0s autopkgtest [21:52:01]: starting date and time: 2024-06-27 21:52:01+0000 0s autopkgtest [21:52:01]: git checkout: 85adf9a1 setup-testbed: prevent /tmp from getting a tmpfs mount 0s autopkgtest [21:52:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j5gqjee7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:requests --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=requests/2.32.3+dfsg-1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-2.secgroup --name adt-oracular-arm64-python-skbio-20240627-215201-juju-7f2275-prod-proposed-migration-environment-2-ab2cc25e-dc20-4c94-ab8a-e6f44de7df14 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 95s autopkgtest [21:53:36]: testbed dpkg architecture: arm64 96s autopkgtest [21:53:37]: testbed apt version: 2.9.5 96s autopkgtest [21:53:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 96s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 97s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [49.4 kB] 97s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [382 kB] 97s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 97s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7052 B] 97s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [78.1 kB] 97s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [32.5 kB] 97s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [366 kB] 97s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7928 B] 97s Fetched 1036 kB in 1s (976 kB/s) 97s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade... 102s The following packages will be upgraded: 102s binutils binutils-aarch64-linux-gnu binutils-common btrfs-progs cloud-init 102s e2fsprogs e2fsprogs-l10n libbinutils libcom-err2 libctf-nobfd0 libctf0 102s libext2fs2t64 libgprofng0 libsframe1 libss2 logsave lsb-release 102s openssh-client openssh-server openssh-sftp-server python3-requests 102s sensible-utils tmux vim-common vim-tiny xxd 103s 26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 11.0 MB of archives. 103s After this operation, 135 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 e2fsprogs-l10n all 1.47.1-1ubuntu1 [6798 B] 103s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 logsave arm64 1.47.1-1ubuntu1 [24.8 kB] 103s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libext2fs2t64 arm64 1.47.1-1ubuntu1 [228 kB] 103s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 e2fsprogs arm64 1.47.1-1ubuntu1 [603 kB] 103s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-sftp-server arm64 1:9.6p1-3ubuntu14 [36.8 kB] 103s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-server arm64 1:9.6p1-3ubuntu14 [502 kB] 103s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-client arm64 1:9.6p1-3ubuntu14 [888 kB] 103s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libcom-err2 arm64 1.47.1-1ubuntu1 [25.1 kB] 103s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libss2 arm64 1.47.1-1ubuntu1 [17.4 kB] 103s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 sensible-utils all 0.0.24 [24.8 kB] 103s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 lsb-release all 12.1-1 [5910 B] 103s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 vim-tiny arm64 2:9.1.0496-1ubuntu2 [781 kB] 103s Get:13 http://ftpmaster.internal/ubuntu oracular/main arm64 vim-common all 2:9.1.0496-1ubuntu2 [387 kB] 103s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 xxd arm64 2:9.1.0496-1ubuntu2 [63.6 kB] 103s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libgprofng0 arm64 2.42.50.20240625-1ubuntu1 [777 kB] 103s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf0 arm64 2.42.50.20240625-1ubuntu1 [96.7 kB] 103s Get:17 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf-nobfd0 arm64 2.42.50.20240625-1ubuntu1 [101 kB] 103s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-aarch64-linux-gnu arm64 2.42.50.20240625-1ubuntu1 [3319 kB] 103s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 libbinutils arm64 2.42.50.20240625-1ubuntu1 [774 kB] 103s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils arm64 2.42.50.20240625-1ubuntu1 [18.2 kB] 103s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-common arm64 2.42.50.20240625-1ubuntu1 [243 kB] 103s Get:22 http://ftpmaster.internal/ubuntu oracular/main arm64 libsframe1 arm64 2.42.50.20240625-1ubuntu1 [14.4 kB] 103s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 btrfs-progs arm64 6.6.3-1.2 [958 kB] 103s Get:24 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 python3-requests all 2.32.3+dfsg-1ubuntu1 [52.6 kB] 103s Get:25 http://ftpmaster.internal/ubuntu oracular/main arm64 tmux arm64 3.4-7 [464 kB] 103s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 cloud-init all 24.2~5g8c396a4b-0ubuntu1 [599 kB] 104s Preconfiguring packages ... 104s Fetched 11.0 MB in 1s (10.6 MB/s) 105s (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 ... 78321 files and directories currently installed.) 105s Preparing to unpack .../e2fsprogs-l10n_1.47.1-1ubuntu1_all.deb ... 105s Unpacking e2fsprogs-l10n (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 105s Preparing to unpack .../logsave_1.47.1-1ubuntu1_arm64.deb ... 