0s autopkgtest [12:51:33]: starting date and time: 2025-02-19 12:51:33+0000 0s autopkgtest [12:51:33]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:51:33]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c63g4bzg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-34.secgroup --name adt-plucky-arm64-python-skbio-20250219-125133-juju-7f2275-prod-proposed-migration-environment-15-3be24773-ec73-4fa9-a125-8d755016d10f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 160s autopkgtest [12:54:13]: testbed dpkg architecture: arm64 161s autopkgtest [12:54:14]: testbed apt version: 2.9.29 161s autopkgtest [12:54:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 161s autopkgtest [12:54:14]: testbed release detected to be: None 162s autopkgtest [12:54:15]: updating testbed package index (apt update) 162s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 163s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 163s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 163s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 163s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 163s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 163s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 163s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 163s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 163s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 163s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 163s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 163s Fetched 1752 kB in 1s (1899 kB/s) 164s Reading package lists... 165s + lsb_release --codename --short 165s + RELEASE=plucky 165s + cat 165s + [ plucky != trusty ] 165s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 166s Calculating upgrade... 166s The following NEW packages will be installed: 166s libapt-pkg7.0 166s The following packages will be upgraded: 166s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 166s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 4842 kB of archives. 166s After this operation, 3409 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 167s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 167s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 167s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 168s Preconfiguring packages ... 168s Fetched 4842 kB in 1s (4605 kB/s) 168s Selecting previously unselected package libapt-pkg7.0:arm64. 168s (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 ... 116620 files and directories currently installed.) 168s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 168s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 168s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 168s (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 ... 116669 files and directories currently installed.) 168s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 168s Unpacking apt (2.9.30) over (2.9.29) ... 169s Setting up apt (2.9.30) ... 169s (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 ... 116669 files and directories currently installed.) 169s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 169s Unpacking apt-utils (2.9.30) over (2.9.29) ... 169s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 169s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 170s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 170s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 170s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 170s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 170s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 170s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 170s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 170s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 170s Setting up apt-utils (2.9.30) ... 170s Setting up liblsof0 (4.99.4+dfsg-1) ... 170s Setting up iproute2 (6.13.0-1ubuntu1) ... 170s Setting up rsyslog (8.2412.0-2ubuntu1) ... 170s info: The user `syslog' is already a member of `adm'. 171s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 171s Setting up lsof (4.99.4+dfsg-1) ... 171s Processing triggers for man-db (2.13.0-1) ... 173s Processing triggers for libc-bin (2.40-4ubuntu1) ... 173s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 173s + /usr/lib/apt/apt-helper analyze-pattern ?true 173s + uname -r 173s + sed s/\./\\./g 173s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 173s + apt list ?obsolete 173s + tail -n+2 173s + cut -d/ -f1 173s + grep -v ^linux-.*6\.12\.0-15-generic.* 175s + true 175s + obsolete_pkgs= 175s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s + grep -q trusty /etc/lsb-release 177s + [ ! -d /usr/share/doc/unattended-upgrades ] 177s + [ ! -d /usr/share/doc/lxd ] 177s + [ ! -d /usr/share/doc/lxd-client ] 177s + [ ! -d /usr/share/doc/snapd ] 177s + type iptables 177s + cat 177s + chmod 755 /etc/rc.local 177s + . /etc/rc.local 177s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 177s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 177s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 177s + uname -m 177s + [ aarch64 = ppc64le ] 177s + [ -d /run/systemd/system ] 177s + systemd-detect-virt --quiet --vm 177s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 177s + cat 177s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 177s + echo COMPRESS=lz4 177s autopkgtest [12:54:29]: upgrading testbed (apt dist-upgrade and autopurge) 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s Entering ResolveByKeep 178s 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s autopkgtest [12:54:34]: rebooting testbed after setup commands that affected boot 205s autopkgtest [12:54:58]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 208s autopkgtest [12:55:01]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-4build1 (dsc) [2921 B] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-4build1 (tar) [2204 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-skbio 0.6.2-4build1 (diff) [12.0 kB] 211s gpgv: Signature made Fri Jan 31 09:41:17 2025 UTC 211s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.6.2-4build1.dsc: no acceptable signature found 211s autopkgtest [12:55:04]: testing package python-skbio version 0.6.2-4build1 212s autopkgtest [12:55:05]: build not needed 213s autopkgtest [12:55:06]: test pybuild-autopkgtest: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 215s The following NEW packages will be installed: 215s architecture-properties autoconf automake autopoint autotools-dev blt 215s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 215s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 215s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 215s fonts-lyx fonts-mathjax fonts-open-sans g++ g++-14 g++-14-aarch64-linux-gnu 215s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 215s gcc-aarch64-linux-gnu gettext intltool-debian libaec0 libarchive-zip-perl 215s libasan8 libblas3 libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev 215s libfile-stripnondeterminism-perl libfontconfig1 libgcc-14-dev libgfortran5 215s libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhwasan0 215s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 215s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 215s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 215s libmpc3 libopenjp2-7 libpython3-all-dev libpython3-dev libpython3.12-dev 215s libpython3.13-dev libqhull-r8.0 libraqm0 libsharpyuv0 libsimde-dev 215s libssw-dev libssw0 libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 215s libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxft2 215s libxrender1 libxslt1.1 libxss1 m4 node-fortawesome-fontawesome-free 215s po-debconf pybuild-plugin-autopkgtest python-biom-format-doc 215s python-matplotlib-data python-numpy-doc python-pandas-doc python-scipy-doc 215s python-skbio-doc python3-accessible-pygments python3-alabaster python3-all 215s python3-all-dev python3-asttokens python3-biom-format python3-brotli 215s python3-bs4 python3-cachecontrol python3-click python3-contourpy 215s python3-cycler python3-dateutil python3-decorator python3-defusedxml 215s python3-dev python3-doc python3-docutils python3-executing python3-fonttools 215s python3-fs python3-h5py python3-h5py-serial python3-hdmedians 215s python3-imagesize python3-iniconfig python3-ipython python3-jedi 215s python3-joblib python3-kiwisolver python3-lxml python3-lz4 215s python3-matplotlib python3-matplotlib-inline python3-mpmath python3-msgpack 215s python3-natsort python3-numpy python3-numpydoc python3-packaging 215s python3-pandas python3-pandas-lib python3-parso python3-patsy 215s python3-pexpect python3-pil python3-pil.imagetk python3-platformdirs 215s python3-pluggy python3-prompt-toolkit python3-ptyprocess python3-pure-eval 215s python3-pydata-sphinx-theme python3-pytest python3-pytz python3-roman 215s python3-scipy python3-skbio python3-sklearn python3-sklearn-lib 215s python3-snowballstemmer python3-soupsieve python3-sphinx 215s python3-sphinx-copybutton python3-sphinx-design python3-stack-data 215s python3-statsmodels python3-statsmodels-lib python3-sympy python3-tabulate 215s python3-threadpoolctl python3-tk python3-traitlets python3-typeshed 215s python3-tz python3-ufolib2 python3-wcwidth python3.12 python3.12-dev 215s python3.12-minimal python3.12-tk python3.13-dev python3.13-doc python3.13-tk 215s sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core 215s zlib1g-dev 215s 0 upgraded, 199 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 227 MB of archives. 