69s Selecting previously unselected package libtool. 69s Preparing to unpack .../051-libtool_2.5.4-7_all.deb ... 69s 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dwz. 69s Preparing to unpack .../057-dwz_0.16-2_amd64.deb ... 69s Unpacking dwz (0.16-2) ... 69s Selecting previously unselected package gettext. 69s Preparing to unpack .../058-gettext_0.23.2-1_amd64.deb ... 69s Unpacking gettext (0.23.2-1) ... 69s Selecting previously unselected package intltool-debian. 69s Preparing to unpack .../059-intltool-debian_0.35.0+20060710.6_all.deb ... 69s Unpacking intltool-debian (0.35.0+20060710.6) ... 69s Selecting previously unselected package po-debconf. 69s Preparing to unpack .../060-po-debconf_1.0.21+nmu1_all.deb ... 69s Unpacking po-debconf (1.0.21+nmu1) ... 69s Selecting previously unselected package debhelper. 69s Preparing to unpack .../061-debhelper_13.24.2ubuntu1_all.deb ... 69s Unpacking debhelper (13.24.2ubuntu1) ... 69s Selecting previously unselected package dh-python. 69s Preparing to unpack .../062-dh-python_6.20250414_all.deb ... 69s Unpacking dh-python (6.20250414) ... 69s Selecting previously unselected package sgml-base. 69s 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Selecting previously unselected package libhdf5-310:amd64. 70s Preparing to unpack .../075-libhdf5-310_1.14.5+repack-4_amd64.deb ... 70s Unpacking libhdf5-310:amd64 (1.14.5+repack-4) ... 70s Selecting previously unselected package libhdf5-hl-310:amd64. 70s Preparing to unpack .../076-libhdf5-hl-310_1.14.5+repack-4_amd64.deb ... 70s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-4) ... 70s Selecting previously unselected package libimagequant0:amd64. 70s Preparing to unpack .../077-libimagequant0_2.18.0-1build1_amd64.deb ... 70s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 70s Selecting previously unselected package libjpeg-turbo8:amd64. 70s Preparing to unpack .../078-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 70s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 70s Selecting previously unselected package libjpeg8:amd64. 70s Preparing to unpack .../079-libjpeg8_8c-2ubuntu11_amd64.deb ... 70s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 70s Selecting previously unselected package libjs-jquery. 70s Preparing to unpack .../080-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 70s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 70s Selecting previously unselected package libjs-underscore. 70s Preparing to unpack .../081-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 70s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 70s Selecting previously unselected package libjs-sphinxdoc. 70s Preparing to unpack .../082-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 70s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 70s Selecting previously unselected package libjson-perl. 70s Preparing to unpack .../083-libjson-perl_4.10000-1_all.deb ... 70s Unpacking libjson-perl (4.10000-1) ... 70s Selecting previously unselected package liblcms2-2:amd64. 70s Preparing to unpack .../084-liblcms2-2_2.16-2_amd64.deb ... 70s Unpacking liblcms2-2:amd64 (2.16-2) ... 70s Selecting previously unselected package liblerc4:amd64. 70s Preparing to unpack .../085-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 70s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 70s Selecting previously unselected package liblzf1:amd64. 70s Preparing to unpack .../086-liblzf1_3.6-4_amd64.deb ... 70s Unpacking liblzf1:amd64 (3.6-4) ... 70s Selecting previously unselected package zlib1g-dev:amd64. 70s Preparing to unpack .../087-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_amd64.deb ... 70s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 70s Selecting previously unselected package libpython3.13-dev:amd64. 70s Preparing to unpack .../088-libpython3.13-dev_3.13.9-1_amd64.deb ... 70s Unpacking libpython3.13-dev:amd64 (3.13.9-1) ... 70s Selecting previously unselected package libpython3-dev:amd64. 70s Preparing to unpack .../089-libpython3-dev_3.13.7-1_amd64.deb ... 70s Unpacking libpython3-dev:amd64 (3.13.7-1) ... 70s Selecting previously unselected package libpython3-all-dev:amd64. 70s Preparing to unpack .../090-libpython3-all-dev_3.13.7-1_amd64.deb ... 70s Unpacking libpython3-all-dev:amd64 (3.13.7-1) ... 70s Selecting previously unselected package libqhull-r8.0:amd64. 70s Preparing to unpack .../091-libqhull-r8.0_2020.2-7_amd64.deb ... 70s Unpacking libqhull-r8.0:amd64 (2020.2-7) ... 70s Selecting previously unselected package libraqm0:amd64. 