105s Unpacking logsave (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 105s Preparing to unpack .../libext2fs2t64_1.47.1-1ubuntu1_arm64.deb ... 106s Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2 to /lib/aarch64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' 106s Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2.3 to /lib/aarch64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 106s Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2 to /lib/aarch64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' 106s Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2.4 to /lib/aarch64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 106s Unpacking libext2fs2t64:arm64 (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 107s Setting up libext2fs2t64:arm64 (1.47.1-1ubuntu1) ... 107s (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 ... 78321 files and directories currently installed.) 107s Preparing to unpack .../00-e2fsprogs_1.47.1-1ubuntu1_arm64.deb ... 107s Unpacking e2fsprogs (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 108s Preparing to unpack .../01-openssh-sftp-server_1%3a9.6p1-3ubuntu14_arm64.deb ... 108s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 108s Preparing to unpack .../02-openssh-server_1%3a9.6p1-3ubuntu14_arm64.deb ... 109s Unpacking openssh-server (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 109s Preparing to unpack .../03-openssh-client_1%3a9.6p1-3ubuntu14_arm64.deb ... 109s Unpacking openssh-client (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 110s Preparing to unpack .../04-libcom-err2_1.47.1-1ubuntu1_arm64.deb ... 110s Unpacking libcom-err2:arm64 (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 110s Preparing to unpack .../05-libss2_1.47.1-1ubuntu1_arm64.deb ... 110s Unpacking libss2:arm64 (1.47.1-1ubuntu1) over (1.47.0-2.4~exp1ubuntu4) ... 110s Preparing to unpack .../06-sensible-utils_0.0.24_all.deb ... 110s Unpacking sensible-utils (0.0.24) over (0.0.23) ... 110s Preparing to unpack .../07-lsb-release_12.1-1_all.deb ... 110s Unpacking lsb-release (12.1-1) over (12.0-2) ... 110s Preparing to unpack .../08-vim-tiny_2%3a9.1.0496-1ubuntu2_arm64.deb ... 110s Unpacking vim-tiny (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 110s Preparing to unpack .../09-vim-common_2%3a9.1.0496-1ubuntu2_all.deb ... 110s Unpacking vim-common (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 111s Preparing to unpack .../10-xxd_2%3a9.1.0496-1ubuntu2_arm64.deb ... 111s Unpacking xxd (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 111s Preparing to unpack .../11-libgprofng0_2.42.50.20240625-1ubuntu1_arm64.deb ... 111s Unpacking libgprofng0:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 111s Preparing to unpack .../12-libctf0_2.42.50.20240625-1ubuntu1_arm64.deb ... 111s Unpacking libctf0:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 111s Preparing to unpack .../13-libctf-nobfd0_2.42.50.20240625-1ubuntu1_arm64.deb ... 111s Unpacking libctf-nobfd0:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 111s Preparing to unpack .../14-binutils-aarch64-linux-gnu_2.42.50.20240625-1ubuntu1_arm64.deb ... 111s Unpacking binutils-aarch64-linux-gnu (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 111s Preparing to unpack .../15-libbinutils_2.42.50.20240625-1ubuntu1_arm64.deb ... 111s Unpacking libbinutils:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 112s Preparing to unpack .../16-binutils_2.42.50.20240625-1ubuntu1_arm64.deb ... 112s Unpacking binutils (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 112s Preparing to unpack .../17-binutils-common_2.42.50.20240625-1ubuntu1_arm64.deb ... 112s Unpacking binutils-common:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 112s Preparing to unpack .../18-libsframe1_2.42.50.20240625-1ubuntu1_arm64.deb ... 112s Unpacking libsframe1:arm64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 112s Preparing to unpack .../19-btrfs-progs_6.6.3-1.2_arm64.deb ... 112s Unpacking btrfs-progs (6.6.3-1.2) over (6.6.3-1.1build2) ... 112s Preparing to unpack .../20-python3-requests_2.32.3+dfsg-1ubuntu1_all.deb ... 112s Unpacking python3-requests (2.32.3+dfsg-1ubuntu1) over (2.31.0+dfsg-1ubuntu3) ... 112s Preparing to unpack .../21-tmux_3.4-7_arm64.deb ... 112s Unpacking tmux (3.4-7) over (3.4-6) ... 112s Preparing to unpack .../22-cloud-init_24.2~5g8c396a4b-0ubuntu1_all.deb ... 112s Unpacking cloud-init (24.2~5g8c396a4b-0ubuntu1) over (24.2~4g5f40426f-0ubuntu1) ... 113s Setting up openssh-client (1:9.6p1-3ubuntu14) ... 113s Setting up binutils-common:arm64 (2.42.50.20240625-1ubuntu1) ... 113s Setting up libctf-nobfd0:arm64 (2.42.50.20240625-1ubuntu1) ... 113s Setting up libcom-err2:arm64 (1.47.1-1ubuntu1) ... 113s Setting up xxd (2:9.1.0496-1ubuntu2) ... 113s Setting up libsframe1:arm64 (2.42.50.20240625-1ubuntu1) ... 113s Setting up vim-common (2:9.1.0496-1ubuntu2) ... 113s Setting up python3-requests (2.32.3+dfsg-1ubuntu1) ... 113s Setting up libss2:arm64 (1.47.1-1ubuntu1) ... 113s Setting up logsave (1.47.1-1ubuntu1) ... 113s Setting up sensible-utils (0.0.24) ... 