215s After this operation, 1347 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 216s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 216s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 216s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 architecture-properties arm64 0.2.5 [2150 B] 216s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-5 [244 kB] 216s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 216s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 216s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3 [572 kB] 216s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 216s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 216s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 216s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 216s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 216s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 216s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 216s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 216s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 216s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 216s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 216s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 216s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 216s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 216s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 216s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [10.6 MB] 217s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu1 [1032 B] 217s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 217s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 217s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250213-1ubuntu1 [44.2 kB] 217s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 217s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250213-1ubuntu1 [28.0 kB] 217s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250213-1ubuntu1 [2928 kB] 217s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250213-1ubuntu1 [1319 kB] 217s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250213-1ubuntu1 [2695 kB] 217s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250213-1ubuntu1 [1178 kB] 217s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250213-1ubuntu1 [1642 kB] 217s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu1 [2593 kB] 217s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [20.9 MB] 218s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu1 [526 kB] 218s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 218s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 218s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu1 [2499 kB] 218s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [12.1 MB] 219s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu1 [21.8 kB] 219s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 219s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 219s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 219s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu1 [2974 kB] 219s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 219s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-3build1 [168 kB] 219s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 219s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 219s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 219s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 219s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 219s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 219s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 219s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 219s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 219s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 219s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250108 [117 kB] 219s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 219s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 219s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 219s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 219s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-open-sans all 1.11-2 [635 kB] 219s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 219s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 219s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 219s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 219s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 219s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 219s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 219s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 219s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 219s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 219s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 219s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 219s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 219s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 219s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 219s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 219s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 219s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 219s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 219s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 219s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 219s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 219s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 219s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 219s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB] 220s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.1-1~exp2 [10.5 kB] 220s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.9-1 [5569 kB] 220s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.13.1-1~exp2 [922 B] 220s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 220s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 220s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 220s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsimde-dev all 0.8.2-1 [466 kB] 220s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw0 arm64 1.1-15 [21.8 kB] 220s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw-dev arm64 1.1-15 [23.6 kB] 220s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 220s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 220s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 220s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 220s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 220s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 220s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-fortawesome-fontawesome-free all 6.7.2+ds1-1 [1653 kB] 221s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20250108 [1744 B] 221s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1build2 [57.5 kB] 221s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 222s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 python-numpy-doc all 1:1.26.4+ds-13 [5471 kB] 222s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 223s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-pandas-doc all 2.2.3+dfsg-8 [10.7 MB] 224s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-skbio-doc all 0.6.2-4build1 [2342 kB] 224s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-accessible-pygments all 0.0.5-2 [790 kB] 224s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 224s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB] 224s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.1-1~exp2 [26.7 kB] 224s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.9-1 [505 kB] 224s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.13.1-1~exp2 [918 B] 224s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 224s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 224s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.12.1-1 [1453 kB] 224s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.12.1-1 [7970 B] 224s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.8-1 [79.8 kB] 224s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 224s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 224s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 224s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 224s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 224s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 224s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 226s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build2 [165 kB] 226s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 226s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-soupsieve all 2.6-1 [33.0 kB] 226s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-bs4 all 4.13.3-1 [136 kB] 226s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build3 [106 kB] 226s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cachecontrol all 0.14.2-1 [18.7 kB] 226s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 226s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 226s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 226s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-doc all 3.13.2-1 [14.2 MB] 226s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-doc all 3.13.1-1~exp2 [10.4 kB] 226s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 5.0-1 [10.3 kB] 226s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 226s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.2.0-0.1 [25.0 kB] 226s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 226s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 226s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 227s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 227s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 227s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 227s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 227s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 228s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 228s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdmedians arm64 0.14.2-6 [181 kB] 228s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 228s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 228s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 228s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 228s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 228s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 228s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 228s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 228s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 228s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 228s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 228s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 228s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 228s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.30.0-2 [569 kB] 228s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-2 [205 kB] 228s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 228s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 228s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 228s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 228s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 228s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 228s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 228s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 228s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 228s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 228s Get:181 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 sphinx-common all 8.1.3-5 [663 kB] 228s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 228s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 228s Get:184 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-sphinx all 8.1.3-5 [474 kB] 228s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 228s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numpydoc all 1.8.0-1 [52.4 kB] 228s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-patsy all 1.0.1-1 [180 kB] 229s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 229s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pydata-sphinx-theme all 0.16.1+dfsg-1 [958 kB] 229s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 229s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1build2 [2511 kB] 229s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels all 0.14.4+dfsg-1build2 [5012 kB] 229s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-skbio arm64 0.6.2-4build1 [1499 kB] 229s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 229s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7build1 [6372 kB] 230s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 230s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-copybutton all 0.5.2-2 [16.6 kB] 230s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-design all 0.6.1-1 [894 kB] 230s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-scipy-doc all 1.14.1-4ubuntu1 [32.6 kB] 231s Fetched 227 MB in 16s (14.6 MB/s) 231s Selecting previously unselected package python3.12-minimal. 