0s autopkgtest [16:33:15]: starting date and time: 2024-11-18 16:33:15+0000 0s autopkgtest [16:33:15]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:33:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ef4_kez0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:openmpi,src:sphinx-rtd-theme --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu1 openmpi/5.0.5-6 sphinx-rtd-theme/3.0.2+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-6.secgroup --name adt-plucky-arm64-python-skbio-20241118-163315-juju-7f2275-prod-proposed-migration-environment-20-d3a7f61e-01f3-498c-8796-c215925b87ab --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 111s autopkgtest [16:35:06]: testbed dpkg architecture: arm64 111s autopkgtest [16:35:06]: testbed apt version: 2.9.8 111s autopkgtest [16:35:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 113s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [103 kB] 113s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 113s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [638 kB] 113s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6696 B] 113s Fetched 1778 kB in 1s (1737 kB/s) 113s Reading package lists... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 118s The following NEW packages will be installed: 118s liblsof0 118s The following packages will be upgraded: 118s libnvme1t64 linux-firmware lsof 118s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 538 MB of archives. 118s After this operation, 1548 kB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.3+dfsg-2 [53.5 kB] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.3+dfsg-2 [235 kB] 119s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libnvme1t64 arm64 1.11.1-1 [83.7 kB] 119s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 linux-firmware arm64 20241118.git6e4e94b0-0ubuntu1 [537 MB] 141s Fetched 538 MB in 22s (24.1 MB/s) 141s Selecting previously unselected package liblsof0. 141s (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 ... 79972 files and directories currently installed.) 141s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_arm64.deb ... 141s Unpacking liblsof0 (4.99.3+dfsg-2) ... 142s Preparing to unpack .../lsof_4.99.3+dfsg-2_arm64.deb ... 142s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 142s Preparing to unpack .../libnvme1t64_1.11.1-1_arm64.deb ... 142s Unpacking libnvme1t64 (1.11.1-1) over (1.11-2) ... 142s Preparing to unpack .../linux-firmware_20241118.git6e4e94b0-0ubuntu1_arm64.deb ... 142s Unpacking linux-firmware (20241118.git6e4e94b0-0ubuntu1) over (20241108.git3bbb13a7-0ubuntu1) ... 145s Setting up linux-firmware (20241118.git6e4e94b0-0ubuntu1) ... 145s Setting up liblsof0 (4.99.3+dfsg-2) ... 145s Setting up libnvme1t64 (1.11.1-1) ... 145s Setting up lsof (4.99.3+dfsg-2) ... 145s Processing triggers for man-db (2.13.0-1) ... 145s Processing triggers for libc-bin (2.40-1ubuntu3) ... 145s Processing triggers for initramfs-tools (0.142ubuntu35) ... 145s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 145s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 163s System running in EFI mode, skipping. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 165s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 165s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 165s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 165s Reading package lists... 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Calculating upgrade... 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s autopkgtest [16:36:03]: rebooting testbed after setup commands that affected boot 172s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 194s autopkgtest [16:36:29]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 196s autopkgtest [16:36:31]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 200s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-3 (dsc) [2897 B] 200s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-3 (tar) [2204 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-3 (diff) [11.1 kB] 200s gpgv: Signature made Sat Sep 28 10:29:34 2024 UTC 200s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 200s gpgv: Can't check signature: No public key 200s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.6.2-3.dsc: no acceptable signature found 200s autopkgtest [16:36:35]: testing package python-skbio version 0.6.2-3 200s autopkgtest [16:36:35]: build not needed 201s autopkgtest [16:36:36]: test pybuild-autopkgtest: preparing testbed 202s Reading package lists... 203s Building dependency tree... 203s Reading state information... 203s Starting pkgProblemResolver with broken count: 0 203s Starting 2 pkgProblemResolver with broken count: 0 203s Done 204s The following additional packages will be installed: 204s architecture-properties autoconf automake autopoint autotools-dev blt 204s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 204s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 204s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 204s fonts-lyx fonts-mathjax fonts-open-sans g++ g++-14 g++-14-aarch64-linux-gnu 204s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 204s gcc-aarch64-linux-gnu gettext intltool-debian libaec0 libarchive-zip-perl 204s libasan8 libblas3 libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev 204s libfile-stripnondeterminism-perl libfontconfig1 libgcc-14-dev libgfortran5 204s libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 204s libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 204s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 204s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 204s libmpc3 libopenjp2-7 libpython3-all-dev libpython3-dev libpython3.12-dev 204s libqhull-r8.0 libraqm0 libsharpyuv0 libsimde-dev libssw-dev libssw0 204s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 204s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 204s libxss1 m4 po-debconf pybuild-plugin-autopkgtest python-biom-format-doc 204s python-matplotlib-data python-numpy-doc python-pandas-doc python-scipy-doc 204s python-skbio-doc python3-alabaster python3-all python3-all-dev 204s python3-appdirs python3-asttokens python3-biom-format python3-brotli 204s python3-bs4 python3-cachecontrol python3-click python3-colorama 204s python3-contourpy python3-cycler python3-dateutil python3-decorator 204s python3-defusedxml python3-dev python3-doc python3-docutils 204s python3-executing python3-fonttools python3-fs python3-h5py 204s python3-h5py-serial python3-hdmedians python3-imagesize python3-iniconfig 204s python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lxml 204s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mpmath 204s python3-msgpack python3-natsort python3-numpy python3-numpydoc 204s python3-packaging python3-pandas python3-pandas-lib python3-parso 204s python3-patsy python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 204s python3-prompt-toolkit python3-ptyprocess python3-pure-eval 204s python3-pydata-sphinx-theme python3-pytest python3-roman python3-scipy 204s python3-six python3-skbio python3-sklearn python3-sklearn-lib 204s python3-snowballstemmer python3-soupsieve python3-sphinx 204s python3-sphinx-copybutton python3-sphinx-design python3-stack-data 204s python3-statsmodels python3-statsmodels-lib python3-sympy python3-tabulate 204s python3-threadpoolctl python3-tk python3-traitlets python3-typeshed 204s python3-tz python3-ufolib2 python3-wcwidth python3.12-dev python3.12-doc 204s python3.12-tk python3.13-tk sgml-base sphinx-common tk8.6-blt2.5 204s unicode-data x11-common xml-core zlib1g-dev 204s Suggested packages: 204s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 204s cpp-14-doc cython-doc dh-make flit python3-build python3-installer 204s python3-wheel gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 204s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 204s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc 204s liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran 204s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python-imageio-doc 204s python-pytest-doc python-skimage-doc python-cycler-doc python3-examples 204s docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 204s texlive-latex-base texlive-latex-recommended python-h5py-doc 204s python-ipython-doc python-joblib-doc python-lxml-doc cm-super-minimal dvipng 204s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 204s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 204s python3-gobject python3-pyqt5 python3-sip python3-tornado 204s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 204s python-natsort-doc gfortran python-patsy-doc python-pexpect-doc 204s python-pil-doc python3-dap