113s Setting up libbinutils:arm64 (2.42.50.20240625-1ubuntu1) ... 113s Setting up lsb-release (12.1-1) ... 113s Setting up tmux (3.4-7) ... 113s Setting up libctf0:arm64 (2.42.50.20240625-1ubuntu1) ... 113s Setting up openssh-sftp-server (1:9.6p1-3ubuntu14) ... 113s Setting up cloud-init (24.2~5g8c396a4b-0ubuntu1) ... 113s 113s Configuration file '/etc/cloud/cloud.cfg' 113s ==> Modified (by you or by a script) since installation. 113s ==> Package distributor has shipped an updated version. 113s ==> Using new file as you requested. 113s Installing new version of config file /etc/cloud/cloud.cfg ... 115s Setting up openssh-server (1:9.6p1-3ubuntu14) ... 115s Replacing config file /etc/ssh/sshd_config with new version 117s Setting up btrfs-progs (6.6.3-1.2) ... 117s Setting up e2fsprogs (1.47.1-1ubuntu1) ... 117s Installing new version of config file /etc/cron.d/e2scrub_all ... 117s Installing new version of config file /etc/mke2fs.conf ... 117s update-initramfs: deferring update (trigger activated) 118s Setting up vim-tiny (2:9.1.0496-1ubuntu2) ... 118s Setting up libgprofng0:arm64 (2.42.50.20240625-1ubuntu1) ... 118s Setting up e2fsprogs-l10n (1.47.1-1ubuntu1) ... 118s Setting up binutils-aarch64-linux-gnu (2.42.50.20240625-1ubuntu1) ... 118s Setting up binutils (2.42.50.20240625-1ubuntu1) ... 118s Processing triggers for debianutils (5.19) ... 118s Processing triggers for initramfs-tools (0.142ubuntu28) ... 118s update-initramfs: Generating /boot/initrd.img-6.8.0-31-generic 118s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 150s System running in EFI mode, skipping. 150s Processing triggers for libc-bin (2.39-0ubuntu9) ... 150s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 150s Processing triggers for ufw (0.36.2-6) ... 151s Processing triggers for man-db (2.12.1-2) ... 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 154s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 154s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 154s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 156s Reading package lists... 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [21:54:41]: rebooting testbed after setup commands that affected boot 164s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 197s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 204s autopkgtest [21:55:25]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 207s autopkgtest [21:55:28]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 212s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (dsc) [2803 B] 212s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (tar) [3559 kB] 212s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (diff) [15.7 kB] 213s gpgv: Signature made Wed Apr 10 15:30:06 2024 UTC 213s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 213s gpgv: Can't check signature: No public key 213s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4build1.dsc: no acceptable signature found 214s autopkgtest [21:55:35]: testing package python-skbio version 0.5.9-4build1 214s autopkgtest [21:55:35]: build not needed 215s autopkgtest [21:55:36]: test import-skbio: preparing testbed 217s Reading package lists... 217s Building dependency tree... 217s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 219s The following additional packages will be installed: 219s blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 libgraphite2-3 219s libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjs-jquery 219s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libopenjp2-7 219s libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 219s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 219s python3-appdirs python3-asttokens python3-brotli python3-contourpy 219s python3-cycler python3-dateutil python3-decorator python3-executing 219s python3-fonttools python3-fs python3-h5py python3-h5py-serial 219s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 219s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 219s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 219s python3-packaging python3-pandas python3-pandas-lib python3-parso 219s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 219s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 219s python3-scipy python3-setuptools python3-skbio python3-stack-data 219s python3-sympy python3-tk python3-traitlets python3-typeshed python3-ufolib2 219s python3-unicodedata2 python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 219s Suggested packages: 219s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 219s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 219s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 219s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 219s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 219s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 219s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 219s python-pexpect-doc python-pil-doc python-scipy-doc python-setuptools-doc 219s python-skbio-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 219s Recommended packages: 219s javascript-common python3-bs4 python3-cssselect python3-html5lib 