231s (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 ... 116670 files and directories currently installed.) 231s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 231s Unpacking python3.12-minimal (3.12.9-1) ... 232s Selecting previously unselected package sgml-base. 232s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 232s Unpacking sgml-base (1.31) ... 232s Selecting previously unselected package python3.12. 232s Preparing to unpack .../002-python3.12_3.12.9-1_arm64.deb ... 232s Unpacking python3.12 (3.12.9-1) ... 232s Selecting previously unselected package architecture-properties:arm64. 232s Preparing to unpack .../003-architecture-properties_0.2.5_arm64.deb ... 232s Unpacking architecture-properties:arm64 (0.2.5) ... 232s Selecting previously unselected package m4. 232s Preparing to unpack .../004-m4_1.4.19-5_arm64.deb ... 232s Unpacking m4 (1.4.19-5) ... 232s Selecting previously unselected package autoconf. 232s Preparing to unpack .../005-autoconf_2.72-3_all.deb ... 232s Unpacking autoconf (2.72-3) ... 232s Selecting previously unselected package autotools-dev. 232s Preparing to unpack .../006-autotools-dev_20220109.1_all.deb ... 232s Unpacking autotools-dev (20220109.1) ... 232s Selecting previously unselected package automake. 232s Preparing to unpack .../007-automake_1%3a1.17-3_all.deb ... 232s Unpacking automake (1:1.17-3) ... 232s Selecting previously unselected package autopoint. 232s Preparing to unpack .../008-autopoint_0.23.1-1_all.deb ... 232s Unpacking autopoint (0.23.1-1) ... 232s Selecting previously unselected package libtcl8.6:arm64. 232s Preparing to unpack .../009-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 232s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 232s Selecting previously unselected package fonts-dejavu-mono. 232s Preparing to unpack .../010-fonts-dejavu-mono_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-mono (2.37-8) ... 232s Selecting previously unselected package fonts-dejavu-core. 232s Preparing to unpack .../011-fonts-dejavu-core_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-core (2.37-8) ... 232s Selecting previously unselected package fontconfig-config. 232s Preparing to unpack .../012-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 233s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 233s Selecting previously unselected package libfontconfig1:arm64. 233s Preparing to unpack .../013-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 233s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 233s Selecting previously unselected package libxrender1:arm64. 233s Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 233s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 233s Selecting previously unselected package libxft2:arm64. 233s Preparing to unpack .../015-libxft2_2.3.6-1build1_arm64.deb ... 233s Unpacking libxft2:arm64 (2.3.6-1build1) ... 233s Selecting previously unselected package x11-common. 233s Preparing to unpack .../016-x11-common_1%3a7.7+23ubuntu3_all.deb ... 233s Unpacking x11-common (1:7.7+23ubuntu3) ... 233s Selecting previously unselected package libxss1:arm64. 233s Preparing to unpack .../017-libxss1_1%3a1.2.3-1build3_arm64.deb ... 233s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 233s Selecting previously unselected package libtk8.6:arm64. 233s Preparing to unpack .../018-libtk8.6_8.6.16-1_arm64.deb ... 233s Unpacking libtk8.6:arm64 (8.6.16-1) ... 233s Selecting previously unselected package tk8.6-blt2.5. 233s Preparing to unpack .../019-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 233s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 233s Selecting previously unselected package blt. 233s Preparing to unpack .../020-blt_2.5.3+dfsg-7build1_arm64.deb ... 233s Unpacking blt (2.5.3+dfsg-7build1) ... 233s Selecting previously unselected package libisl23:arm64. 233s Preparing to unpack .../021-libisl23_0.27-1_arm64.deb ... 233s Unpacking libisl23:arm64 (0.27-1) ... 233s Selecting previously unselected package libmpc3:arm64. 233s Preparing to unpack .../022-libmpc3_1.3.1-1build2_arm64.deb ... 233s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 233s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 233s Preparing to unpack .../023-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 233s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 233s Selecting previously unselected package cpp-14. 233s Preparing to unpack .../024-cpp-14_14.2.0-17ubuntu1_arm64.deb ... 233s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 233s Selecting previously unselected package cpp-aarch64-linux-gnu. 233s Preparing to unpack .../025-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 233s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 233s Selecting previously unselected package cpp. 233s Preparing to unpack .../026-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 233s Unpacking cpp (4:14.2.0-1ubuntu1) ... 234s Selecting previously unselected package libcc1-0:arm64. 234s Preparing to unpack .../027-libcc1-0_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libcc1-0:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libgomp1:arm64. 234s Preparing to unpack .../028-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libitm1:arm64. 234s Preparing to unpack .../029-libitm1_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libitm1:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libasan8:arm64. 234s Preparing to unpack .../030-libasan8_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libasan8:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package liblsan0:arm64. 234s Preparing to unpack .../031-liblsan0_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking liblsan0:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libtsan2:arm64. 234s Preparing to unpack .../032-libtsan2_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libtsan2:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libubsan1:arm64. 234s Preparing to unpack .../033-libubsan1_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libubsan1:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libhwasan0:arm64. 234s Preparing to unpack .../034-libhwasan0_15-20250213-1ubuntu1_arm64.deb ... 234s Unpacking libhwasan0:arm64 (15-20250213-1ubuntu1) ... 234s Selecting previously unselected package libgcc-14-dev:arm64. 234s Preparing to unpack .../035-libgcc-14-dev_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 234s Preparing to unpack .../036-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 235s Selecting previously unselected package gcc-14. 235s Preparing to unpack .../037-gcc-14_14.2.0-17ubuntu1_arm64.deb ... 235s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 235s Selecting previously unselected package gcc-aarch64-linux-gnu. 235s Preparing to unpack .../038-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 235s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 235s Selecting previously unselected package gcc. 235s Preparing to unpack .../039-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 235s Unpacking gcc (4:14.2.0-1ubuntu1) ... 235s Selecting previously unselected package libstdc++-14-dev:arm64. 235s Preparing to unpack .../040-libstdc++-14-dev_14.2.0-17ubuntu1_arm64.deb ... 235s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 235s Selecting previously unselected package g++-14-aarch64-linux-gnu. 235s Preparing to unpack .../041-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 235s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 236s Selecting previously unselected package g++-14. 236s Preparing to unpack .../042-g++-14_14.2.0-17ubuntu1_arm64.deb ... 236s Unpacking g++-14 (14.2.0-17ubuntu1) ... 236s Selecting previously unselected package g++-aarch64-linux-gnu. 236s Preparing to unpack .../043-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 236s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 236s Selecting previously unselected package g++. 236s Preparing to unpack .../044-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 236s Unpacking g++ (4:14.2.0-1ubuntu1) ... 236s Selecting previously unselected package build-essential. 236s Preparing to unpack .../045-build-essential_12.10ubuntu1_arm64.deb ... 236s Unpacking build-essential (12.10ubuntu1) ... 236s Selecting previously unselected package cython3. 236s Preparing to unpack .../046-cython3_3.0.11+dfsg-2ubuntu1_arm64.deb ... 236s Unpacking cython3 (3.0.11+dfsg-2ubuntu1) ... 236s Selecting previously unselected package libdebhelper-perl. 236s Preparing to unpack .../047-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 236s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 236s Selecting previously unselected package libtool. 236s Preparing to unpack .../048-libtool_2.5.4-3build1_all.deb ... 236s Unpacking libtool (2.5.4-3build1) ... 236s Selecting previously unselected package dh-autoreconf. 236s Preparing to unpack .../049-dh-autoreconf_20_all.deb ... 236s Unpacking dh-autoreconf (20) ... 236s Selecting previously unselected package libarchive-zip-perl. 236s Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... 236s Unpacking libarchive-zip-perl (1.68-1) ... 236s Selecting previously unselected package libfile-stripnondeterminism-perl. 236s Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 236s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 236s Selecting previously unselected package dh-strip-nondeterminism. 236s Preparing to unpack .../052-dh-strip-nondeterminism_1.14.1-2_all.deb ... 236s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 236s Selecting previously unselected package debugedit. 237s Preparing to unpack .../053-debugedit_1%3a5.1-2_arm64.deb ... 237s Unpacking debugedit (1:5.1-2) ... 237s Selecting previously unselected package dwz. 237s Preparing to unpack .../054-dwz_0.15-1build6_arm64.deb ... 237s Unpacking dwz (0.15-1build6) ... 237s Selecting previously unselected package gettext. 237s Preparing to unpack .../055-gettext_0.23.1-1_arm64.deb ... 237s Unpacking gettext (0.23.1-1) ... 237s Selecting previously unselected package intltool-debian. 237s Preparing to unpack .../056-intltool-debian_0.35.0+20060710.6_all.deb ... 237s Unpacking intltool-debian (0.35.0+20060710.6) ... 237s Selecting previously unselected package po-debconf. 237s Preparing to unpack .../057-po-debconf_1.0.21+nmu1_all.deb ... 237s Unpacking po-debconf (1.0.21+nmu1) ... 237s Selecting previously unselected package debhelper. 237s Preparing to unpack .../058-debhelper_13.24.1ubuntu2_all.deb ... 237s Unpacking debhelper (13.24.1ubuntu2) ... 237s Selecting previously unselected package dh-python. 