70s Preparing to unpack .../092-libraqm0_0.10.3-1_amd64.deb ... 70s Unpacking libraqm0:amd64 (0.10.3-1) ... 70s Selecting previously unselected package libsharpyuv0:amd64. 70s Preparing to unpack .../093-libsharpyuv0_1.5.0-0.1_amd64.deb ... 70s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 70s Selecting previously unselected package libsimde-dev. 70s Preparing to unpack .../094-libsimde-dev_0.8.2-3_all.deb ... 70s Unpacking libsimde-dev (0.8.2-3) ... 70s Selecting previously unselected package libssw0:amd64. 70s Preparing to unpack .../095-libssw0_1.1-15_amd64.deb ... 70s Unpacking libssw0:amd64 (1.1-15) ... 70s Selecting previously unselected package libssw-dev:amd64. 70s Preparing to unpack .../096-libssw-dev_1.1-15_amd64.deb ... 70s Unpacking libssw-dev:amd64 (1.1-15) ... 70s Selecting previously unselected package libjbig0:amd64. 70s Preparing to unpack .../097-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 70s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 70s Selecting previously unselected package libwebp7:amd64. 70s Preparing to unpack .../098-libwebp7_1.5.0-0.1_amd64.deb ... 70s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 70s Selecting previously unselected package libtiff6:amd64. 70s Preparing to unpack .../099-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 70s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 70s Selecting previously unselected package libwebpdemux2:amd64. 70s Preparing to unpack .../100-libwebpdemux2_1.5.0-0.1_amd64.deb ... 70s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 70s Selecting previously unselected package libwebpmux3:amd64. 70s Preparing to unpack .../101-libwebpmux3_1.5.0-0.1_amd64.deb ... 70s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 70s Selecting previously unselected package libxslt1.1:amd64. 70s Preparing to unpack .../102-libxslt1.1_1.1.43-0.3_amd64.deb ... 70s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 70s Selecting previously unselected package libzopfli1. 70s Preparing to unpack .../103-libzopfli1_1.0.3-3_amd64.deb ... 70s Unpacking libzopfli1 (1.0.3-3) ... 70s Selecting previously unselected package node-fortawesome-fontawesome-free. 70s Preparing to unpack .../104-node-fortawesome-fontawesome-free_6.7.2+ds1-1_all.deb ... 70s Unpacking node-fortawesome-fontawesome-free (6.7.2+ds1-1) ... 70s Selecting previously unselected package pybuild-plugin-autopkgtest. 70s Preparing to unpack .../105-pybuild-plugin-autopkgtest_6.20250414_all.deb ... 70s Unpacking pybuild-plugin-autopkgtest (6.20250414) ... 70s Selecting previously unselected package python-biom-format-doc. 70s Preparing to unpack .../106-python-biom-format-doc_2.1.16-1build3_all.deb ... 70s Unpacking python-biom-format-doc (2.1.16-1build3) ... 70s Selecting previously unselected package python-matplotlib-data. 70s Preparing to unpack .../107-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 70s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 70s Selecting previously unselected package python-numpy-doc. 70s Preparing to unpack .../108-python-numpy-doc_1%3a2.2.4+ds-1ubuntu1_all.deb ... 70s Unpacking python-numpy-doc (1:2.2.4+ds-1ubuntu1) ... 71s Selecting previously unselected package libjs-mathjax. 71s Preparing to unpack .../109-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 71s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 71s Selecting previously unselected package python-pandas-doc. 71s Preparing to unpack .../110-python-pandas-doc_2.3.3+dfsg-1ubuntu1_all.deb ... 71s Unpacking python-pandas-doc (2.3.3+dfsg-1ubuntu1) ... 72s Selecting previously unselected package python-skbio-doc. 72s Preparing to unpack .../111-python-skbio-doc_0.6.2-4build2_all.deb ... 72s Unpacking python-skbio-doc (0.6.2-4build2) ... 72s Selecting previously unselected package python3-accessible-pygments. 72s Preparing to unpack .../112-python3-accessible-pygments_0.0.5-2_all.deb ... 72s Unpacking python3-accessible-pygments (0.0.5-2) ... 72s Selecting previously unselected package python3-all. 72s Preparing to unpack .../113-python3-all_3.13.7-1_amd64.deb ... 72s Unpacking python3-all (3.13.7-1) ... 72s Selecting previously unselected package python3.13-dev. 72s Preparing to unpack .../114-python3.13-dev_3.13.9-1_amd64.deb ... 72s Unpacking python3.13-dev (3.13.9-1) ... 72s Selecting previously unselected package python3-dev. 72s Preparing to unpack .../115-python3-dev_3.13.7-1_amd64.deb ... 72s Unpacking python3-dev (3.13.7-1) ... 