219s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 219s python3-tables python3-olefile g++ | c++-compiler isympy-common 219s The following NEW packages will be installed: 219s autopkgtest-satdep blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 219s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 219s libimagequant0 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 219s liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 219s libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 219s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 219s python3-contourpy python3-cycler python3-dateutil python3-decorator 219s python3-executing python3-fonttools python3-fs python3-h5py 219s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 219s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 219s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 219s python3-packaging python3-pandas python3-pandas-lib python3-parso 219s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 219s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 219s python3-scipy python3-setuptools python3-skbio python3-stack-data 219s python3-sympy python3-tk python3-traitlets python3-typeshed python3-ufolib2 219s python3-unicodedata2 python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 219s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 219s Need to get 67.7 MB/67.7 MB of archives. 219s After this operation, 313 MB of additional disk space will be used. 219s Get:1 /tmp/autopkgtest.jhfkQj/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 219s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] 220s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 220s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 220s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 220s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 220s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] 220s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 220s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 220s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 fonts-lyx all 2.4.0-1 [171 kB] 220s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 220s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 220s Get:13 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 220s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14.1.0-1ubuntu1 [144 kB] 220s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 220s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 libharfbuzz0b arm64 8.3.0-2build2 [463 kB] 220s Get:17 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 220s Get:18 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu4 [1192 kB] 220s Get:19 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu4 [55.8 kB] 220s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 220s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 220s Get:22 http://ftpmaster.internal/ubuntu oracular/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 220s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 220s Get:24 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 220s Get:25 http://ftpmaster.internal/ubuntu oracular/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 220s Get:26 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 220s Get:27 http://ftpmaster.internal/ubuntu oracular/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 220s Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 220s Get:29 http://ftpmaster.internal/ubuntu oracular/universe arm64 libssw0 arm64 1.1-14build1 [21.4 kB] 220s Get:30 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 220s Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 220s Get:32 http://ftpmaster.internal/ubuntu oracular/main arm64 libxslt1.1 arm64 1.1.39-0exp1build1 [166 kB] 220s Get:33 http://ftpmaster.internal/ubuntu oracular/universe arm64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 220s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 220s Get:35 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-asttokens all 2.4.1-1 [20.9 kB] 220s Get:36 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 220s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 220s Get:38 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-contourpy arm64 1.0.7-3 [163 kB] 220s Get:39 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 220s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 220s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 220s Get:42 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-executing all 2.0.1-0.1 [23.3 kB] 220s Get:43 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.12.0-2 [15.9 MB] 221s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 221s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 221s Get:46 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sympy all 1.12-8 [3966 kB] 221s Get:47 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 221s Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-lxml arm64 5.2.1-1 [1179 kB] 221s Get:49 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 221s Get:50 