237s Preparing to unpack .../059-dh-python_6.20250108_all.deb ... 237s Unpacking dh-python (6.20250108) ... 237s Selecting previously unselected package xml-core. 237s Preparing to unpack .../060-xml-core_0.19_all.deb ... 237s Unpacking xml-core (0.19) ... 237s Selecting previously unselected package docutils-common. 237s Preparing to unpack .../061-docutils-common_0.21.2+dfsg-2_all.deb ... 237s Unpacking docutils-common (0.21.2+dfsg-2) ... 237s Selecting previously unselected package fonts-lyx. 237s Preparing to unpack .../062-fonts-lyx_2.4.3-1_all.deb ... 237s Unpacking fonts-lyx (2.4.3-1) ... 238s Selecting previously unselected package fonts-mathjax. 238s Preparing to unpack .../063-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 238s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 238s Selecting previously unselected package fonts-open-sans. 238s Preparing to unpack .../064-fonts-open-sans_1.11-2_all.deb ... 238s Unpacking fonts-open-sans (1.11-2) ... 238s Selecting previously unselected package libaec0:arm64. 238s Preparing to unpack .../065-libaec0_1.1.3-1_arm64.deb ... 238s Unpacking libaec0:arm64 (1.1.3-1) ... 238s Selecting previously unselected package libblas3:arm64. 238s Preparing to unpack .../066-libblas3_3.12.1-2_arm64.deb ... 238s Unpacking libblas3:arm64 (3.12.1-2) ... 238s Selecting previously unselected package libdeflate0:arm64. 238s Preparing to unpack .../067-libdeflate0_1.23-1_arm64.deb ... 238s Unpacking libdeflate0:arm64 (1.23-1) ... 238s Selecting previously unselected package libexpat1-dev:arm64. 238s Preparing to unpack .../068-libexpat1-dev_2.6.4-1_arm64.deb ... 238s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 238s Selecting previously unselected package libgfortran5:arm64. 238s Preparing to unpack .../069-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 238s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 238s Selecting previously unselected package libgraphite2-3:arm64. 238s Preparing to unpack .../070-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 238s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 238s Selecting previously unselected package libharfbuzz0b:arm64. 238s Preparing to unpack .../071-libharfbuzz0b_10.2.0-1_arm64.deb ... 238s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 238s Selecting previously unselected package libsz2:arm64. 238s Preparing to unpack .../072-libsz2_1.1.3-1_arm64.deb ... 238s Unpacking libsz2:arm64 (1.1.3-1) ... 238s Selecting previously unselected package libhdf5-310:arm64. 238s Preparing to unpack .../073-libhdf5-310_1.14.5+repack-3_arm64.deb ... 238s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 238s Selecting previously unselected package libhdf5-hl-310:arm64. 238s Preparing to unpack .../074-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 238s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 238s Selecting previously unselected package libimagequant0:arm64. 238s Preparing to unpack .../075-libimagequant0_2.18.0-1build1_arm64.deb ... 238s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 238s Selecting previously unselected package libjpeg-turbo8:arm64. 238s Preparing to unpack .../076-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 238s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 238s Selecting previously unselected package libjpeg8:arm64. 239s Preparing to unpack .../077-libjpeg8_8c-2ubuntu11_arm64.deb ... 239s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 239s Selecting previously unselected package libjs-jquery. 239s Preparing to unpack .../078-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 239s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 239s Selecting previously unselected package libjs-jquery-ui. 239s Preparing to unpack .../079-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 239s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 239s Selecting previously unselected package libjs-underscore. 239s Preparing to unpack .../080-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 239s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 239s Selecting previously unselected package libjs-sphinxdoc. 239s Preparing to unpack .../081-libjs-sphinxdoc_8.1.3-5_all.deb ... 239s Unpacking libjs-sphinxdoc (8.1.3-5) ... 239s Selecting previously unselected package libjson-perl. 239s Preparing to unpack .../082-libjson-perl_4.10000-1_all.deb ... 239s Unpacking libjson-perl (4.10000-1) ... 239s Selecting previously unselected package liblapack3:arm64. 239s Preparing to unpack .../083-liblapack3_3.12.1-2_arm64.deb ... 239s Unpacking liblapack3:arm64 (3.12.1-2) ... 239s Selecting previously unselected package liblbfgsb0:arm64. 239s Preparing to unpack .../084-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 239s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 239s Selecting previously unselected package liblcms2-2:arm64. 239s Preparing to unpack .../085-liblcms2-2_2.16-2_arm64.deb ... 239s Unpacking liblcms2-2:arm64 (2.16-2) ... 239s Selecting previously unselected package liblerc4:arm64. 239s Preparing to unpack .../086-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 239s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 239s Selecting previously unselected package liblzf1:arm64. 239s Preparing to unpack .../087-liblzf1_3.6-4_arm64.deb ... 239s Unpacking liblzf1:arm64 (3.6-4) ... 239s Selecting previously unselected package zlib1g-dev:arm64. 239s Preparing to unpack .../088-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 239s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 239s Selecting previously unselected package libpython3.13-dev:arm64. 239s Preparing to unpack .../089-libpython3.13-dev_3.13.2-1_arm64.deb ... 239s Unpacking libpython3.13-dev:arm64 (3.13.2-1) ... 240s Selecting previously unselected package libpython3-dev:arm64. 240s Preparing to unpack .../090-libpython3-dev_3.13.1-1~exp2_arm64.deb ... 240s Unpacking libpython3-dev:arm64 (3.13.1-1~exp2) ... 240s Selecting previously unselected package libpython3.12-dev:arm64. 240s Preparing to unpack .../091-libpython3.12-dev_3.12.9-1_arm64.deb ... 240s Unpacking libpython3.12-dev:arm64 (3.12.9-1) ... 240s Selecting previously unselected package libpython3-all-dev:arm64. 240s Preparing to unpack .../092-libpython3-all-dev_3.13.1-1~exp2_arm64.deb ... 240s Unpacking libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 240s Selecting previously unselected package libqhull-r8.0:arm64. 240s Preparing to unpack .../093-libqhull-r8.0_2020.2-6build1_arm64.deb ... 240s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 240s Selecting previously unselected package libraqm0:arm64. 240s Preparing to unpack .../094-libraqm0_0.10.2-1_arm64.deb ... 240s Unpacking libraqm0:arm64 (0.10.2-1) ... 240s Selecting previously unselected package libsharpyuv0:arm64. 240s Preparing to unpack .../095-libsharpyuv0_1.5.0-0.1_arm64.deb ... 240s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 240s Selecting previously unselected package libsimde-dev. 240s Preparing to unpack .../096-libsimde-dev_0.8.2-1_all.deb ... 240s Unpacking libsimde-dev (0.8.2-1) ... 240s Selecting previously unselected package libssw0:arm64. 240s Preparing to unpack .../097-libssw0_1.1-15_arm64.deb ... 240s Unpacking libssw0:arm64 (1.1-15) ... 240s Selecting previously unselected package libssw-dev:arm64. 240s Preparing to unpack .../098-libssw-dev_1.1-15_arm64.deb ... 240s Unpacking libssw-dev:arm64 (1.1-15) ... 240s Selecting previously unselected package libjbig0:arm64. 240s Preparing to unpack .../099-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 240s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 240s Selecting previously unselected package libwebp7:arm64. 240s Preparing to unpack .../100-libwebp7_1.5.0-0.1_arm64.deb ... 240s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 241s Selecting previously unselected package libtiff6:arm64. 241s Preparing to unpack .../101-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 241s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 241s Selecting previously unselected package libwebpdemux2:arm64. 241s Preparing to unpack .../102-libwebpdemux2_1.5.0-0.1_arm64.deb ... 241s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 241s Selecting previously unselected package libwebpmux3:arm64. 241s Preparing to unpack .../103-libwebpmux3_1.5.0-0.1_arm64.deb ... 241s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 241s Selecting previously unselected package libxslt1.1:arm64. 241s Preparing to unpack .../104-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 241s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 241s Selecting previously unselected package node-fortawesome-fontawesome-free. 241s Preparing to unpack .../105-node-fortawesome-fontawesome-free_6.7.2+ds1-1_all.deb ... 241s Unpacking node-fortawesome-fontawesome-free (6.7.2+ds1-1) ... 241s Selecting previously unselected package pybuild-plugin-autopkgtest. 241s Preparing to unpack .../106-pybuild-plugin-autopkgtest_6.20250108_all.deb ... 241s Unpacking pybuild-plugin-autopkgtest (6.20250108) ... 241s Selecting previously unselected package python-biom-format-doc. 241s Preparing to unpack .../107-python-biom-format-doc_2.1.16-1build2_all.deb ... 241s Unpacking python-biom-format-doc (2.1.16-1build2) ... 241s Selecting previously unselected package python-matplotlib-data. 241s Preparing to unpack .../108-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 241s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 241s Selecting previously unselected package python-numpy-doc. 241s Preparing to unpack .../109-python-numpy-doc_1%3a1.26.4+ds-13_all.deb ... 241s Unpacking python-numpy-doc (1:1.26.4+ds-13) ... 242s Selecting previously unselected package libjs-mathjax. 242s Preparing to unpack .../110-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 242s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 243s Selecting previously unselected package python-pandas-doc. 243s Preparing to unpack .../111-python-pandas-doc_2.2.3+dfsg-8_all.deb ... 243s Unpacking python-pandas-doc (2.2.3+dfsg-8) ... 244s Selecting previously unselected package python-skbio-doc. 244s Preparing to unpack .../112-python-skbio-doc_0.6.2-4build1_all.deb ... 244s Unpacking python-skbio-doc (0.6.2-4build1) ... 244s Selecting previously unselected package python3-accessible-pygments. 245s Preparing to unpack .../113-python3-accessible-pygments_0.0.5-2_all.deb ... 245s Unpacking python3-accessible-pygments (0.0.5-2) ... 245s Selecting previously unselected package python3-all. 245s Preparing to unpack .../114-python3-all_3.13.1-1~exp2_arm64.deb ... 245s Unpacking python3-all (3.13.1-1~exp2) ... 245s Selecting previously unselected package python3.13-dev. 245s Preparing to unpack .../115-python3.13-dev_3.13.2-1_arm64.deb ... 245s Unpacking python3.13-dev (3.13.2-1) ... 245s Selecting previously unselected package python3-dev. 245s Preparing to unpack .../116-python3-dev_3.13.1-1~exp2_arm64.deb ... 245s Unpacking python3-dev (3.13.1-1~exp2) ... 