python-sklearn-doc python3-stemmer dvisvgm 204s fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme 204s sphinx-doc tex-gyre texlive-fonts-extra texlive-fonts-recommended 204s texlive-plain-generic python-sphinx-copybutton-doc python-statsmodels-doc 204s python-sympy-doc tix python3-tk-dbg python-traitlets-doc sgml-base-doc 204s Recommended packages: 204s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 204s libmail-sendmail-perl libpaper-utils python3-simplejson python3-psutil 204s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 204s python3-odf python3-openpyxl python3-tables python3-olefile 204s python3-accessible-pygments python3-cvxopt isympy-common 205s The following NEW packages will be installed: 205s architecture-properties autoconf automake autopkgtest-satdep autopoint 205s autotools-dev blt build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu 205s cpp-aarch64-linux-gnu cython3 debhelper debugedit dh-autoreconf dh-python 205s dh-strip-nondeterminism docutils-common dwz fontconfig-config 205s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-mathjax fonts-open-sans 205s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 205s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 205s libaec0 libarchive-zip-perl libasan8 libblas3 libcc1-0 libdebhelper-perl 205s libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 205s libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 205s libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23 205s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 205s libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 205s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libopenjp2-7 205s libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 205s libsharpyuv0 libsimde-dev libssw-dev libssw0 libstdc++-14-dev libsz2 205s libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 205s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 m4 205s po-debconf pybuild-plugin-autopkgtest python-biom-format-doc 205s python-matplotlib-data python-numpy-doc python-pandas-doc python-scipy-doc 205s python-skbio-doc python3-alabaster python3-all python3-all-dev 205s python3-appdirs python3-asttokens python3-biom-format python3-brotli 205s python3-bs4 python3-cachecontrol python3-click python3-colorama 205s python3-contourpy python3-cycler python3-dateutil python3-decorator 205s python3-defusedxml python3-dev python3-doc python3-docutils 205s python3-executing python3-fonttools python3-fs python3-h5py 205s python3-h5py-serial python3-hdmedians python3-imagesize python3-iniconfig 205s python3-ipython python3-jedi python3-joblib python3-kiwisolver python3-lxml 205s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mpmath 205s python3-msgpack python3-natsort python3-numpy python3-numpydoc 205s python3-packaging python3-pandas python3-pandas-lib python3-parso 205s python3-patsy python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 205s python3-prompt-toolkit python3-ptyprocess python3-pure-eval 205s python3-pydata-sphinx-theme python3-pytest python3-roman python3-scipy 205s python3-six python3-skbio python3-sklearn python3-sklearn-lib 205s python3-snowballstemmer python3-soupsieve python3-sphinx 205s python3-sphinx-copybutton python3-sphinx-design python3-stack-data 205s python3-statsmodels python3-statsmodels-lib python3-sympy python3-tabulate 205s python3-threadpoolctl python3-tk python3-traitlets python3-typeshed 205s python3-tz python3-ufolib2 python3-wcwidth python3.12-dev python3.12-doc 205s python3.12-tk python3.13-tk sgml-base sphinx-common tk8.6-blt2.5 205s unicode-data x11-common xml-core zlib1g-dev 205s 0 upgraded, 195 newly installed, 0 to remove and 0 not upgraded. 205s Need to get 207 MB/207 MB of archives. 205s After this operation, 1228 MB of additional disk space will be used. 205s Get:1 /tmp/autopkgtest.nZe3r8/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [980 B] 205s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 205s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 architecture-properties arm64 0.2.3 [2058 B] 205s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 205s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 205s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 205s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 205s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 205s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 205s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 205s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 205s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 205s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 205s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 205s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 205s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 205s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 205s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 205s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 205s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 205s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 205s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 205s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 206s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 206s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 206s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 206s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 206s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 206s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 206s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 206s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 206s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 206s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 206s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 206s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 206s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 209s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 209s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 209s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 209s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 209s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 209s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 209s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 209s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 209s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 209s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu2 [2977 kB] 209s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 209s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-8 [166 kB] 209s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 209s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 209s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 209s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 209s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 209s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 209s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 209s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 209s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 209s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 209s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 209s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 209s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 209s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 209s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 209s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-open-sans all 1.11-2 [635 kB] 209s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 209s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 209s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 209s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 209s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 209s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 209s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 209s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 209s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 209s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 209s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 209s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 209s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 209s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 209s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 209s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 209s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 209s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 