72s Selecting previously unselected package python3-all-dev. 72s Preparing to unpack .../116-python3-all-dev_3.13.7-1_amd64.deb ... 72s Unpacking python3-all-dev (3.13.7-1) ... 72s Selecting previously unselected package python3-asttokens. 72s 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Selecting previously unselected package python3-cycler. 73s Preparing to unpack .../133-python3-cycler_0.12.1-2_all.deb ... 73s Unpacking python3-cycler (0.12.1-2) ... 73s Selecting previously unselected package python3-defusedxml. 73s Preparing to unpack .../134-python3-defusedxml_0.7.1-3_all.deb ... 73s Unpacking python3-defusedxml (0.7.1-3) ... 73s Selecting previously unselected package python3.13-doc. 73s Preparing to unpack .../135-python3.13-doc_3.13.9-1_all.deb ... 73s Unpacking python3.13-doc (3.13.9-1) ... 73s Selecting previously unselected package python3-doc. 73s Preparing to unpack .../136-python3-doc_3.13.7-1_all.deb ... 73s Unpacking python3-doc (3.13.7-1) ... 73s Selecting previously unselected package python3-roman. 73s Preparing to unpack .../137-python3-roman_5.1-1_all.deb ... 73s Unpacking python3-roman (5.1-1) ... 73s Selecting previously unselected package python3-docutils. 73s Preparing to unpack .../138-python3-docutils_0.21.2+dfsg-2_all.deb ... 73s Unpacking python3-docutils (0.21.2+dfsg-2) ... 73s Selecting previously unselected package python3-executing. 73s Preparing to unpack .../139-python3-executing_2.2.0-0.2_all.deb ... 73s Unpacking python3-executing (2.2.0-0.2) ... 73s Selecting previously unselected package python3-platformdirs. 73s Preparing to unpack .../140-python3-platformdirs_4.3.7-1_all.deb ... 73s Unpacking python3-platformdirs (4.3.7-1) ... 73s Selecting previously unselected package python3-fs. 73s Preparing to unpack .../141-python3-fs_2.4.16-9ubuntu1_all.deb ... 73s Unpacking python3-fs (2.4.16-9ubuntu1) ... 73s Selecting previously unselected package python3-lxml:amd64. 73s Preparing to unpack .../142-python3-lxml_6.0.2-1_amd64.deb ... 73s Unpacking python3-lxml:amd64 (6.0.2-1) ... 73s Selecting previously unselected package python3-lz4. 73s Preparing to unpack .../143-python3-lz4_4.4.4+dfsg-3_amd64.deb ... 73s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 73s Selecting previously unselected package python3-mpmath. 73s 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up libfile-stripnondeterminism-perl (1.15.0-1) ... 80s Setting up python3-sympy (1.14.0-2) ... 84s Setting up liblapack3:amd64 (3.12.1-7) ... 84s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 84s Setting up gettext (0.23.2-1) ... 84s Setting up libgcc-15-dev:amd64 (15.2.0-7ubuntu1) ... 84s Setting up python3-jedi (0.19.1+ds1-1) ... 84s Setting up libssw-dev:amd64 (1.1-15) ... 84s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 84s Setting up python3-pytest (8.3.5-2) ... 84s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 84s Setting up cpp-15-x86-64-linux-gnu (15.2.0-7ubuntu1) ... 84s Setting up python3-bs4 (4.13.4-3) ... 84s Setting up python3-zopfli (0.4.0-1) ... 84s Setting up intltool-debian (0.35.0+20060710.6) ... 84s Setting up python3-matplotlib-inline (0.1.7-1) ... 85s Setting up gcc-15-x86-64-linux-gnu (15.2.0-7ubuntu1) ... 85s Setting up 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Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 90s Setting up gcc-15 (15.2.0-7ubuntu1) ... 90s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 93s Setting up libpython3-all-dev:amd64 (3.13.7-1) ... 93s Setting up sphinx-common (8.2.3-1ubuntu2) ... 93s Setting up python3-dev (3.13.7-1) ... 93s Setting up python3-h5py (3.13.0-1ubuntu1) ... 93s Setting up python3-sklearn (1.7.2+dfsg-3ubuntu1) ... 94s Setting up python3-statsmodels (0.14.5+dfsg-1ubuntu1) ... 96s Setting up cpp (4:15.2.0-4ubuntu1) ... 96s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 96s Setting up g++-15 (15.2.0-7ubuntu1) ... 96s Setting up python3-all-dev (3.13.7-1) ... 96s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 96s Setting up python3.14-tk (3.14.0-4) ... 96s Setting up libtool (2.5.4-7) ... 96s Setting up blt (2.5.3+dfsg-8) ... 96s Setting up python3-tk:amd64 (3.13.9-1) ... 96s Setting up gcc (4:15.2.0-4ubuntu1) ... 96s Setting up dh-autoreconf (21) ... 96s Setting up python3-biom-format (2.1.16-1build3) ... 96s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 96s Setting up python3-skbio (0.6.2-4build2) ... 97s Setting up g++ (4:15.2.0-4ubuntu1) ... 97s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 97s Setting up build-essential (12.12ubuntu1) ... 97s Setting up debhelper (13.24.2ubuntu1) ... 