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 221s Get:51 http://ftpmaster.internal/ubuntu oracular/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 221s Get:52 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 221s Get:53 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu3 [888 kB] 221s Get:54 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 221s Get:55 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-hdmedians arm64 0.14.2-5.1build1 [116 kB] 221s Get:56 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 221s Get:57 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 221s Get:58 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 221s Get:59 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 221s Get:60 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 221s Get:61 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 221s Get:62 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 221s Get:63 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 221s Get:64 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 221s Get:65 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-prompt-toolkit all 3.0.47-1 [256 kB] 221s Get:66 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pure-eval all 0.2.2-2 [11.1 kB] 221s Get:67 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 222s Get:68 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 222s Get:69 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 222s Get:70 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-kiwisolver arm64 1.4.5-1 [48.9 kB] 222s Get:71 http://ftpmaster.internal/ubuntu oracular/main arm64 libopenjp2-7 arm64 2.5.0-2build3 [171 kB] 222s Get:72 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pil arm64 10.3.0-2 [446 kB] 222s Get:73 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-tk arm64 3.12.3-0ubuntu1 [102 kB] 222s Get:74 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pil.imagetk arm64 10.3.0-2 [9268 B] 222s Get:75 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 222s Get:76 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-matplotlib arm64 3.6.3-2ubuntu1 [5963 kB] 222s Get:77 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 222s Get:78 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-8 [4178 kB] 222s Get:79 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 222s Get:80 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 222s Get:81 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 222s Get:82 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-skbio arm64 0.5.9-4build1 [744 kB] 224s Fetched 67.7 MB in 3s (23.9 MB/s) 224s Selecting previously unselected package libtcl8.6:arm64. 224s (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 ... 78320 files and directories currently installed.) 224s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_arm64.deb ... 224s Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 224s Selecting previously unselected package libxrender1:arm64. 224s Preparing to unpack .../01-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 224s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 224s Selecting previously unselected package libxft2:arm64. 224s Preparing to unpack .../02-libxft2_2.3.6-1build1_arm64.deb ... 224s Unpacking libxft2:arm64 (2.3.6-1build1) ... 224s Selecting previously unselected package x11-common. 224s Preparing to unpack .../03-x11-common_1%3a7.7+23ubuntu3_all.deb ... 224s Unpacking x11-common (1:7.7+23ubuntu3) ... 224s Selecting previously unselected package libxss1:arm64. 224s Preparing to unpack .../04-libxss1_1%3a1.2.3-1build3_arm64.deb ... 224s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 224s Selecting previously unselected package libtk8.6:arm64. 224s Preparing to unpack .../05-libtk8.6_8.6.14-1build1_arm64.deb ... 224s Unpacking libtk8.6:arm64 (8.6.14-1build1) ... 224s Selecting previously unselected package tk8.6-blt2.5. 225s Preparing to unpack .../06-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 225s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 225s Selecting previously unselected package blt. 225s Preparing to unpack .../07-blt_2.5.3+dfsg-7build1_arm64.deb ... 225s Unpacking blt (2.5.3+dfsg-7build1) ... 225s Selecting previously unselected package fonts-lyx. 226s Preparing to unpack .../08-fonts-lyx_2.4.0-1_all.deb ... 226s Unpacking fonts-lyx (2.4.0-1) ... 226s Selecting previously unselected package libaec0:arm64. 226s Preparing to unpack .../09-libaec0_1.1.3-1_arm64.deb ... 226s Unpacking libaec0:arm64 (1.1.3-1) ... 226s Selecting previously unselected package libblas3:arm64. 226s Preparing to unpack .../10-libblas3_3.12.0-3build1_arm64.deb ... 226s Unpacking libblas3:arm64 (3.12.0-3build1) ... 226s Selecting previously unselected package libgfortran5:arm64. 227s Preparing to unpack .../11-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 227s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 227s Selecting previously unselected package libgomp1:arm64. 228s Preparing to unpack .../12-libgomp1_14.1.0-1ubuntu1_arm64.deb ... 228s Unpacking libgomp1:arm64 (14.1.0-1ubuntu1) ... 