209s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 209s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 209s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 209s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 209s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 209s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 209s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 209s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB] 209s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B] 209s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 209s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 209s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 209s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsimde-dev all 0.8.2-1 [466 kB] 209s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw0 arm64 1.1-15 [21.8 kB] 209s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw-dev arm64 1.1-15 [23.6 kB] 209s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 209s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 209s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 209s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 209s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 209s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 210s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 210s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1 [57.5 kB] 210s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 210s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python-numpy-doc all 1:1.26.4+ds-11ubuntu1 [5481 kB] 210s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 210s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-pandas-doc all 2.2.3+dfsg-5ubuntu1 [9117 kB] 211s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-skbio-doc all 0.6.2-3 [2071 kB] 211s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 211s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 211s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB] 211s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B] 211s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 211s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 2.4.1-2 [20.8 kB] 211s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 211s Get:118 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu1 [1449 kB] 211s Get:119 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py all 3.11.0-8ubuntu1 [7982 B] 211s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 211s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 211s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 211s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 211s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB] 211s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 211s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 211s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5ubuntu1 [19.1 MB] 212s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1 [137 kB] 212s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 212s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-soupsieve all 2.6-1 [33.0 kB] 212s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-bs4 all 4.12.3-3 [109 kB] 212s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build3 [106 kB] 212s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cachecontrol all 0.14.1-1 [19.0 kB] 212s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2build1 [220 kB] 212s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 212s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] 212s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-doc all 3.12.7-3 [12.4 MB] 212s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-doc all 3.12.6-0ubuntu1 [10.2 kB] 212s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB] 212s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 212s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 212s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 212s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 212s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1build1 [1591 kB] 212s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 212s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 212s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 212s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 212s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 213s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.54.1-4ubuntu1 [1614 kB] 213s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdmedians arm64 0.14.2-5.1build2 [180 kB] 213s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 213s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 213s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 213s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 213s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 213s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 213s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 213s Get:159 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 213s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 213s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 213s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 213s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 213s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 213s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.29.0-1 [569 kB] 213s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 213s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 213s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 213s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 213s Get:170 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 213s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 213s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 213s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 213s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 213s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 213s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 213s Get:177 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB] 213s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 213s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 213s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB] 213s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 213s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numpydoc all 1.6.0-2 [50.5 kB] 213s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-patsy all 1.0.1-1 [180 kB] 213s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 213s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pydata-sphinx-theme all 0.15.4+dfsg-2 [41.5 kB] 213s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 213s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1build1 [2512 kB] 213s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels all 0.14.4+dfsg-1build1 [5011 kB] 213s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-skbio arm64 0.6.2-3 [1391 kB] 213s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 213s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 213s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 214s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-copybutton all 0.5.2-2 [16.6 kB] 214s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-design all 0.6.1-1 [894 kB] 214s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-scipy-doc all 1.13.1-5ubuntu1 [31.2 kB] 214s Fetched 207 MB in 9s (22.3 MB/s) 214s Selecting previously unselected package sgml-base. 214s (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 ... 80002 files and directories currently installed.) 214s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 214s Unpacking sgml-base (1.31) ... 215s Selecting previously unselected package architecture-properties:arm64. 215s Preparing to unpack .../001-architecture-properties_0.2.3_arm64.deb ... 215s Unpacking architecture-properties:arm64 (0.2.3) ... 215s Selecting previously unselected package m4. 215s Preparing to unpack .../002-m4_1.4.19-4build1_arm64.deb ... 215s Unpacking m4 (1.4.19-4build1) ... 215s Selecting previously unselected package autoconf. 215s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 215s Unpacking autoconf (2.72-3) ... 215s Selecting previously unselected package autotools-dev. 215s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 215s Unpacking autotools-dev (20220109.1) ... 215s Selecting previously unselected package automake. 215s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 215s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 215s Selecting previously unselected package autopoint. 