97s Setting up pybuild-plugin-autopkgtest (6.20250414) ... 97s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 97s Setting up python3-fonttools (4.57.0-2build1) ... 97s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 98s Processing triggers for libc-bin (2.42-2ubuntu2) ... 98s Processing triggers for man-db (2.13.1-1) ... 99s Processing triggers for install-info (7.2-5) ... 100s Processing triggers for sgml-base (1.31+nmu1) ... 100s Setting up docutils-common (0.21.2+dfsg-2) ... 100s Processing triggers for sgml-base (1.31+nmu1) ... 100s Setting up python3-docutils (0.21.2+dfsg-2) ... 100s Setting up python3-sphinx (8.2.3-1ubuntu2) ... 100s Setting up python3-sphinx-copybutton (0.5.2-3) ... 100s Setting up python3-sphinx-design (0.6.1-2) ... 101s Setting up python3-numpydoc (1.9.0-1) ... 101s Setting up python3-pydata-sphinx-theme (0.16.1+dfsg-3) ... 102s autopkgtest [20:21:41]: test pybuild-autopkgtest: pybuild-autopkgtest 102s autopkgtest [20:21:41]: test pybuild-autopkgtest: [----------------------- 102s pybuild-autopkgtest 102s I: pybuild base:311: cd /tmp/autopkgtest.h6DdLt/autopkgtest_tmp/build; python3.13 -m pytest --pyargs skbio 104s ============================= test session starts ============================== 104s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 104s rootdir: /tmp/autopkgtest.h6DdLt/autopkgtest_tmp/build 104s configfile: pyproject.toml 104s plugins: typeguard-4.4.2 104s collected 2793 items 104s 104s alignment/tests/test_pairwise.py ......................... [ 0%] 104s alignment/tests/test_path.py ................. [ 1%] 104s alignment/tests/test_ssw.py ........................... [ 2%] 104s alignment/tests/test_tabular_msa.py .................................... [ 3%] 105s ........................................................................ [ 6%] 105s ........................................................................ [ 8%] 106s ........................................................................ [ 11%] 106s ........................................................................ [ 14%] 106s ........................................................................ [ 16%] 106s ..... [ 16%] 106s diversity/alpha/tests/test_ace.py .. [ 16%] 107s diversity/alpha/tests/test_base.py ............................... [ 18%] 107s diversity/alpha/tests/test_chao1.py ... [ 18%] 107s diversity/alpha/tests/test_gini.py .... [ 18%] 110s diversity/alpha/tests/test_lladser.py ............ [ 18%] 111s diversity/alpha/tests/test_pd.py ................ [ 19%] 111s diversity/beta/tests/test_unifrac.py ............................ [ 20%] 111s diversity/tests/test_block.py ........... [ 20%] 111s diversity/tests/test_driver.py ..................................... [ 21%] 111s diversity/tests/test_util.py ................ [ 22%] 111s embedding/tests/test_embedding.py ................... [ 23%] 111s embedding/tests/test_protein.py .............. [ 23%] 111s io/format/tests/test_base.py ................................ [ 24%] 111s io/format/tests/test_binary_dm.py ......... [ 25%] 111s io/format/tests/test_biom.py ... [ 25%] 111s io/format/tests/test_blast6.py ........... [ 25%] 111s io/format/tests/test_blast7.py .............. [ 26%] 111s io/format/tests/test_clustal.py ............. [ 26%] 111s io/format/tests/test_embed.py ........ [ 26%] 113s io/format/tests/test_embl.py ............................... [ 28%] 113s io/format/tests/test_emptyfile.py .. [ 28%] 118s io/format/tests/test_fasta.py ................ [ 28%] 121s io/format/tests/test_fastq.py ............... [ 29%] 121s io/format/tests/test_genbank.py ..................... [ 30%] 122s io/format/tests/test_gff3.py ........................ [ 30%] 122s io/format/tests/test_lsmat.py ....... [ 31%] 122s io/format/tests/test_newick.py ....... [ 31%] 122s io/format/tests/test_ordination.py ..... [ 31%] 123s io/format/tests/test_phylip.py ....... [ 31%] 124s io/format/tests/test_qseq.py ...... [ 32%] 124s io/format/tests/test_sample_metadata.py .... [ 32%] 124s io/format/tests/test_sequence_feature_vocabulary.py .... [ 32%] 124s io/format/tests/test_stockholm.py ...................................... [ 33%] 125s ..................................... [ 34%] 125s io/format/tests/test_taxdump.py ...... [ 35%] 125s io/tests/test_iosources.py .......... [ 35%] 125s io/tests/test_registry.py .............................................. [ 37%] 125s ................................................ [ 38%] 127s io/tests/test_util.py .........................................sssssssss [ 40%] 129s sssssssssssssssssssss................................................... [ 43%] 133s ........................................................................ [ 45%] 134s .......................... [ 46%] 135s metadata/tests/test_enan.py ... [ 46%] 135s metadata/tests/test_intersection.py ............... [ 47%] 135s metadata/tests/test_interval.py ........................................ [ 48%] 135s ............................... [ 49%] 136s metadata/tests/test_io.py .............................................. [ 51%] 136s ............................................................ [ 53%] 136s metadata/tests/test_metadata.py ........................................ [ 55%] 136s .................... [ 55%] 137s metadata/tests/test_metadata_column.py ................................. [ 57%] 137s ........................................ [ 58%] 137s metadata/tests/test_missing.py ................ [ 59%] 137s metadata/tests/test_mixin.py ........................................... [ 60%] 137s ....................................................... [ 62%] 137s sequence/tests/test_alphabet.py ..... [ 62%] 137s sequence/tests/test_distance.py .......................... [ 63%] 137s sequence/tests/test_dna.py ... [ 63%] 137s sequence/tests/test_genetic_code.py .......................... [ 64%] 137s sequence/tests/test_grammared_sequence.py .............................. [ 65%] 137s ................... [ 66%] 137s sequence/tests/test_nucleotide_sequences.py ............................ [ 67%] 137s . [ 67%] 137s sequence/tests/test_protein.py ........... [ 67%] 137s sequence/tests/test_rna.py ... [ 68%] 137s sequence/tests/test_sequence.py ........................................ [ 69%] 137s ........................................................................ [ 72%] 137s ........................................................................ [ 74%] 137s ........................................................................ [ 77%] 137s ....... [ 77%] 137s sequence/tests/test_substitution.py ........ [ 77%] 137s stats/distance/tests/test_anosim.py .... [ 77%] 137s stats/distance/tests/test_base.py ...................................... [ 79%] 137s .......................................................... [ 81%] 141s stats/distance/tests/test_bioenv.py ................. [ 81%] 142s stats/distance/tests/test_mantel.py .................................... [ 83%] 143s ........ [ 83%] 143s stats/distance/tests/test_permanova.py ..... [ 83%] 151s stats/distance/tests/test_permdisp.py .............. [ 84%] 151s stats/evolve/tests/test_hommola.py ............ [ 84%] 151s stats/ordination/tests/test_canonical_correspondence_analysis.py ...... [ 84%] 151s stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%] 151s stats/ordination/tests/test_ordination_results.py ............. [ 85%] 151s stats/ordination/tests/test_principal_coordinate_analysis.py ........... [ 86%] 151s . [ 86%] 151s stats/ordination/tests/test_redundancy_analysis.py .... [ 86%] 151s stats/ordination/tests/test_util.py .......... [ 86%] 152s stats/tests/test_composition.py ........................................ [ 87%] 163s .......................................... [ 89%] 163s stats/tests/test_gradient.py .......................... [ 90%] 163s stats/tests/test_misc.py ... [ 90%] 164s stats/tests/test_power.py ........................................... [ 92%] 165s stats/tests/test_subsample.py ............ [ 92%] 165s table/tests/test_base.py . [ 92%] 165s tests/test_base.py ..... [ 92%] 165s tests/test_workflow.py ................. [ 93%] 165s tree/tests/test_majority_rule.py ...... [ 93%] 165s tree/tests/test_nj.py ............................ [ 94%] 165s tree/tests/test_tree.py ................................................ [ 96%] 165s ........................................................ [ 98%] 165s util/tests/test_decorator.py ........ [ 98%] 165s util/tests/test_misc.py .................... [ 99%] 166s util/tests/test_plotting.py ...... [ 99%] 166s util/tests/test_testing.py ............... [100%] 166s 166s =============================== warnings summary =============================== 166s alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: make_identity_substitution_matrix is deprecated as of 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional details at https://github.com/scikit-bio/scikit-bio/pull/1913. 166s warn( 166s 166s alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It will be removed in favor of more general purpose and performant aligners. Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814. 