228s Selecting previously unselected package libgraphite2-3:arm64. 228s Preparing to unpack .../13-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 228s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 228s Selecting previously unselected package libharfbuzz0b:arm64. 228s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_arm64.deb ... 228s Unpacking libharfbuzz0b:arm64 (8.3.0-2build2) ... 228s Selecting previously unselected package libsz2:arm64. 229s Preparing to unpack .../15-libsz2_1.1.3-1_arm64.deb ... 229s Unpacking libsz2:arm64 (1.1.3-1) ... 229s Selecting previously unselected package libhdf5-103-1t64:arm64. 229s Preparing to unpack .../16-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 229s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 229s Selecting previously unselected package libhdf5-hl-100t64:arm64. 230s Preparing to unpack .../17-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 230s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 230s Selecting previously unselected package libimagequant0:arm64. 230s Preparing to unpack .../18-libimagequant0_2.18.0-1build1_arm64.deb ... 230s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 230s Selecting previously unselected package libjs-jquery. 231s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 231s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 231s Selecting previously unselected package libjs-jquery-ui. 231s Preparing to unpack .../20-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 231s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 232s Selecting previously unselected package liblapack3:arm64. 232s Preparing to unpack .../21-liblapack3_3.12.0-3build1_arm64.deb ... 232s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 233s Selecting previously unselected package liblbfgsb0:arm64. 233s Preparing to unpack .../22-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 233s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 233s Selecting previously unselected package liblcms2-2:arm64. 233s Preparing to unpack .../23-liblcms2-2_2.14-2build1_arm64.deb ... 233s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 233s Selecting previously unselected package liblzf1:arm64. 233s Preparing to unpack .../24-liblzf1_3.6-4_arm64.deb ... 233s Unpacking liblzf1:arm64 (3.6-4) ... 233s Selecting previously unselected package libqhull-r8.0:arm64. 233s Preparing to unpack .../25-libqhull-r8.0_2020.2-6build1_arm64.deb ... 233s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 233s Selecting previously unselected package libraqm0:arm64. 233s Preparing to unpack .../26-libraqm0_0.10.1-1build1_arm64.deb ... 233s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 233s Selecting previously unselected package libssw0:arm64. 233s Preparing to unpack .../27-libssw0_1.1-14build1_arm64.deb ... 233s Unpacking libssw0:arm64 (1.1-14build1) ... 233s Selecting previously unselected package libwebpdemux2:arm64. 233s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_arm64.deb ... 233s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package libwebpmux3:arm64. 234s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_arm64.deb ... 234s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package libxslt1.1:arm64. 234s Preparing to unpack .../30-libxslt1.1_1.1.39-0exp1build1_arm64.deb ... 234s Unpacking libxslt1.1:arm64 (1.1.39-0exp1build1) ... 234s Selecting previously unselected package python-matplotlib-data. 234s Preparing to unpack .../31-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 234s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 234s Selecting previously unselected package python3-appdirs. 234s Preparing to unpack .../32-python3-appdirs_1.4.4-4_all.deb ... 234s Unpacking python3-appdirs (1.4.4-4) ... 234s Selecting previously unselected package python3-asttokens. 234s Preparing to unpack .../33-python3-asttokens_2.4.1-1_all.deb ... 234s Unpacking python3-asttokens (2.4.1-1) ... 234s Selecting previously unselected package python3-brotli. 234s Preparing to unpack .../34-python3-brotli_1.1.0-2build2_arm64.deb ... 234s Unpacking python3-brotli (1.1.0-2build2) ... 234s Selecting previously unselected package python3-numpy. 234s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 234s Unpacking python3-numpy (1:1.26.4+ds-10) ... 235s Selecting previously unselected package python3-contourpy. 235s Preparing to unpack .../36-python3-contourpy_1.0.7-3_arm64.deb ... 235s Unpacking python3-contourpy (1.0.7-3) ... 235s Selecting previously unselected package python3-cycler. 236s Preparing to unpack .../37-python3-cycler_0.12.1-1_all.deb ... 236s Unpacking python3-cycler (0.12.1-1) ... 236s Selecting previously unselected package python3-dateutil. 237s Preparing to unpack .../38-python3-dateutil_2.9.0-2_all.deb ... 237s Unpacking python3-dateutil (2.9.0-2) ... 237s Selecting previously unselected package python3-decorator. 237s Preparing to unpack .../39-python3-decorator_5.1.1-5_all.deb ... 237s Unpacking python3-decorator (5.1.1-5) ... 237s Selecting previously unselected package python3-executing. 237s Preparing to unpack .../40-python3-executing_2.0.1-0.1_all.deb ... 