215s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 215s Unpacking autopoint (0.22.5-2) ... 215s Selecting previously unselected package libtcl8.6:arm64. 215s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 215s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 215s Selecting previously unselected package fonts-dejavu-mono. 215s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 215s Unpacking fonts-dejavu-mono (2.37-8) ... 215s Selecting previously unselected package fonts-dejavu-core. 215s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 215s Unpacking fonts-dejavu-core (2.37-8) ... 215s Selecting previously unselected package fontconfig-config. 215s Preparing to unpack .../010-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 215s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 215s Selecting previously unselected package libfontconfig1:arm64. 215s Preparing to unpack .../011-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 215s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 215s Selecting previously unselected package libxrender1:arm64. 215s Preparing to unpack .../012-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 215s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 215s Selecting previously unselected package libxft2:arm64. 215s Preparing to unpack .../013-libxft2_2.3.6-1build1_arm64.deb ... 215s Unpacking libxft2:arm64 (2.3.6-1build1) ... 215s Selecting previously unselected package x11-common. 216s Preparing to unpack .../014-x11-common_1%3a7.7+23ubuntu3_all.deb ... 216s Unpacking x11-common (1:7.7+23ubuntu3) ... 216s Selecting previously unselected package libxss1:arm64. 216s Preparing to unpack .../015-libxss1_1%3a1.2.3-1build3_arm64.deb ... 216s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 216s Selecting previously unselected package libtk8.6:arm64. 216s Preparing to unpack .../016-libtk8.6_8.6.15-1_arm64.deb ... 216s Unpacking libtk8.6:arm64 (8.6.15-1) ... 216s Selecting previously unselected package tk8.6-blt2.5. 216s Preparing to unpack .../017-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 216s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 216s Selecting previously unselected package blt. 216s Preparing to unpack .../018-blt_2.5.3+dfsg-7build1_arm64.deb ... 216s Unpacking blt (2.5.3+dfsg-7build1) ... 216s Selecting previously unselected package libisl23:arm64. 216s Preparing to unpack .../019-libisl23_0.27-1_arm64.deb ... 216s Unpacking libisl23:arm64 (0.27-1) ... 216s Selecting previously unselected package libmpc3:arm64. 216s Preparing to unpack .../020-libmpc3_1.3.1-1build2_arm64.deb ... 216s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 216s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 216s Preparing to unpack .../021-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 216s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 216s Selecting previously unselected package cpp-14. 216s Preparing to unpack .../022-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 216s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 216s Selecting previously unselected package cpp-aarch64-linux-gnu. 216s Preparing to unpack .../023-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 216s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 216s Selecting previously unselected package cpp. 216s Preparing to unpack .../024-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 216s Unpacking cpp (4:14.1.0-2ubuntu1) ... 216s Selecting previously unselected package libcc1-0:arm64. 216s Preparing to unpack .../025-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 216s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 216s Selecting previously unselected package libgomp1:arm64. 216s Preparing to unpack .../026-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 216s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 216s Selecting previously unselected package libitm1:arm64. 216s Preparing to unpack .../027-libitm1_14.2.0-8ubuntu1_arm64.deb ... 216s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package libasan8:arm64. 217s Preparing to unpack .../028-libasan8_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package liblsan0:arm64. 217s Preparing to unpack .../029-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package libtsan2:arm64. 217s Preparing to unpack .../030-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package libubsan1:arm64. 217s Preparing to unpack .../031-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package libhwasan0:arm64. 217s Preparing to unpack .../032-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package libgcc-14-dev:arm64. 217s Preparing to unpack .../033-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 217s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 217s Preparing to unpack .../034-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 217s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 218s Selecting previously unselected package gcc-14. 218s Preparing to unpack .../035-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 218s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 218s Selecting previously unselected package gcc-aarch64-linux-gnu. 218s Preparing to unpack .../036-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 218s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 218s Selecting previously unselected package gcc. 218s Preparing to unpack .../037-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 218s Unpacking gcc (4:14.1.0-2ubuntu1) ... 218s Selecting previously unselected package libstdc++-14-dev:arm64. 218s Preparing to unpack .../038-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 218s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 218s Selecting previously unselected package g++-14-aarch64-linux-gnu. 218s Preparing to unpack .../039-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 218s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 219s Selecting previously unselected package g++-14. 219s Preparing to unpack .../040-g++-14_14.2.0-8ubuntu1_arm64.deb ... 219s Unpacking g++-14 (14.2.0-8ubuntu1) ... 219s Selecting previously unselected package g++-aarch64-linux-gnu. 219s Preparing to unpack .../041-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 219s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 219s Selecting previously unselected package g++. 219s Preparing to unpack .../042-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 219s Unpacking g++ (4:14.1.0-2ubuntu1) ... 219s Selecting previously unselected package build-essential. 219s Preparing to unpack .../043-build-essential_12.10ubuntu1_arm64.deb ... 219s Unpacking build-essential (12.10ubuntu1) ... 219s Selecting previously unselected package cython3. 219s Preparing to unpack .../044-cython3_3.0.11+dfsg-1ubuntu2_arm64.deb ... 219s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 219s Selecting previously unselected package libdebhelper-perl. 219s Preparing to unpack .../045-libdebhelper-perl_13.20ubuntu1_all.deb ... 219s Unpacking libdebhelper-perl (13.20ubuntu1) ... 219s Selecting previously unselected package libtool. 219s Preparing to unpack .../046-libtool_2.4.7-8_all.deb ... 219s Unpacking libtool (2.4.7-8) ... 219s Selecting previously unselected package dh-autoreconf. 219s Preparing to unpack .../047-dh-autoreconf_20_all.deb ... 219s Unpacking dh-autoreconf (20) ... 219s Selecting previously unselected package libarchive-zip-perl. 219s Preparing to unpack .../048-libarchive-zip-perl_1.68-1_all.deb ... 219s Unpacking libarchive-zip-perl (1.68-1) ... 219s Selecting previously unselected package libfile-stripnondeterminism-perl. 219s Preparing to unpack .../049-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 219s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 219s Selecting previously unselected package dh-strip-nondeterminism. 219s Preparing to unpack .../050-dh-strip-nondeterminism_1.14.0-1_all.deb ... 219s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 219s Selecting previously unselected package debugedit. 219s Preparing to unpack .../051-debugedit_1%3a5.1-1_arm64.deb ... 219s Unpacking debugedit (1:5.1-1) ... 219s Selecting previously unselected package dwz. 219s Preparing to unpack .../052-dwz_0.15-1build6_arm64.deb ... 219s Unpacking dwz (0.15-1build6) ... 219s Selecting previously unselected package gettext. 219s Preparing to unpack .../053-gettext_0.22.5-2_arm64.deb ... 219s Unpacking gettext (0.22.5-2) ... 219s Selecting previously unselected package intltool-debian. 219s Preparing to unpack .../054-intltool-debian_0.35.0+20060710.6_all.deb ... 219s Unpacking intltool-debian (0.35.0+20060710.6) ... 