166s warn( 166s 166s alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 166s /usr/lib/python3/dist-packages/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 166s gap_freqs /= length 166s 166s diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading. 166s warn( 166s 166s diversity/tests/test_driver.py::BetaDiversityTests::test_available_metrics 166s diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549 166s diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549 166s /usr/lib/python3/dist-packages/scipy/spatial/distance.py:2322: DeprecationWarning: The sokalmichener metric is deprecated since SciPy 1.15.0 and will be removed in SciPy 1.17.0. Replace usage of 'sokalmichener(u, v)' with 'rogerstanimoto(u, v)'. 166s return pdist_fn(X, out=out, **kwargs) 166s 166s embedding/tests/test_protein.py: 3 warnings 166s sequence/tests/test_protein.py: 18 warnings 166s /usr/lib/python3/dist-packages/skbio/sequence/_protein.py:257: DeprecationWarning: `in1d` is deprecated. Use `np.isin` instead. 166s return np.in1d(self._bytes, self._stop_codes) 166s 166s metadata/tests/test_io.py: 10 warnings 166s /usr/lib/python3/dist-packages/skbio/metadata/io.py:411: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 166s series = series.replace("", np.nan) 166s 166s metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 166s metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 166s metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 166s /usr/lib/python3/dist-packages/skbio/metadata/_metadata.py:1102: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['missing']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first. 166s series[missing.index] = missing 166s 166s metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 166s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 166s /usr/lib/python3/dist-packages/skbio/metadata/tests/test_missing.py:53: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 166s pdt.assert_series_equal(missing, series.astype(object)) 166s 166s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 166s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 166s /usr/lib/python3/dist-packages/skbio/metadata/tests/test_missing.py:31: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 166s pdt.assert_series_equal(missing, series[1:].astype(object)) 166s 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 166s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 166s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 166s 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 166s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 166s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 166s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 166s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 166s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 166s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 166s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 166s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 166s 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 166s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 166s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 166s 166s sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 166s /usr/lib/python3/dist-packages/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 166s obs_counts = obs_counts / len(self) 166s 166s sequence/tests/test_sequence.py: 12 warnings 166s /usr/lib/python3/dist-packages/skbio/sequence/_sequence.py:2209: DeprecationWarning: `in1d` is deprecated. Use `np.isin` instead. 166s gaps = np.in1d(seq, gap_chars) 166s 166s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 166s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 166s warnings.warn(ConstantInputWarning()) 166s 166s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 166s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 166s warnings.warn(ConstantInputWarning()) 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 166s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.006573677549550485 and the largest is 0.17668321589384078. 166s warn( 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 166s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.54184654426961 and the largest is 16.5872013747859. 166s warn( 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 166s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395208 and the largest is 20.90315427793891. 