245s Selecting previously unselected package python3.12-dev. 245s Preparing to unpack .../117-python3.12-dev_3.12.9-1_arm64.deb ... 245s Unpacking python3.12-dev (3.12.9-1) ... 245s Selecting previously unselected package python3-all-dev. 245s Preparing to unpack .../118-python3-all-dev_3.13.1-1~exp2_arm64.deb ... 245s Unpacking python3-all-dev (3.13.1-1~exp2) ... 245s Selecting previously unselected package python3-asttokens. 245s Preparing to unpack .../119-python3-asttokens_3.0.0-1_all.deb ... 245s Unpacking python3-asttokens (3.0.0-1) ... 245s Selecting previously unselected package python3-numpy. 245s Preparing to unpack .../120-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 245s Unpacking python3-numpy (1:1.26.4+ds-13) ... 245s Selecting previously unselected package python3-h5py-serial. 245s Preparing to unpack .../121-python3-h5py-serial_3.12.1-1_arm64.deb ... 245s Unpacking python3-h5py-serial (3.12.1-1) ... 245s Selecting previously unselected package python3-h5py. 245s Preparing to unpack .../122-python3-h5py_3.12.1-1_all.deb ... 245s Unpacking python3-h5py (3.12.1-1) ... 245s Selecting previously unselected package python3-click. 245s Preparing to unpack .../123-python3-click_8.1.8-1_all.deb ... 245s Unpacking python3-click (8.1.8-1) ... 245s Selecting previously unselected package python3-dateutil. 245s Preparing to unpack .../124-python3-dateutil_2.9.0-3_all.deb ... 245s Unpacking python3-dateutil (2.9.0-3) ... 245s Selecting previously unselected package python3-pytz. 245s Preparing to unpack .../125-python3-pytz_2025.1-3_all.deb ... 245s Unpacking python3-pytz (2025.1-3) ... 246s Selecting previously unselected package python3-tz. 246s Preparing to unpack .../126-python3-tz_2025.1-3_all.deb ... 246s Unpacking python3-tz (2025.1-3) ... 246s Selecting previously unselected package python3-pandas-lib:arm64. 246s Preparing to unpack .../127-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 246s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 246s Selecting previously unselected package python3-pandas. 246s Preparing to unpack .../128-python3-pandas_2.2.3+dfsg-8_all.deb ... 246s Unpacking python3-pandas (2.2.3+dfsg-8) ... 246s Selecting previously unselected package python3-decorator. 246s Preparing to unpack .../129-python3-decorator_5.1.1-5_all.deb ... 246s Unpacking python3-decorator (5.1.1-5) ... 246s Selecting previously unselected package python3-scipy. 246s Preparing to unpack .../130-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 246s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 247s Selecting previously unselected package python3-biom-format. 247s Preparing to unpack .../131-python3-biom-format_2.1.16-1build2_arm64.deb ... 247s Unpacking python3-biom-format (2.1.16-1build2) ... 247s Selecting previously unselected package python3-brotli. 247s Preparing to unpack .../132-python3-brotli_1.1.0-2build3_arm64.deb ... 247s Unpacking python3-brotli (1.1.0-2build3) ... 247s Selecting previously unselected package python3-soupsieve. 247s Preparing to unpack .../133-python3-soupsieve_2.6-1_all.deb ... 247s Unpacking python3-soupsieve (2.6-1) ... 247s Selecting previously unselected package python3-bs4. 247s Preparing to unpack .../134-python3-bs4_4.13.3-1_all.deb ... 247s Unpacking python3-bs4 (4.13.3-1) ... 247s Selecting previously unselected package python3-msgpack. 247s Preparing to unpack .../135-python3-msgpack_1.0.3-3build3_arm64.deb ... 247s Unpacking python3-msgpack (1.0.3-3build3) ... 247s Selecting previously unselected package python3-cachecontrol. 247s Preparing to unpack .../136-python3-cachecontrol_0.14.2-1_all.deb ... 247s Unpacking python3-cachecontrol (0.14.2-1) ... 247s Selecting previously unselected package python3-contourpy. 247s Preparing to unpack .../137-python3-contourpy_1.3.1-1_arm64.deb ... 247s Unpacking python3-contourpy (1.3.1-1) ... 247s Selecting previously unselected package python3-cycler. 247s Preparing to unpack .../138-python3-cycler_0.12.1-1_all.deb ... 247s Unpacking python3-cycler (0.12.1-1) ... 247s Selecting previously unselected package python3-defusedxml. 247s Preparing to unpack .../139-python3-defusedxml_0.7.1-3_all.deb ... 247s Unpacking python3-defusedxml (0.7.1-3) ... 247s Selecting previously unselected package python3.13-doc. 247s Preparing to unpack .../140-python3.13-doc_3.13.2-1_all.deb ... 247s Unpacking python3.13-doc (3.13.2-1) ... 248s Selecting previously unselected package python3-doc. 248s Preparing to unpack .../141-python3-doc_3.13.1-1~exp2_all.deb ... 248s Unpacking python3-doc (3.13.1-1~exp2) ... 248s Selecting previously unselected package python3-roman. 248s Preparing to unpack .../142-python3-roman_5.0-1_all.deb ... 248s Unpacking python3-roman (5.0-1) ... 248s Selecting previously unselected package python3-docutils. 248s Preparing to unpack .../143-python3-docutils_0.21.2+dfsg-2_all.deb ... 248s Unpacking python3-docutils (0.21.2+dfsg-2) ... 248s Selecting previously unselected package python3-executing. 248s Preparing to unpack .../144-python3-executing_2.2.0-0.1_all.deb ... 248s Unpacking python3-executing (2.2.0-0.1) ... 248s Selecting previously unselected package python3-platformdirs. 248s Preparing to unpack .../145-python3-platformdirs_4.3.6-1_all.deb ... 248s Unpacking python3-platformdirs (4.3.6-1) ... 248s Selecting previously unselected package python3-fs. 248s Preparing to unpack .../146-python3-fs_2.4.16-6_all.deb ... 248s Unpacking python3-fs (2.4.16-6) ... 248s Selecting previously unselected package python3-lxml:arm64. 248s Preparing to unpack .../147-python3-lxml_5.3.1-1_arm64.deb ... 248s Unpacking python3-lxml:arm64 (5.3.1-1) ... 248s Selecting previously unselected package python3-lz4. 248s Preparing to unpack .../148-python3-lz4_4.4.0+dfsg-1_arm64.deb ... 248s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 248s Selecting previously unselected package python3-mpmath. 249s Preparing to unpack .../149-python3-mpmath_1.3.0-1_all.deb ... 249s Unpacking python3-mpmath (1.3.0-1) ... 249s Selecting previously unselected package python3-sympy. 249s Preparing to unpack .../150-python3-sympy_1.13.3-1_all.deb ... 249s Unpacking python3-sympy (1.13.3-1) ... 249s Selecting previously unselected package python3-ufolib2. 249s Preparing to unpack .../151-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 249s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 249s Selecting previously unselected package unicode-data. 249s Preparing to unpack .../152-unicode-data_15.1.0-1_all.deb ... 249s Unpacking unicode-data (15.1.0-1) ... 249s Selecting previously unselected package python3-fonttools. 249s Preparing to unpack .../153-python3-fonttools_4.55.3-2_arm64.deb ... 249s Unpacking python3-fonttools (4.55.3-2) ... 249s Selecting previously unselected package python3-hdmedians. 249s Preparing to unpack .../154-python3-hdmedians_0.14.2-6_arm64.deb ... 249s Unpacking python3-hdmedians (0.14.2-6) ... 249s Selecting previously unselected package python3-imagesize. 249s Preparing to unpack .../155-python3-imagesize_1.4.1-1_all.deb ... 249s Unpacking python3-imagesize (1.4.1-1) ... 249s Selecting previously unselected package python3-iniconfig. 249s Preparing to unpack .../156-python3-iniconfig_1.1.1-2_all.deb ... 249s Unpacking python3-iniconfig (1.1.1-2) ... 250s Selecting previously unselected package python3-parso. 250s Preparing to unpack .../157-python3-parso_0.8.4-1_all.deb ... 250s Unpacking python3-parso (0.8.4-1) ... 250s Selecting previously unselected package python3-typeshed. 250s Preparing to unpack .../158-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 250s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 250s Selecting previously unselected package python3-jedi. 250s Preparing to unpack .../159-python3-jedi_0.19.1+ds1-1_all.deb ... 250s Unpacking python3-jedi (0.19.1+ds1-1) ... 250s Selecting previously unselected package python3-traitlets. 250s Preparing to unpack .../160-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 250s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 250s Selecting previously unselected package python3-matplotlib-inline. 250s Preparing to unpack .../161-python3-matplotlib-inline_0.1.6-2_all.deb ... 250s Unpacking python3-matplotlib-inline (0.1.6-2) ... 250s Selecting previously unselected package python3-wcwidth. 251s Preparing to unpack .../162-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 251s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 251s Selecting previously unselected package python3-prompt-toolkit. 251s 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python3-ipython (8.30.0-2) ... 251s Selecting previously unselected package python3-joblib. 251s Preparing to unpack .../169-python3-joblib_1.4.2-2_all.deb ... 251s Unpacking python3-joblib (1.4.2-2) ... 251s Selecting previously unselected package python3-kiwisolver. 251s Preparing to unpack .../170-python3-kiwisolver_1.4.7-3_arm64.deb ... 251s Unpacking python3-kiwisolver (1.4.7-3) ... 251s Selecting previously unselected package libopenjp2-7:arm64. 251s Preparing to unpack .../171-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 251s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 251s Selecting previously unselected package python3-pil:arm64. 251s Preparing to unpack .../172-python3-pil_11.1.0-5_arm64.deb ... 251s Unpacking python3-pil:arm64 (11.1.0-5) ... 251s Selecting previously unselected package python3.12-tk. 251s Preparing to unpack .../173-python3.12-tk_3.12.9-1_arm64.deb ... 251s Unpacking python3.12-tk (3.12.9-1) ... 251s Selecting previously unselected package python3.13-tk. 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... 261s Setting up libblas3:arm64 (3.12.1-2) ... 261s 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 261s Setting up python3-packaging (24.2-1) ... 262s Setting up libexpat1-dev:arm64 (2.6.4-1) ... 262s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 262s Setting up python3-accessible-pygments (0.0.5-2) ... 262s Setting up python3-typeshed (0.0~git20241223.ea91db2-1) ... 262s Setting up python3-executing (2.2.0-0.1) ... 262s Setting up python3-snowballstemmer (2.2.0-4build1) ... 263s Setting up python3-brotli (1.1.0-2build3) ... 263s Setting up liblzf1:arm64 (3.6-4) ... 263s Setting up python3-cycler (0.12.1-1) ... 263s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 263s Setting up fonts-dejavu-mono (2.37-8) ... 263s Setting up python3-kiwisolver (1.4.7-3) ... 264s Setting up libmpc3:arm64 (1.3.1-1build2) ... 264s Setting up cython3 (3.0.11+dfsg-2ubuntu1) ... 265s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 265s Setting up autopoint (0.23.1-1) ... 265s Setting up fonts-dejavu-core (2.37-8) ... 265s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 265s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 265s Setting up autoconf (2.72-3) ... 265s Setting up python3-pluggy (1.5.0-1) ... 266s Setting up libwebp7:arm64 (1.5.0-0.1) ... 266s Setting up libubsan1:arm64 (15-20250213-1ubuntu1) ... 266s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 266s Setting up dwz (0.15-1build6) ... 266s Setting up libhwasan0:arm64 (15-20250213-1ubuntu1) ... 