219s Selecting previously unselected package po-debconf. 219s Preparing to unpack .../055-po-debconf_1.0.21+nmu1_all.deb ... 219s Unpacking po-debconf (1.0.21+nmu1) ... 219s Selecting previously unselected package debhelper. 219s Preparing to unpack .../056-debhelper_13.20ubuntu1_all.deb ... 219s Unpacking debhelper (13.20ubuntu1) ... 220s Selecting previously unselected package dh-python. 220s Preparing to unpack .../057-dh-python_6.20241024_all.deb ... 220s Unpacking dh-python (6.20241024) ... 220s Selecting previously unselected package xml-core. 220s Preparing to unpack .../058-xml-core_0.19_all.deb ... 220s Unpacking xml-core (0.19) ... 220s Selecting previously unselected package docutils-common. 220s Preparing to unpack .../059-docutils-common_0.21.2+dfsg-2_all.deb ... 220s Unpacking docutils-common (0.21.2+dfsg-2) ... 220s Selecting previously unselected package fonts-lyx. 220s Preparing to unpack .../060-fonts-lyx_2.4.2.1-1_all.deb ... 220s Unpacking fonts-lyx (2.4.2.1-1) ... 220s Selecting previously unselected package fonts-mathjax. 220s Preparing to unpack .../061-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 220s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 220s Selecting previously unselected package fonts-open-sans. 220s Preparing to unpack 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Selecting previously unselected package libgraphite2-3:arm64. 220s Preparing to unpack .../068-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 220s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 220s Selecting previously unselected package libharfbuzz0b:arm64. 220s Preparing to unpack .../069-libharfbuzz0b_10.0.1-1_arm64.deb ... 220s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 220s Selecting previously unselected package libsz2:arm64. 220s Preparing to unpack .../070-libsz2_1.1.3-1_arm64.deb ... 220s Unpacking libsz2:arm64 (1.1.3-1) ... 220s Selecting previously unselected package libhdf5-103-1t64:arm64. 220s Preparing to unpack .../071-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 220s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 220s Selecting previously unselected package libhdf5-hl-100t64:arm64. 220s Preparing to unpack .../072-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 220s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 220s Selecting previously unselected package libimagequant0:arm64. 220s Preparing to unpack .../073-libimagequant0_2.18.0-1build1_arm64.deb ... 220s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 220s Selecting previously unselected package libjpeg-turbo8:arm64. 220s Preparing to unpack .../074-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 220s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 221s Selecting previously unselected package libjpeg8:arm64. 221s Preparing to unpack .../075-libjpeg8_8c-2ubuntu11_arm64.deb ... 221s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 221s Selecting previously unselected package libjs-jquery. 221s Preparing to unpack .../076-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 221s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 221s Selecting previously unselected package libjs-jquery-ui. 221s Preparing to unpack .../077-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 221s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 221s Selecting previously unselected package libjs-underscore. 221s Preparing to unpack .../078-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 221s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 221s Selecting previously unselected package libjs-sphinxdoc. 221s Preparing to unpack .../079-libjs-sphinxdoc_7.4.7-4_all.deb ... 221s Unpacking libjs-sphinxdoc (7.4.7-4) ... 221s Selecting previously unselected package libjson-perl. 221s Preparing to unpack .../080-libjson-perl_4.10000-1_all.deb ... 221s Unpacking libjson-perl (4.10000-1) ... 221s Selecting previously unselected package liblapack3:arm64. 221s Preparing to unpack .../081-liblapack3_3.12.0-3build2_arm64.deb ... 221s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 221s Selecting previously unselected package liblbfgsb0:arm64. 221s Preparing to unpack .../082-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 221s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 221s Selecting previously unselected package liblcms2-2:arm64. 221s Preparing to unpack .../083-liblcms2-2_2.16-2_arm64.deb ... 221s Unpacking liblcms2-2:arm64 (2.16-2) ... 221s Selecting previously unselected package liblerc4:arm64. 221s Preparing to unpack .../084-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 221s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 221s Selecting previously unselected package liblzf1:arm64. 221s Preparing to unpack .../085-liblzf1_3.6-4_arm64.deb ... 221s Unpacking liblzf1:arm64 (3.6-4) ... 221s Selecting previously unselected package zlib1g-dev:arm64. 221s Preparing to unpack .../086-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 221s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 221s Selecting previously unselected package libpython3.12-dev:arm64. 221s Preparing to unpack .../087-libpython3.12-dev_3.12.7-3_arm64.deb ... 221s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 221s Selecting previously unselected package libpython3-dev:arm64. 221s Preparing to unpack .../088-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ... 221s Unpacking libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 221s Selecting previously unselected package libpython3-all-dev:arm64. 221s Preparing to unpack .../089-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 221s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 221s Selecting previously unselected package libqhull-r8.0:arm64. 221s Preparing to unpack .../090-libqhull-r8.0_2020.2-6build1_arm64.deb ... 221s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 222s Selecting previously unselected package libraqm0:arm64. 222s Preparing to unpack .../091-libraqm0_0.10.1-1build1_arm64.deb ... 222s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 222s Selecting previously unselected package libsharpyuv0:arm64. 222s Preparing to unpack .../092-libsharpyuv0_1.4.0-0.1_arm64.deb ... 222s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 222s Selecting previously unselected package libsimde-dev. 222s Preparing to unpack .../093-libsimde-dev_0.8.2-1_all.deb ... 222s Unpacking libsimde-dev (0.8.2-1) ... 222s Selecting previously unselected package libssw0:arm64. 222s Preparing to unpack .../094-libssw0_1.1-15_arm64.deb ... 222s Unpacking libssw0:arm64 (1.1-15) ... 222s Selecting previously unselected package libssw-dev:arm64. 222s Preparing to unpack .../095-libssw-dev_1.1-15_arm64.deb ... 222s Unpacking libssw-dev:arm64 (1.1-15) ... 222s Selecting previously unselected package libjbig0:arm64. 222s Preparing to unpack .../096-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 222s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 222s Selecting previously unselected package libwebp7:arm64. 222s Preparing to unpack .../097-libwebp7_1.4.0-0.1_arm64.deb ... 222s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 222s Selecting previously unselected package libtiff6:arm64. 222s Preparing to unpack .../098-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 222s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 222s Selecting previously unselected package libwebpdemux2:arm64. 222s Preparing to unpack .../099-libwebpdemux2_1.4.0-0.1_arm64.deb ... 222s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 222s Selecting previously unselected package libwebpmux3:arm64. 222s Preparing to unpack .../100-libwebpmux3_1.4.0-0.1_arm64.deb ... 222s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 222s Selecting previously unselected package libxslt1.1:arm64. 222s Preparing to unpack .../101-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 222s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 222s Selecting previously unselected package pybuild-plugin-autopkgtest. 222s Preparing to unpack .../102-pybuild-plugin-autopkgtest_6.20241024_all.deb ... 222s Unpacking pybuild-plugin-autopkgtest (6.20241024) ... 222s Selecting previously unselected package python-biom-format-doc. 222s Preparing to unpack .../103-python-biom-format-doc_2.1.16-1_all.deb ... 222s Unpacking python-biom-format-doc (2.1.16-1) ... 222s Selecting previously unselected package python-matplotlib-data. 222s Preparing to unpack .../104-python-matplotlib-data_3.8.3-3_all.deb ... 222s Unpacking python-matplotlib-data (3.8.3-3) ... 222s Selecting previously unselected package python-numpy-doc. 222s Preparing to unpack .../105-python-numpy-doc_1%3a1.26.4+ds-11ubuntu1_all.deb ... 