237s Unpacking python3-executing (2.0.1-0.1) ... 237s Selecting previously unselected package python3-scipy. 238s Preparing to unpack .../41-python3-scipy_1.12.0-2_arm64.deb ... 238s Unpacking python3-scipy (1.12.0-2) ... 238s Selecting previously unselected package python3-ufolib2. 238s Preparing to unpack .../42-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 238s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 238s Selecting previously unselected package python3-mpmath. 239s Preparing to unpack .../43-python3-mpmath_1.3.0-1_all.deb ... 239s Unpacking python3-mpmath (1.3.0-1) ... 239s Selecting previously unselected package python3-sympy. 240s Preparing to unpack .../44-python3-sympy_1.12-8_all.deb ... 240s Unpacking python3-sympy (1.12-8) ... 240s Selecting previously unselected package python3-fs. 241s Preparing to unpack .../45-python3-fs_2.4.16-4_all.deb ... 241s Unpacking python3-fs (2.4.16-4) ... 241s Selecting previously unselected package python3-lxml:arm64. 241s Preparing to unpack .../46-python3-lxml_5.2.1-1_arm64.deb ... 241s Unpacking python3-lxml:arm64 (5.2.1-1) ... 241s Selecting previously unselected package python3-lz4. 242s Preparing to unpack .../47-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 242s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 242s Selecting previously unselected package python3-unicodedata2. 242s Preparing to unpack .../48-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 242s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 242s Selecting previously unselected package unicode-data. 242s Preparing to unpack .../49-unicode-data_15.1.0-1_all.deb ... 242s Unpacking unicode-data (15.1.0-1) ... 242s Selecting previously unselected package python3-fonttools. 242s Preparing to unpack .../50-python3-fonttools_4.46.0-1build2_arm64.deb ... 242s 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PASS 305s autopkgtest [21:57:06]: test testsuite: preparing testbed 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 307s Starting pkgProblemResolver with broken count: 0 308s Starting 2 pkgProblemResolver with broken count: 0 308s Done 308s The following NEW packages will be installed: 308s autopkgtest-satdep 308s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 308s Need to get 0 B/716 B of archives. 308s After this operation, 0 B of additional disk space will be used. 308s Get:1 /tmp/autopkgtest.jhfkQj/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 309s Selecting previously unselected package autopkgtest-satdep. 309s (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 ... 95465 files and directories currently installed.) 309s Preparing to unpack .../2-autopkgtest-satdep.deb ... 309s Unpacking autopkgtest-satdep (0) ... 309s Setting up autopkgtest-satdep (0) ... 313s (Reading database ... 95465 files and directories currently installed.) 313s Removing autopkgtest-satdep (0) ... 314s autopkgtest [21:57:15]: test testsuite: [----------------------- 314s + find . -name _hommola.py -exec sed -i /Run the cospeciation test with 99 permutations. Note that the correlation/,/After permuting host : parasite interactions, we find that the observed/d {} ; 314s + find . -name power.py -exec sed -i /Now, let's use random sampling to estimate the power of our test on/,/Based on this power estimate, as we increase our confidence that we have not/d {} ; 314s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 319s ============================= test session starts ============================== 319s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 319s rootdir: /tmp/autopkgtest.jhfkQj/autopkgtest_tmp 319s collected 2390 items 319s 319s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 319s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 319s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 320s ........................................................................ 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[ 93%] 381s skbio/tree/tests/test_nj.py ........... [ 93%] 382s skbio/tree/tests/test_tree.py .......................................... [ 95%] 382s ................................................... [ 97%] 382s skbio/util/tests/test_decorator.py ....................... [ 98%] 382s skbio/util/tests/test_misc.py .................... [ 99%] 382s skbio/util/tests/test_testing.py ............... [100%] 382s 382s =============================== warnings summary =============================== 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 382s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: local_pairwise_align_ssw is deprecated as of scikit-bio version 0.5.8, and will be removed in version 0.6.0. This will be removed or replaced, in favor of more general-purpose performant aligners. Additional details at https://github.com/biocore/scikit-bio/issues/1814 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 382s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 382s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/metadata/_testing.py:445: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 382s