266s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 266s Setting up libasan8:arm64 (15-20250213-1ubuntu1) ... 266s Setting up libjson-perl (4.10000-1) ... 266s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 266s Setting up debugedit (1:5.1-2) ... 266s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 266s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 266s Setting up python3-dateutil (2.9.0-3) ... 266s Setting up sgml-base (1.31) ... 266s Setting up python3-msgpack (1.0.3-3build3) ... 267s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 267s Setting up python3-cachecontrol (0.14.2-1) ... 267s Setting up libtsan2:arm64 (15-20250213-1ubuntu1) ... 267s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 267s Setting up python3-mpmath (1.3.0-1) ... 268s Setting up libisl23:arm64 (0.27-1) ... 268s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 268s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 268s Setting up python3-stack-data (0.6.3-1) ... 268s Setting up libssw0:arm64 (1.1-15) ... 268s Setting up python3-soupsieve (2.6-1) ... 268s Setting up libcc1-0:arm64 (15-20250213-1ubuntu1) ... 268s Setting up liblsan0:arm64 (15-20250213-1ubuntu1) ... 268s Setting up libsz2:arm64 (1.1.3-1) ... 268s Setting up libitm1:arm64 (15-20250213-1ubuntu1) ... 268s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 268s Setting up python3-imagesize (1.4.1-1) ... 269s Setting up python3-ptyprocess (0.7.0-6) ... 269s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 269s Setting up automake (1:1.17-3) ... 269s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 269s Setting up python3-prompt-toolkit (3.0.50-1) ... 269s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 269s Setting up python3-sympy (1.13.3-1) ... 284s Setting up liblapack3:arm64 (3.12.1-2) ... 284s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 284s Setting up gettext (0.23.1-1) ... 284s Setting up python3-jedi (0.19.1+ds1-1) ... 284s Setting up libssw-dev:arm64 (1.1-15) ... 284s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 284s Setting up python3-pytest (8.3.4-1) ... 285s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 285s Setting up libpython3.12-dev:arm64 (3.12.9-1) ... 285s 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(3.13.1-1~exp2) ... 323s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 323s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 323s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 323s Setting up blt (2.5.3+dfsg-7build1) ... 323s Setting up python3-tk:arm64 (3.13.1-1) ... 323s Setting up gcc-14 (14.2.0-17ubuntu1) ... 323s Setting up python3-biom-format (2.1.16-1build2) ... 323s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 324s Setting up python3-skbio (0.6.2-4build1) ... 325s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 325s Setting up g++-14 (14.2.0-17ubuntu1) ... 325s Setting up libtool (2.5.4-3build1) ... 325s Setting up gcc (4:14.2.0-1ubuntu1) ... 325s Setting up dh-autoreconf (20) ... 325s Setting up g++ (4:14.2.0-1ubuntu1) ... 325s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 325s Setting up build-essential (12.10ubuntu1) ... 325s Setting up debhelper (13.24.1ubuntu2) ... 325s Setting up pybuild-plugin-autopkgtest (6.20250108) ... 325s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 325s Setting up python3-fonttools (4.55.3-2) ... 327s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 331s Processing triggers for libc-bin (2.40-4ubuntu1) ... 331s Processing triggers for systemd (257.2-3ubuntu1) ... 331s Processing triggers for man-db (2.13.0-1) ... 333s Processing triggers for install-info (7.1.1-1) ... 333s Processing triggers for sgml-base (1.31) ... 333s Setting up docutils-common (0.21.2+dfsg-2) ... 333s Processing triggers for sgml-base (1.31) ... 333s Setting up python3-docutils (0.21.2+dfsg-2) ... 334s Setting up python3-sphinx (8.1.3-5) ... 336s Setting up python3-sphinx-copybutton (0.5.2-2) ... 336s Setting up python3-sphinx-design (0.6.1-1) ... 336s Setting up python3-numpydoc (1.8.0-1) ... 336s Setting up python3-pydata-sphinx-theme (0.16.1+dfsg-1) ... 338s autopkgtest [12:57:11]: test pybuild-autopkgtest: pybuild-autopkgtest 338s autopkgtest [12:57:11]: test pybuild-autopkgtest: [----------------------- 338s pybuild-autopkgtest 339s I: pybuild base:311: cd /tmp/autopkgtest.uVi7iW/autopkgtest_tmp/build; python3.12 -m pytest --pyargs skbio 343s ============================= test session starts ============================== 343s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 343s rootdir: /tmp/autopkgtest.uVi7iW/autopkgtest_tmp/build 343s configfile: pyproject.toml 343s plugins: typeguard-4.4.1 343s collected 2793 items 343s 343s alignment/tests/test_pairwise.py ......................... [ 0%] 343s alignment/tests/test_path.py ................. [ 1%] 343s alignment/tests/test_ssw.py ........................... [ 2%] 344s alignment/tests/test_tabular_msa.py .................................... [ 3%] 344s ........................................................................ [ 6%] 345s ........................................................................ [ 8%] 346s ........................................................................ [ 11%] 346s ........................................................................ [ 14%] 346s ........................................................................ [ 16%] 346s ..... [ 16%] 346s diversity/alpha/tests/test_ace.py .. [ 16%] 349s diversity/alpha/tests/test_base.py ............................... [ 18%] 349s diversity/alpha/tests/test_chao1.py ... [ 18%] 349s diversity/alpha/tests/test_gini.py .... [ 18%] 354s diversity/alpha/tests/test_lladser.py ............ [ 18%] 354s diversity/alpha/tests/test_pd.py ................ [ 19%] 354s diversity/beta/tests/test_unifrac.py ............................ [ 20%] 354s diversity/tests/test_block.py ........... [ 20%] 354s diversity/tests/test_driver.py ..................................... [ 21%] 354s diversity/tests/test_util.py ................ [ 22%] 354s embedding/tests/test_embedding.py ................... [ 23%] 354s embedding/tests/test_protein.py .............. [ 23%] 354s io/format/tests/test_base.py ................................ [ 24%] 354s io/format/tests/test_binary_dm.py ......... [ 25%] 355s io/format/tests/test_biom.py ... [ 25%] 355s io/format/tests/test_blast6.py ........... [ 25%] 355s io/format/tests/test_blast7.py .............. [ 26%] 355s io/format/tests/test_clustal.py ............. [ 26%] 356s io/format/tests/test_embed.py ........ [ 26%] 358s io/format/tests/test_embl.py ............................... [ 28%] 358s io/format/tests/test_emptyfile.py .. [ 28%] 368s io/format/tests/test_fasta.py ................ [ 28%] 374s io/format/tests/test_fastq.py ............... [ 29%] 375s io/format/tests/test_genbank.py ..................... [ 30%] 376s io/format/tests/test_gff3.py ........................ [ 30%] 376s io/format/tests/test_lsmat.py ....... [ 31%] 376s io/format/tests/test_newick.py ....... [ 31%] 377s io/format/tests/test_ordination.py ..... [ 31%] 378s io/format/tests/test_phylip.py ....... [ 31%] 379s io/format/tests/test_qseq.py ...... [ 32%] 379s io/format/tests/test_sample_metadata.py .... [ 32%] 379s io/format/tests/test_sequence_feature_vocabulary.py .... [ 32%] 380s io/format/tests/test_stockholm.py ...................................... [ 33%] 380s ..................................... [ 34%] 380s io/format/tests/test_taxdump.py ...... [ 35%] 380s io/tests/test_iosources.py .......... [ 35%] 381s io/tests/test_registry.py .............................................. [ 37%] 381s ................................................ [ 38%] 384s io/tests/test_util.py .........................................sssssssss [ 40%] 389s sssssssssssssssssssss................................................... [ 43%] 396s ........................................................................ [ 45%] 399s .......................... [ 46%] 399s metadata/tests/test_enan.py ... [ 46%] 401s metadata/tests/test_intersection.py ............... [ 47%] 401s metadata/tests/test_interval.py ........................................ [ 48%] 401s ............................... [ 49%] 402s metadata/tests/test_io.py .............................................. [ 51%] 403s ............................................................ [ 53%] 403s metadata/tests/test_metadata.py ........................................ [ 55%] 403s .................... [ 55%] 403s metadata/tests/test_metadata_column.py ................................. [ 57%] 403s ........................................ [ 58%] 403s metadata/tests/test_missing.py ................ [ 59%] 403s metadata/tests/test_mixin.py ........................................... [ 60%] 403s ....................................................... [ 62%] 403s sequence/tests/test_alphabet.py ..... [ 62%] 403s sequence/tests/test_distance.py .......................... [ 63%] 403s sequence/tests/test_dna.py ... [ 63%] 404s sequence/tests/test_genetic_code.py .......................... [ 64%] 404s sequence/tests/test_grammared_sequence.py .............................. [ 65%] 404s ................... [ 66%] 404s sequence/tests/test_nucleotide_sequences.py ............................ [ 67%] 404s . [ 67%] 404s sequence/tests/test_protein.py ........... [ 67%] 404s sequence/tests/test_rna.py ... [ 68%] 404s sequence/tests/test_sequence.py ........................................ [ 69%] 404s ........................................................................ [ 72%] 404s ........................................................................ [ 74%] 404s ........................................................................ [ 77%] 404s ....... [ 77%] 404s sequence/tests/test_substitution.py ........ [ 77%] 404s stats/distance/tests/test_anosim.py .... [ 77%] 404s stats/distance/tests/test_base.py ...................................... [ 79%] 405s .......................................................... [ 81%] 425s stats/distance/tests/test_bioenv.py ................. [ 81%] 429s stats/distance/tests/test_mantel.py .................................... [ 83%] 429s ........ [ 83%] 429s stats/distance/tests/test_permanova.py ..... [ 83%] 446s stats/distance/tests/test_permdisp.py .............. [ 84%] 446s stats/evolve/tests/test_hommola.py ............ [ 84%] 446s stats/ordination/tests/test_canonical_correspondence_analysis.py ...... [ 84%] 447s stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%] 447s stats/ordination/tests/test_ordination_results.py ............. [ 85%] 447s stats/ordination/tests/test_principal_coordinate_analysis.py ........... [ 86%] 447s . [ 86%] 447s stats/ordination/tests/test_redundancy_analysis.py .... [ 86%] 447s stats/ordination/tests/test_util.py .......... [ 86%] 449s stats/tests/test_composition.py ........................................ [ 87%] 470s .......................................... [ 89%] 471s stats/tests/test_gradient.py .......................... [ 90%] 471s stats/tests/test_misc.py ... [ 90%] 473s stats/tests/test_power.py ........................................... [ 92%] 474s stats/tests/test_subsample.py ............ [ 92%] 474s table/tests/test_base.py . [ 92%] 474s tests/test_base.py ..... [ 92%] 474s tests/test_workflow.py ................. [ 93%] 474s tree/tests/test_majority_rule.py ...... [ 93%] 475s tree/tests/test_nj.py ............................ [ 94%] 475s tree/tests/test_tree.py ................................................ [ 96%] 475s ........................................................ [ 98%] 475s util/tests/test_decorator.py ........ [ 98%] 475s util/tests/test_misc.py .................... [ 99%] 476s util/tests/test_plotting.py ...... [ 99%] 476s util/tests/test_testing.py ............... [100%] 476s 476s =============================== warnings summary =============================== 476s alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 476s /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. 476s warn( 476s 476s alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 476s /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. 476s warn( 476s 476s alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 476s /usr/lib/python3/dist-packages/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 476s gap_freqs /= length 476s 476s diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 476s /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. 476s warn( 476s 476s metadata/tests/test_io.py: 10 warnings 476s /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)` 476s series = series.replace("", np.nan) 476s 476s metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 476s metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 476s metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 476s /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. 476s series[missing.index] = missing 476s 476s metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 476s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 476s /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. 476s pdt.assert_series_equal(missing, series.astype(object)) 476s 476s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 476s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 476s /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. 476s pdt.assert_series_equal(missing, series[1:].astype(object)) 476s 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 476s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 476s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 476s 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 476s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 476s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 476s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 476s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 476s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 476s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 476s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 476s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 476s 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 476s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 476s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 476s 476s sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 476s /usr/lib/python3/dist-packages/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 476s obs_counts = obs_counts / len(self) 476s 476s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 476s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 476s warnings.warn(ConstantInputWarning()) 476s 476s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 476s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 476s warnings.warn(ConstantInputWarning()) 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 476s /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. 476s warn( 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 476s /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. 476s warn( 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 476s /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. 476s warn( 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 476s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 476s proportion_explained = eigvals / sum_eigenvalues 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 476s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:605: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 476s res = hypotest_fun_out(*samples, axis=axis, **kwds) 476s 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 476s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 476s /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. 476s warn( 476s 476s stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 476s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 476s return self.run(*args, **kwds) 476s 476s stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 476s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 476s warn(f"{func.__name__} is deprecated as of {ver}.") 476s 476s stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 476s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:573: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 476s res = hypotest_fun_out(*samples, **kwds) 476s 476s stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 476s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 476s warn(f"{func.__name__} is deprecated as of {ver}.") 476s 476s stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 476s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:573: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 476s res = hypotest_fun_out(*samples, **kwds) 476s 476s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 476s /usr/lib/python3/dist-packages/skbio/stats/composition.py:947: RuntimeWarning: divide by zero encountered in log 476s X_log = np.log(mat) 476s 476s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 476s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 476s X -= avg[:, None] 476s 476s stats/tests/test_composition.py::VLRTests::test_vlr 476s /usr/lib/python3/dist-packages/skbio/stats/composition.py:831: RuntimeWarning: divide by zero encountered in log 476s x = np.log(x) 476s 476s stats/tests/test_composition.py::VLRTests::test_vlr 476s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 476s x = asanyarray(arr - arrmean) 476s 476s stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 476s /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. 476s trajectories.loc[idx] = ( 476s 476s tree/tests/test_tree.py::TreeTests::test_root_at 476s /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`. 476s warn( 476s 476s tree/tests/test_tree.py::TreeTests::test_root_at 476s /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`. 476s warn( 476s 476s tree/tests/test_tree.py::TreeTests::test_root_at_midpoint 476s /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`. 476s warn( 476s 476s tree/tests/test_tree.py::TreeTests::test_unrooted_deepcopy 476s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: unrooted_deepcopy is deprecated as of 0.6.2. Use unrooted_copy instead. 476s warn( 476s 476s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 476s ========== 2763 passed, 30 skipped, 70 warnings in 135.18s (0:02:15) =========== 477s I: pybuild base:311: cd /tmp/autopkgtest.uVi7iW/autopkgtest_tmp/build; python3.13 -m pytest --pyargs skbio 480s ============================= test session starts ============================== 480s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 480s rootdir: /tmp/autopkgtest.uVi7iW/autopkgtest_tmp/build 480s configfile: pyproject.toml 480s plugins: typeguard-4.4.1 480s collected 2793 items 480s 480s alignment/tests/test_pairwise.py ......................... [ 0%] 480s alignment/tests/test_path.py ................. [ 1%] 481s alignment/tests/test_ssw.py ........................... [ 2%] 481s alignment/tests/test_tabular_msa.py .................................... [ 3%] 481s ........................................................................ [ 6%] 482s ........................................................................ [ 8%] 484s ........................................................................ [ 11%] 484s ........................................................................ [ 14%] 484s ........................................................................ [ 16%] 484s ..... [ 16%] 484s diversity/alpha/tests/test_ace.py .. [ 16%] 487s diversity/alpha/tests/test_base.py ............................... [ 18%] 487s diversity/alpha/tests/test_chao1.py ... [ 18%] 487s diversity/alpha/tests/test_gini.py .... [ 18%] 492s diversity/alpha/tests/test_lladser.py ............ [ 18%] 492s diversity/alpha/tests/test_pd.py ................ [ 19%] 492s diversity/beta/tests/test_unifrac.py ............................ [ 20%] 492s diversity/tests/test_block.py ........... [ 20%] 492s diversity/tests/test_driver.py ..................................... [ 21%] 492s diversity/tests/test_util.py ................ [ 22%] 492s embedding/tests/test_embedding.py ................... [ 23%] 492s embedding/tests/test_protein.py .............. [ 23%] 492s io/format/tests/test_base.py ................................ [ 24%] 492s io/format/tests/test_binary_dm.py ......... [ 25%] 492s io/format/tests/test_biom.py ... [ 25%] 493s io/format/tests/test_blast6.py ........... [ 25%] 493s io/format/tests/test_blast7.py .............. [ 26%] 493s io/format/tests/test_clustal.py ............. [ 26%] 494s io/format/tests/test_embed.py ........ [ 26%] 496s io/format/tests/test_embl.py ............................... [ 28%] 496s io/format/tests/test_emptyfile.py .. [ 28%] 506s io/format/tests/test_fasta.py ................ [ 28%] 513s io/format/tests/test_fastq.py ............... [ 29%] 514s io/format/tests/test_genbank.py ..................... [ 30%] 515s io/format/tests/test_gff3.py ........................ [ 30%] 515s io/format/tests/test_lsmat.py ....... [ 31%] 515s io/format/tests/test_newick.py ....... [ 31%] 516s io/format/tests/test_ordination.py ..... [ 31%] 518s io/format/tests/test_phylip.py ....... [ 31%] 519s io/format/tests/test_qseq.py ...... [ 32%] 519s io/format/tests/test_sample_metadata.py .... [ 32%] 519s io/format/tests/test_sequence_feature_vocabulary.py .... [ 32%] 520s io/format/tests/test_stockholm.py ...................................... [ 33%] 521s ..................................... [ 34%] 521s io/format/tests/test_taxdump.py ...... [ 35%] 521s io/tests/test_iosources.py .......... [ 35%] 521s io/tests/test_registry.py .............................................. [ 37%] 521s ................................................ [ 38%] 525s io/tests/test_util.py .........................................sssssssss [ 40%] 530s sssssssssssssssssssss................................................... [ 43%] 538s ........................................................................ [ 45%] 541s .......................... [ 46%] 541s metadata/tests/test_enan.py ... [ 46%] 542s metadata/tests/test_intersection.py ............... [ 47%] 543s metadata/tests/test_interval.py ........................................ [ 48%] 543s ............................... [ 49%] 543s metadata/tests/test_io.py .............................................. [ 51%] 544s ............................................................ [ 53%] 545s metadata/tests/test_metadata.py ........................................ [ 55%] 545s .................... [ 55%] 545s metadata/tests/test_metadata_column.py ................................. [ 57%] 545s ........................................ [ 58%] 545s metadata/tests/test_missing.py ................ [ 59%] 545s metadata/tests/test_mixin.py ........................................... [ 60%] 545s ....................................................... [ 62%] 545s sequence/tests/test_alphabet.py ..... [ 62%] 545s sequence/tests/test_distance.py .......................... [ 63%] 545s sequence/tests/test_dna.py ... [ 63%] 545s sequence/tests/test_genetic_code.py .......................... [ 64%] 545s sequence/tests/test_grammared_sequence.py .............................. [ 65%] 545s ................... [ 66%] 545s sequence/tests/test_nucleotide_sequences.py ............................ [ 67%] 545s . [ 67%] 545s sequence/tests/test_protein.py ........... [ 67%] 545s sequence/tests/test_rna.py ... [ 68%] 545s sequence/tests/test_sequence.py ........................................ [ 69%] 545s ........................................................................ [ 72%] 545s ........................................................................ [ 74%] 546s ........................................................................ [ 77%] 546s ....... [ 77%] 546s sequence/tests/test_substitution.py ........ [ 77%] 546s stats/distance/tests/test_anosim.py .... [ 77%] 546s stats/distance/tests/test_base.py ...................................... [ 79%] 546s .......................................................... [ 81%] 563s stats/distance/tests/test_bioenv.py ................. [ 81%] 567s stats/distance/tests/test_mantel.py .................................... [ 83%] 567s ........ [ 83%] 567s stats/distance/tests/test_permanova.py ..... [ 83%] 584s stats/distance/tests/test_permdisp.py .............. [ 84%] 584s stats/evolve/tests/test_hommola.py ............ [ 84%] 584s stats/ordination/tests/test_canonical_correspondence_analysis.py ...... [ 84%] 584s stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%] 584s stats/ordination/tests/test_ordination_results.py ............. [ 85%] 585s stats/ordination/tests/test_principal_coordinate_analysis.py ........... [ 86%] 585s . [ 86%] 585s stats/ordination/tests/test_redundancy_analysis.py .... [ 86%] 585s stats/ordination/tests/test_util.py .......... [ 86%] 587s stats/tests/test_composition.py ........................................ [ 87%] 610s .......................................... [ 89%] 610s stats/tests/test_gradient.py .......................... [ 90%] 610s stats/tests/test_misc.py ... [ 90%] 612s stats/tests/test_power.py ........................................... [ 92%] 613s stats/tests/test_subsample.py ............ [ 92%] 613s table/tests/test_base.py . [ 92%] 613s tests/test_base.py ..... [ 92%] 613s tests/test_workflow.py ................. [ 93%] 613s tree/tests/test_majority_rule.py ...... [ 93%] 614s tree/tests/test_nj.py ............................ [ 94%] 614s tree/tests/test_tree.py ................................................ [ 96%] 615s ........................................................ [ 98%] 615s util/tests/test_decorator.py ........ [ 98%] 615s util/tests/test_misc.py .................... [ 99%] 615s util/tests/test_plotting.py ...... [ 99%] 615s util/tests/test_testing.py ............... [100%] 615s 615s =============================== warnings summary =============================== 615s alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 615s /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. 615s warn( 615s 615s alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 615s /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. 615s warn( 615s 615s alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 615s /usr/lib/python3/dist-packages/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 615s gap_freqs /= length 615s 615s diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 615s /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. 615s warn( 615s 615s metadata/tests/test_io.py: 10 warnings 615s /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)` 615s series = series.replace("", np.nan) 615s 615s metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 615s metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 615s metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 615s /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. 615s series[missing.index] = missing 615s 615s metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 615s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 615s /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. 615s pdt.assert_series_equal(missing, series.astype(object)) 615s 615s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 615s metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 615s /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. 615s pdt.assert_series_equal(missing, series[1:].astype(object)) 615s 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 615s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 615s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 615s 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 615s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 615s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 615s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 615s sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 615s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 615s sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 615s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 615s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 615s 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 615s /usr/lib/python3/dist-packages/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 615s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 615s 615s sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 615s /usr/lib/python3/dist-packages/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 615s obs_counts = obs_counts / len(self) 615s 615s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 615s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 615s warnings.warn(ConstantInputWarning()) 615s 615s stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 615s /usr/lib/python3/dist-packages/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 615s warnings.warn(ConstantInputWarning()) 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 615s /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. 615s warn( 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 615s /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. 615s warn( 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 615s /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. 615s warn( 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 615s /usr/lib/python3/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 615s proportion_explained = eigvals / sum_eigenvalues 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 615s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:605: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 615s res = hypotest_fun_out(*samples, axis=axis, **kwds) 615s 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 615s stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 615s /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. 615s warn( 615s 615s stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 615s /usr/lib/python3.13/unittest/case.py:707: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 615s return self.run(*args, **kwds) 615s 615s stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 615s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 615s warn(f"{func.__name__} is deprecated as of {ver}.") 615s 615s stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 615s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:573: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 615s res = hypotest_fun_out(*samples, **kwds) 615s 615s stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 615s /usr/lib/python3/dist-packages/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 615s warn(f"{func.__name__} is deprecated as of {ver}.") 615s 615s stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 615s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:573: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 615s res = hypotest_fun_out(*samples, **kwds) 615s 615s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 615s /usr/lib/python3/dist-packages/skbio/stats/composition.py:947: RuntimeWarning: divide by zero encountered in log 615s X_log = np.log(mat) 615s 615s stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 615s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 615s X -= avg[:, None] 615s 615s stats/tests/test_composition.py::VLRTests::test_vlr 615s /usr/lib/python3/dist-packages/skbio/stats/composition.py:831: RuntimeWarning: divide by zero encountered in log 615s x = np.log(x) 615s 615s stats/tests/test_composition.py::VLRTests::test_vlr 615s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 615s x = asanyarray(arr - arrmean) 615s 615s stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 615s /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. 615s trajectories.loc[idx] = ( 615s 615s tree/tests/test_tree.py::TreeTests::test_root_at 615s /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`. 615s warn( 615s 615s tree/tests/test_tree.py::TreeTests::test_root_at 615s /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`. 615s warn( 615s 615s tree/tests/test_tree.py::TreeTests::test_root_at_midpoint 615s /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`. 615s warn( 615s 615s tree/tests/test_tree.py::TreeTests::test_unrooted_deepcopy 615s /usr/lib/python3/dist-packages/skbio/util/_warning.py:56: DeprecationWarning: unrooted_deepcopy is deprecated as of 0.6.2. Use unrooted_copy instead. 615s warn( 615s 615s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 615s ========== 2763 passed, 30 skipped, 70 warnings in 137.00s (0:02:16) =========== 617s autopkgtest [13:01:50]: test pybuild-autopkgtest: -----------------------] 617s pybuild-autopkgtest PASS 617s autopkgtest [13:01:50]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 618s autopkgtest [13:01:51]: @@@@@@@@@@@@@@@@@@@@ summary 618s pybuild-autopkgtest PASS 635s nova [W] Using flock in prodstack6-arm64 635s flock: timeout while waiting to get lock 635s Creating nova instance adt-plucky-arm64-python-skbio-20250219-125133-juju-7f2275-prod-proposed-migration-environment-15-3be24773-ec73-4fa9-a125-8d755016d10f from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 635s nova [W] Timed out waiting for c8afc4c4-e090-48ef-abf2-717031320a31 to get deleted.