222s Unpacking python-numpy-doc (1:1.26.4+ds-11ubuntu1) ... 223s Selecting previously unselected package libjs-mathjax. 223s Preparing to unpack .../106-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 223s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 224s Selecting previously unselected package python-pandas-doc. 224s Preparing to unpack .../107-python-pandas-doc_2.2.3+dfsg-5ubuntu1_all.deb ... 224s Unpacking python-pandas-doc (2.2.3+dfsg-5ubuntu1) ... 225s Selecting previously unselected package python-skbio-doc. 225s Preparing to unpack .../108-python-skbio-doc_0.6.2-3_all.deb ... 225s Unpacking python-skbio-doc (0.6.2-3) ... 225s Selecting previously unselected package python3-all. 226s Preparing to unpack .../109-python3-all_3.12.6-0ubuntu1_arm64.deb ... 226s Unpacking python3-all (3.12.6-0ubuntu1) ... 226s Selecting previously unselected package python3.12-dev. 226s Preparing to unpack .../110-python3.12-dev_3.12.7-3_arm64.deb ... 226s Unpacking python3.12-dev (3.12.7-3) ... 226s Selecting previously unselected package python3-dev. 226s Preparing to unpack .../111-python3-dev_3.12.6-0ubuntu1_arm64.deb ... 226s Unpacking python3-dev (3.12.6-0ubuntu1) ... 226s Selecting previously unselected package python3-all-dev. 226s Preparing to unpack .../112-python3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 226s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 226s Selecting previously unselected package python3-appdirs. 226s Preparing to unpack .../113-python3-appdirs_1.4.4-4_all.deb ... 226s Unpacking python3-appdirs (1.4.4-4) ... 226s Selecting previously unselected package python3-asttokens. 226s Preparing to unpack .../114-python3-asttokens_2.4.1-2_all.deb ... 226s Unpacking python3-asttokens (2.4.1-2) ... 226s Selecting previously unselected package python3-numpy. 226s Preparing to unpack .../115-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 226s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 226s Selecting previously unselected package python3-h5py-serial. 226s Preparing to unpack .../116-python3-h5py-serial_3.11.0-8ubuntu1_arm64.deb ... 226s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 226s Selecting previously unselected package python3-h5py. 226s Preparing to unpack .../117-python3-h5py_3.11.0-8ubuntu1_all.deb ... 226s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 226s Selecting previously unselected package python3-colorama. 226s Preparing to unpack .../118-python3-colorama_0.4.6-4_all.deb ... 226s Unpacking python3-colorama (0.4.6-4) ... 226s Selecting previously unselected package python3-click. 226s Preparing to unpack .../119-python3-click_8.1.7-2_all.deb ... 226s Unpacking python3-click (8.1.7-2) ... 226s Selecting previously unselected package python3-dateutil. 226s Preparing to unpack .../120-python3-dateutil_2.9.0-3_all.deb ... 226s Unpacking python3-dateutil (2.9.0-3) ... 226s Selecting previously unselected package python3-tz. 226s Preparing to unpack .../121-python3-tz_2024.1-2_all.deb ... 226s Unpacking python3-tz (2024.1-2) ... 227s Selecting previously unselected package python3-pandas-lib:arm64. 227s Preparing to unpack .../122-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ... 227s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 227s Selecting previously unselected package python3-pandas. 227s Preparing to unpack .../123-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 227s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 227s Selecting previously unselected package python3-decorator. 227s Preparing to unpack .../124-python3-decorator_5.1.1-5_all.deb ... 227s Unpacking python3-decorator (5.1.1-5) ... 227s Selecting previously unselected package python3-scipy. 227s Preparing to unpack .../125-python3-scipy_1.13.1-5ubuntu1_arm64.deb ... 227s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 228s Selecting previously unselected package python3-biom-format. 228s Preparing to unpack .../126-python3-biom-format_2.1.16-1_arm64.deb ... 228s Unpacking python3-biom-format (2.1.16-1) ... 228s Selecting previously unselected package python3-brotli. 228s Preparing to unpack .../127-python3-brotli_1.1.0-2build3_arm64.deb ... 228s Unpacking python3-brotli (1.1.0-2build3) ... 228s Selecting previously unselected package python3-soupsieve. 228s Preparing to unpack .../128-python3-soupsieve_2.6-1_all.deb ... 228s Unpacking python3-soupsieve (2.6-1) ... 228s Selecting previously unselected package python3-bs4. 228s Preparing to unpack .../129-python3-bs4_4.12.3-3_all.deb ... 228s Unpacking python3-bs4 (4.12.3-3) ... 228s Selecting previously unselected package python3-msgpack. 228s Preparing to unpack .../130-python3-msgpack_1.0.3-3build3_arm64.deb ... 228s Unpacking python3-msgpack (1.0.3-3build3) ... 228s Selecting previously unselected package python3-cachecontrol. 228s Preparing to unpack .../131-python3-cachecontrol_0.14.1-1_all.deb ... 228s Unpacking python3-cachecontrol (0.14.1-1) ... 228s Selecting previously unselected package python3-contourpy. 228s Preparing to unpack .../132-python3-contourpy_1.3.0-2build1_arm64.deb ... 228s Unpacking python3-contourpy (1.3.0-2build1) ... 229s Selecting previously unselected package python3-cycler. 229s Preparing to unpack .../133-python3-cycler_0.12.1-1_all.deb ... 229s Unpacking python3-cycler (0.12.1-1) ... 229s Selecting previously unselected package python3-defusedxml. 229s Preparing to unpack .../134-python3-defusedxml_0.7.1-2_all.deb ... 229s Unpacking python3-defusedxml (0.7.1-2) ... 229s Selecting previously unselected package python3.12-doc. 229s Preparing to unpack .../135-python3.12-doc_3.12.7-3_all.deb ... 229s Unpacking python3.12-doc (3.12.7-3) ... 229s Selecting previously unselected package python3-doc. 229s Preparing to unpack .../136-python3-doc_3.12.6-0ubuntu1_all.deb ... 229s Unpacking python3-doc (3.12.6-0ubuntu1) ... 229s Selecting previously unselected package python3-roman. 229s Preparing to unpack .../137-python3-roman_4.2-1_all.deb ... 229s Unpacking python3-roman (4.2-1) ... 229s Selecting previously unselected package python3-docutils. 229s Preparing to unpack .../138-python3-docutils_0.21.2+dfsg-2_all.deb ... 229s Unpacking python3-docutils (0.21.2+dfsg-2) ... 229s Selecting previously unselected package python3-executing. 229s Preparing to unpack .../139-python3-executing_2.1.0-0.1_all.deb ... 229s Unpacking python3-executing (2.1.0-0.1) ... 229s Selecting previously unselected package python3-six. 229s Preparing to unpack .../140-python3-six_1.16.0-7_all.deb ... 229s Unpacking python3-six (1.16.0-7) ... 229s Selecting previously unselected package python3-fs. 229s Preparing to unpack .../141-python3-fs_2.4.16-4_all.deb ... 229s Unpacking python3-fs (2.4.16-4) ... 230s Selecting previously unselected package python3-lxml:arm64. 230s Preparing to unpack .../142-python3-lxml_5.3.0-1build1_arm64.deb ... 230s Unpacking python3-lxml:arm64 (5.3.0-1build1) ... 230s Selecting previously unselected package python3-lz4. 230s Preparing to unpack .../143-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 230s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 230s Selecting previously unselected package python3-mpmath. 230s Preparing to unpack .../144-python3-mpmath_1.3.0-1_all.deb ... 230s Unpacking python3-mpmath (1.3.0-1) ... 230s Selecting previously unselected package python3-sympy. 230s Preparing to unpack .../145-python3-sympy_1.13.3-1_all.deb ... 230s Unpacking python3-sympy (1.13.3-1) ... 230s Selecting previously unselected package python3-ufolib2. 230s Preparing to unpack .../146-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 230s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 230s Selecting previously unselected package unicode-data. 230s Preparing to unpack .../147-unicode-data_15.1.0-1_all.deb ... 230s Unpacking unicode-data (15.1.0-1) ... 230s Selecting previously unselected package python3-fonttools. 230s Preparing to unpack .../148-python3-fonttools_4.54.1-4ubuntu1_arm64.deb ... 230s Unpacking python3-fonttools (4.54.1-4ubuntu1) ... 231s Selecting previously unselected package python3-hdmedians. 231s Preparing to unpack .../149-python3-hdmedians_0.14.2-5.1build2_arm64.deb ... 231s Unpacking python3-hdmedians (0.14.2-5.1build2) ... 231s Selecting previously unselected package python3-imagesize. 231s Preparing to unpack .../150-python3-imagesize_1.4.1-1_all.deb ... 231s Unpacking python3-imagesize (1.4.1-1) ... 231s Selecting previously unselected package python3-iniconfig. 231s Preparing to unpack .../151-python3-iniconfig_1.1.1-2_all.deb ... 231s Unpacking python3-iniconfig (1.1.1-2) ... 231s Selecting previously unselected package python3-parso. 