166s warn( 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 166s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 166s proportion_explained = eigvals / sum_eigenvalues 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 166s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:618: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 166s res = hypotest_fun_out(*samples, axis=axis, **kwds) 166s 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 166s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 166s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780521 and the largest is 2.7077929489469237. 166s warn( 166s 166s stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 166s /usr/lib/python3.13/unittest/case.py:707: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 166s return self.run(*args, **kwds) 166s 166s stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 166s warn(f"{func.__name__} is deprecated as of {ver}.") 166s 166s stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 166s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:586: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 166s res = hypotest_fun_out(*samples, **kwds) 166s 166s stats/tests/test_composition.py::AncomTests::test_ancom_fail_multiple_groups 166s /usr/lib/python3/dist-packages/skbio/stats/composition.py:1628: DeprecationWarning: You are passing as positional arguments: axis. Please change your invocation to use keyword arguments. From SciPy 1.17.0, passing these as positional arguments will result in an error. 166s return test(*[x[cats == k] for k in cs]) 166s 166s stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 166s warn(f"{func.__name__} is deprecated as of {ver}.") 166s 166s stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 166s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:586: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 166s res = hypotest_fun_out(*samples, **kwds) 166s 166s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 166s /usr/lib/python3/dist-packages/skbio/stats/composition.py:947: RuntimeWarning: divide by zero encountered in log 166s X_log = np.log(mat) 166s 166s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 166s /usr/lib/python3/dist-packages/numpy/lib/_function_base_impl.py:2888: RuntimeWarning: invalid value encountered in subtract 166s X -= avg[:, None] 166s 166s stats/tests/test_composition.py::VLRTests::test_vlr 166s /usr/lib/python3/dist-packages/skbio/stats/composition.py:831: RuntimeWarning: divide by zero encountered in log 166s x = np.log(x) 166s 166s stats/tests/test_composition.py::VLRTests::test_vlr 166s /usr/lib/python3/dist-packages/numpy/_core/_methods.py:191: RuntimeWarning: invalid value encountered in subtract 166s x = asanyarray(arr - arrmean) 166s 166s stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 166s /usr/lib/python3/dist-packages/skbio/stats/gradient.py:167: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 166s trajectories.loc[idx] = ( 166s 166s tree/tests/test_tree.py::TreeTests::test_root_at 166s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:1327: FutureWarning: The default behavior of `root_at` is subject to change in 0.7.0. The new default behavior can be achieved by specifying `reset=True, branch_attrs=[], root_name=None`. 166s warn( 166s 166s tree/tests/test_tree.py::TreeTests::test_root_at 166s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:776: FutureWarning: The default behavior of `unrooted_copy` is subject to change in 0.7.0. The new default behavior can be achieved by specifying `branch_attrs={"length", "support"}, root_name=None`. 166s warn( 166s 166s tree/tests/test_tree.py::TreeTests::test_root_at_midpoint 166s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:1472: FutureWarning: The default behavior of `root_at_midpoint` is subject to change in 0.7.0. The new default behavior can be achieved by specifying `reset=True, branch_attrs=[], root_name=None`. 166s warn( 166s 166s tree/tests/test_tree.py::TreeTests::test_unrooted_deepcopy 166s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: unrooted_deepcopy is deprecated as of 0.6.2. Use unrooted_copy instead. 166s warn( 166s 166s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 166s ========== 2763 passed, 30 skipped, 107 warnings in 62.97s (0:01:02) =========== 167s autopkgtest [20:22:46]: test pybuild-autopkgtest: -----------------------] 167s pybuild-autopkgtest PASS 167s autopkgtest [20:22:46]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 167s autopkgtest [20:22:46]: @@@@@@@@@@@@@@@@@@@@ summary 167s pybuild-autopkgtest PASS