df['bar'][0].append(42) 382s 382s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 382s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 382s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/metadata/_testing.py:823: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 382s df['bar'][0].append(42) 382s 382s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 382s gap_freqs /= length 382s 382s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 382s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 382s 382s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 382s freqs = counts / counts.sum() 382s 382s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 382s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 382s 382s skbio/diversity/tests/test_block.py: 3 warnings 382s skbio/diversity/tests/test_driver.py: 9 warnings 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading. 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 382s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 382s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definites 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 382s obs_counts = obs_counts / len(self) 382s 382s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 382s warnings.warn(ConstantInputWarning()) 382s 382s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 382s warnings.warn(ConstantInputWarning()) 382s 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.541846544269621 and the largest is 16.587201374785895. 382s warn( 382s 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395201 and the largest is 20.903154277938906. 382s warn( 382s 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 382s proportion_explained = eigvals / sum_eigenvalues 382s 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/distance/_permdisp.py:290: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 382s stat, _ = f_oneway(*groups) 382s 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 382s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780542 and the largest is 2.7077929489469237. 382s warn( 382s 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations. 382s fig.tight_layout() 382s 382s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 382s plot = scatter_fn(c=point_colors, cmap=cmap) 382s 382s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 382s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 382s return self.run(*args, **kwds) 382s 382s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/ordination/tests/test_redundancy_analysis.py:248: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 382s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 382s 382s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 382s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 382s res = hypotest_fun_out(*samples, **kwds) 382s 382s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/composition.py:1589: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 382s return significance_test(*[x[cats == k] for k in cs]) 382s 382s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 382s X_log = np.log(mat) 382s 382s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 382s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 382s X -= avg[:, None] 382s 382s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 382s x = np.log(x) 382s 382s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 382s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 382s x = asanyarray(arr - arrmean) 382s 382s skbio/stats/tests/test_gradient.py: 13 warnings 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/gradient.py:168: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 382s np.abs((w_vector[i] - w_vector[i-1])) 382s 382s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/gradient.py:166: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 382s trajectories.loc[idx] = ( 382s 382s skbio/stats/tests/test_power.py: 27 warnings 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/stats/power.py:1122: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 382s pwr[id2] = _calculate_power(ps, a) 382s 382s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 382s /tmp/autopkgtest.jhfkQj/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will be removed in version 0.1.4. You should now use skbio.g(). 382s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 382s 382s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 382s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 119 warnings in 67.89s (0:01:07) = 386s autopkgtest [21:58:27]: test testsuite: -----------------------] 386s autopkgtest [21:58:27]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 386s testsuite PASS 387s autopkgtest [21:58:28]: @@@@@@@@@@@@@@@@@@@@ summary 387s import-skbio PASS 387s testsuite PASS 399s nova [W] Skipping flock in bos03-arm64 399s Creating nova instance adt-oracular-arm64-python-skbio-20240627-215201-juju-7f2275-prod-proposed-migration-environment-2-ab2cc25e-dc20-4c94-ab8a-e6f44de7df14 from image adt/ubuntu-oracular-arm64-server-20240626.img (UUID e9e82f35-c378-4d21-81eb-4b45711533b8)...