231s Preparing to unpack .../152-python3-parso_0.8.3-1_all.deb ... 231s Unpacking python3-parso (0.8.3-1) ... 231s Selecting previously unselected package python3-typeshed. 231s Preparing to unpack .../153-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 231s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 231s Selecting previously unselected package python3-jedi. 231s Preparing to unpack .../154-python3-jedi_0.19.1+ds1-1_all.deb ... 231s Unpacking python3-jedi (0.19.1+ds1-1) ... 231s Selecting previously unselected package python3-traitlets. 232s Preparing to unpack .../155-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 232s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 232s Selecting previously unselected package python3-matplotlib-inline. 232s Preparing to unpack .../156-python3-matplotlib-inline_0.1.6-2_all.deb ... 232s Unpacking python3-matplotlib-inline (0.1.6-2) ... 232s Selecting previously unselected package python3-wcwidth. 232s Preparing to unpack .../157-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 232s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 232s Selecting previously unselected package python3-prompt-toolkit. 232s Preparing to unpack .../158-python3-prompt-toolkit_3.0.48-1_all.deb ... 232s Unpacking python3-prompt-toolkit (3.0.48-1) ... 232s Selecting previously unselected package python3-pure-eval. 232s Preparing to unpack .../159-python3-pure-eval_0.2.3-1_all.deb ... 232s Unpacking python3-pure-eval (0.2.3-1) ... 232s Selecting previously unselected package python3-stack-data. 232s Preparing to unpack .../160-python3-stack-data_0.6.3-1_all.deb ... 232s Unpacking python3-stack-data (0.6.3-1) ... 232s Selecting previously unselected package python3-ptyprocess. 232s Preparing to unpack .../161-python3-ptyprocess_0.7.0-6_all.deb ... 232s Unpacking python3-ptyprocess (0.7.0-6) ... 232s Selecting previously unselected package python3-pexpect. 232s Preparing to unpack .../162-python3-pexpect_4.9-2_all.deb ... 232s Unpacking python3-pexpect (4.9-2) ... 232s Selecting previously unselected package python3-ipython. 232s Preparing to unpack .../163-python3-ipython_8.29.0-1_all.deb ... 232s Unpacking python3-ipython (8.29.0-1) ... 232s Selecting previously unselected package python3-joblib. 232s Preparing to unpack .../164-python3-joblib_1.3.2-5_all.deb ... 232s Unpacking python3-joblib (1.3.2-5) ... 232s Selecting previously unselected package python3-kiwisolver. 232s Preparing to unpack .../165-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 232s Unpacking python3-kiwisolver (1.4.7-2build1) ... 232s Selecting previously unselected package libopenjp2-7:arm64. 232s Preparing to unpack .../166-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 232s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 232s Selecting previously unselected package python3-pil:arm64. 232s Preparing to unpack .../167-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 232s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 232s Selecting previously unselected package python3.12-tk. 232s Preparing to unpack .../168-python3.12-tk_3.12.7-3_arm64.deb ... 232s Unpacking python3.12-tk (3.12.7-3) ... 232s Selecting previously unselected package python3.13-tk. 232s Preparing to unpack .../169-python3.13-tk_3.13.0-2_arm64.deb ... 232s Unpacking python3.13-tk (3.13.0-2) ... 232s Selecting previously unselected package python3-tk:arm64. 232s Preparing to unpack .../170-python3-tk_3.12.7-1_arm64.deb ... 232s Unpacking python3-tk:arm64 (3.12.7-1) ... 233s Selecting previously unselected package python3-pil.imagetk:arm64. 233s Preparing to unpack .../171-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 233s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 233s Selecting previously unselected package python3-packaging. 233s Preparing to unpack .../172-python3-packaging_24.2-1_all.deb ... 233s Unpacking python3-packaging (24.2-1) ... 233s Selecting previously unselected package python3-matplotlib. 233s Preparing to unpack .../173-python3-matplotlib_3.8.3-3_arm64.deb ... 233s Unpacking python3-matplotlib (3.8.3-3) ... 233s Selecting previously unselected package python3-natsort. 233s Preparing to unpack .../174-python3-natsort_8.0.2-2_all.deb ... 233s Unpacking python3-natsort (8.0.2-2) ... 233s Selecting previously unselected package sphinx-common. 233s Preparing to unpack .../175-sphinx-common_7.4.7-4_all.deb ... 233s Unpacking sphinx-common (7.4.7-4) ... 233s Selecting previously unselected package python3-alabaster. 233s Preparing to unpack .../176-python3-alabaster_0.7.16-0.1_all.deb ... 233s Unpacking python3-alabaster (0.7.16-0.1) ... 233s Selecting previously unselected package python3-snowballstemmer. 233s Preparing to unpack .../177-python3-snowballstemmer_2.2.0-4build1_all.deb ... 233s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 233s Selecting previously unselected package python3-sphinx. 233s Preparing to unpack .../178-python3-sphinx_7.4.7-4_all.deb ... 233s Unpacking python3-sphinx (7.4.7-4) ... 233s Selecting previously unselected package python3-tabulate. 233s Preparing to unpack .../179-python3-tabulate_0.9.0-1_all.deb ... 233s Unpacking python3-tabulate (0.9.0-1) ... 233s Selecting previously unselected package python3-numpydoc. 233s Preparing to unpack .../180-python3-numpydoc_1.6.0-2_all.deb ... 233s Unpacking python3-numpydoc (1.6.0-2) ... 233s Selecting previously unselected package python3-patsy. 233s Preparing to unpack .../181-python3-patsy_1.0.1-1_all.deb ... 233s Unpacking python3-patsy (1.0.1-1) ... 233s Selecting previously unselected package python3-pluggy. 234s Preparing to unpack .../182-python3-pluggy_1.5.0-1_all.deb ... 234s Unpacking python3-pluggy (1.5.0-1) ... 234s Selecting previously unselected package python3-pydata-sphinx-theme. 234s Preparing to unpack .../183-python3-pydata-sphinx-theme_0.15.4+dfsg-2_all.deb ... 234s Unpacking python3-pydata-sphinx-theme (0.15.4+dfsg-2) ... 234s Selecting previously unselected package python3-pytest. 234s Preparing to unpack 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.../194-1-autopkgtest-satdep.deb ... 235s Unpacking autopkgtest-satdep (0) ... 235s Setting up dh-python (6.20241024) ... 235s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 235s Setting up libsimde-dev (0.8.2-1) ... 235s Setting up liblcms2-2:arm64 (2.16-2) ... 235s Setting up python3-iniconfig (1.1.1-2) ... 235s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 235s Setting up python3-pure-eval (0.2.3-1) ... 236s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 236s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 236s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 236s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 236s Setting up python3-joblib (1.3.2-5) ... 236s Setting up python3-parso (0.8.3-1) ... 236s Setting up python3-colorama (0.4.6-4) ... 236s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 236s Setting up python3-defusedxml (0.7.1-2) ... 236s Setting up libarchive-zip-perl (1.68-1) ... 236s Setting up python3-asttokens (2.4.1-2) ... 237s Setting up architecture-properties:arm64 (0.2.3) ... 237s Setting up python3-alabaster (0.7.16-0.1) ... 237s Setting up fonts-lyx (2.4.2.1-1) ... 237s Setting up libdebhelper-perl (13.20ubuntu1) ... 237s Setting up python3-threadpoolctl (3.1.0-1) ... 237s Setting up x11-common (1:7.7+23ubuntu3) ... 237s Setting up libdeflate0:arm64 (1.22-1) ... 237s Setting up python3-tabulate (0.9.0-1) ... 237s Setting up m4 (1.4.19-4build1) ... 237s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 237s Setting up python3-all (3.12.6-0ubuntu1) ... 237s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 237s Setting up python3-click (8.1.7-2) ... 238s Setting up fonts-open-sans (1.11-2) ... 238s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 238s Setting up libaec0:arm64 (1.1.3-1) ... 238s Setting up python3-tz (2024.1-2) ... 238s Setting up python3-natsort (8.0.2-2) ... 238s Setting up unicode-data (15.1.0-1) ... 238s Setting up python3-six (1.16.0-7) ... 238s Setting up python3-roman (4.2-1) ... 238s Setting up python3-decorator (5.1.1-5) ... 238s Setting up autotools-dev (20220109.1) ... 238s Setting up libblas3:arm64 (3.12.0-3build2) ... 238s 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 238s Setting up python3-packaging (24.2-1) ... 238s Setting up libexpat1-dev:arm64 (2.6.4-1) ... 238s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 239s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 239s Setting up python3-executing (2.1.0-0.1) ... 239s Setting up python3-snowballstemmer (2.2.0-4build1) ... 239s Setting up python3-brotli (1.1.0-2build3) ... 239s Setting up liblzf1:arm64 (3.6-4) ... 239s Setting up python3-cycler (0.12.1-1) ... 239s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 239s Setting up fonts-dejavu-mono (2.37-8) ... 239s Setting up python3-kiwisolver (1.4.7-2build1) ... 239s Setting up libmpc3:arm64 (1.3.1-1build2) ... 239s Setting up 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Removing autopkgtest-satdep (0) ... 289s autopkgtest [16:38:04]: test pybuild-autopkgtest: pybuild-autopkgtest 289s autopkgtest [16:38:04]: test pybuild-autopkgtest: [----------------------- 290s pybuild-autopkgtest 290s I: pybuild base:311: cd /tmp/autopkgtest.nZe3r8/autopkgtest_tmp/build; python3.12 -m pytest --pyargs skbio 294s ============================= test session starts ============================== 294s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 294s rootdir: /tmp/autopkgtest.nZe3r8/autopkgtest_tmp/build 294s configfile: pyproject.toml 294s plugins: typeguard-4.4.1 294s collected 2793 items 294s 294s alignment/tests/test_pairwise.py ......................... 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[ 94%] 410s tree/tests/test_tree.py ................................................ [ 96%] 410s ........................................................ [ 98%] 410s util/tests/test_decorator.py ........ [ 98%] 410s util/tests/test_misc.py .................... [ 99%] 410s util/tests/test_plotting.py ...... [ 99%] 410s util/tests/test_testing.py ............... [100%] 410s 410s =============================== warnings summary =============================== 410s alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 410s /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. 410s warn( 410s 410s alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 410s /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. 410s warn( 410s 410s alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 410s /usr/lib/python3/dist-packages/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 410s gap_freqs /= length 410s 410s diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 410s /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. 410s warn( 410s 410s metadata/tests/test_io.py: 10 warnings 410s /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)` 410s series = series.replace("", np.nan) 410s 410s metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 410s metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 410s metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 410s /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. 410s series[missing.index] = missing 410s 410s metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 410s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 410s /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. 410s pdt.assert_series_equal(missing, series.astype(object)) 410s 410s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 410s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 410s /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. 410s pdt.assert_series_equal(missing, series[1:].astype(object)) 410s 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 410s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 410s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 410s 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 410s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 410s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 410s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 410s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 410s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 410s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 410s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 410s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 410s 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 410s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 410s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 410s 410s sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 410s /usr/lib/python3/dist-packages/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 410s obs_counts = obs_counts / len(self) 410s 410s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 410s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 410s warnings.warn(ConstantInputWarning()) 410s 410s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 410s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 410s warnings.warn(ConstantInputWarning()) 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 410s /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 -0.00657367754955049 and the largest is 0.17668321589384078. 410s warn( 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 410s /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 -13.541846544269621 and the largest is 16.587201374785895. 410s warn( 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 410s /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 -15.629533932395201 and the largest is 20.903154277938906. 410s warn( 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 410s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 410s proportion_explained = eigvals / sum_eigenvalues 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 410s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:563: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 410s res = hypotest_fun_out(*samples, axis=axis, **kwds) 410s 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 410s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 410s /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 -0.007758325147780542 and the largest is 2.7077929489469237. 410s warn( 410s 410s stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 410s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 410s return self.run(*args, **kwds) 410s 410s stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 410s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 410s warn(f"{func.__name__} is deprecated as of {ver}.") 410s 410s stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 410s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 410s res = hypotest_fun_out(*samples, **kwds) 410s 410s stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 410s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 410s warn(f"{func.__name__} is deprecated as of {ver}.") 410s 410s stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 410s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 410s res = hypotest_fun_out(*samples, **kwds) 410s 410s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 410s /usr/lib/python3/dist-packages/skbio/stats/composition.py:947: RuntimeWarning: divide by zero encountered in log 410s X_log = np.log(mat) 410s 410s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 410s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 410s X -= avg[:, None] 410s 410s stats/tests/test_composition.py::VLRTests::test_vlr 410s /usr/lib/python3/dist-packages/skbio/stats/composition.py:831: RuntimeWarning: divide by zero encountered in log 410s x = np.log(x) 410s 410s stats/tests/test_composition.py::VLRTests::test_vlr 410s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 410s x = asanyarray(arr - arrmean) 410s 410s stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 410s /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. 410s trajectories.loc[idx] = ( 410s 410s tree/tests/test_tree.py::TreeTests::test_root_at 410s /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`. 410s warn( 410s 410s tree/tests/test_tree.py::TreeTests::test_root_at 410s /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`. 410s warn( 410s 410s tree/tests/test_tree.py::TreeTests::test_root_at_midpoint 410s /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`. 410s warn( 410s 410s tree/tests/test_tree.py::TreeTests::test_unrooted_deepcopy 410s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: unrooted_deepcopy is deprecated as of 0.6.2. Use unrooted_copy instead. 410s warn( 410s 410s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 410s ========== 2763 passed, 30 skipped, 70 warnings in 118.72s (0:01:58) =========== 411s autopkgtest [16:40:06]: test pybuild-autopkgtest: -----------------------] 412s pybuild-autopkgtest PASS 412s autopkgtest [16:40:07]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 412s autopkgtest [16:40:07]: @@@@@@@@@@@@@@@@@@@@ summary 412s pybuild-autopkgtest PASS 423s nova [W] Skipping flock in bos03-arm64 423s Creating nova instance adt-plucky-arm64-python-skbio-20241118-163315-juju-7f2275-prod-proposed-migration-environment-20-d3a7f61e-01f3-498c-8796-c215925b87ab from image adt/ubuntu-plucky-arm64-server-20241117.img (UUID 346584db-208f-4446-ae16-5eaab5e37305)...