0s autopkgtest [19:11:31]: starting date and time: 2024-06-27 19:11:31+0000 0s autopkgtest [19:11:31]: git checkout: 85adf9a1 setup-testbed: prevent /tmp from getting a tmpfs mount 0s autopkgtest [19:11:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wya18loi/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@lcy02-6.secgroup --name adt-oracular-amd64-python-skbio-20240627-191131-juju-7f2275-prod-proposed-migration-environment-2-e41c312b-a95e-4b54-a51c-986bf6dd5922 --image adt/ubuntu-oracular-amd64-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/ 111s autopkgtest [19:13:22]: testbed dpkg architecture: amd64 111s autopkgtest [19:13:22]: testbed apt version: 2.9.5 111s autopkgtest [19:13:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 112s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7052 B] 112s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [387 kB] 112s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 112s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [52.1 kB] 112s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [95.2 kB] 112s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [74.2 kB] 112s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [28.0 kB] 112s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 112s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [403 kB] 112s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [223 kB] 112s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7968 B] 112s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 112s Fetched 1401 kB in 0s (5746 kB/s) 112s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade... 122s The following packages will be upgraded: 122s binutils binutils-common binutils-x86-64-linux-gnu btrfs-progs cloud-init 122s libbinutils libctf-nobfd0 libctf0 libgprofng0 libsframe1 openssh-client 122s openssh-server openssh-sftp-server python3-requests vim-common vim-tiny xxd 122s 17 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Need to get 8717 kB of archives. 122s After this operation, 12.3 kB disk space will be freed. 122s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-sftp-server amd64 1:9.6p1-3ubuntu14 [37.1 kB] 122s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-server amd64 1:9.6p1-3ubuntu14 [509 kB] 122s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-client amd64 1:9.6p1-3ubuntu14 [904 kB] 122s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 vim-tiny amd64 2:9.1.0496-1ubuntu2 [812 kB] 122s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 vim-common all 2:9.1.0496-1ubuntu2 [387 kB] 122s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 xxd amd64 2:9.1.0496-1ubuntu2 [63.6 kB] 122s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240625-1ubuntu1 [846 kB] 122s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240625-1ubuntu1 [95.6 kB] 122s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240625-1ubuntu1 [97.9 kB] 122s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240625-1ubuntu1 [2482 kB] 122s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240625-1ubuntu1 [576 kB] 122s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240625-1ubuntu1 [18.2 kB] 122s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240625-1ubuntu1 [243 kB] 122s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240625-1ubuntu1 [14.7 kB] 122s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 btrfs-progs amd64 6.6.3-1.2 [978 kB] 122s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python3-requests all 2.32.3+dfsg-1ubuntu1 [52.6 kB] 122s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 cloud-init all 24.2~5g8c396a4b-0ubuntu1 [599 kB] 123s Preconfiguring packages ... 123s Fetched 8717 kB in 0s (69.0 MB/s) 123s (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 ... 74417 files and directories currently installed.) 123s Preparing to unpack .../00-openssh-sftp-server_1%3a9.6p1-3ubuntu14_amd64.deb ... 123s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 123s Preparing to unpack .../01-openssh-server_1%3a9.6p1-3ubuntu14_amd64.deb ... 123s Unpacking openssh-server (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 123s Preparing to unpack .../02-openssh-client_1%3a9.6p1-3ubuntu14_amd64.deb ... 123s Unpacking openssh-client (1:9.6p1-3ubuntu14) over (1:9.6p1-3ubuntu13) ... 123s Preparing to unpack .../03-vim-tiny_2%3a9.1.0496-1ubuntu2_amd64.deb ... 123s Unpacking vim-tiny (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 123s Preparing to unpack .../04-vim-common_2%3a9.1.0496-1ubuntu2_all.deb ... 123s Unpacking vim-common (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 124s Preparing to unpack .../05-xxd_2%3a9.1.0496-1ubuntu2_amd64.deb ... 124s Unpacking xxd (2:9.1.0496-1ubuntu2) over (2:9.1.0377-1ubuntu1) ... 124s Preparing to unpack .../06-libgprofng0_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking libgprofng0:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../07-libctf0_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking libctf0:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../08-libctf-nobfd0_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking libctf-nobfd0:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../09-binutils-x86-64-linux-gnu_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../10-libbinutils_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking libbinutils:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../11-binutils_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking binutils (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../12-binutils-common_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking binutils-common:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../13-libsframe1_2.42.50.20240625-1ubuntu1_amd64.deb ... 124s Unpacking libsframe1:amd64 (2.42.50.20240625-1ubuntu1) over (2.42.50.20240618-1ubuntu1) ... 124s Preparing to unpack .../14-btrfs-progs_6.6.3-1.2_amd64.deb ... 124s Unpacking btrfs-progs (6.6.3-1.2) over (6.6.3-1.1build2) ... 124s Preparing to unpack .../15-python3-requests_2.32.3+dfsg-1ubuntu1_all.deb ... 124s Unpacking python3-requests (2.32.3+dfsg-1ubuntu1) over (2.31.0+dfsg-1ubuntu3) ... 124s Preparing to unpack .../16-cloud-init_24.2~5g8c396a4b-0ubuntu1_all.deb ... 125s Unpacking cloud-init (24.2~5g8c396a4b-0ubuntu1) over (24.2~4g5f40426f-0ubuntu1) ... 125s Setting up openssh-client (1:9.6p1-3ubuntu14) ... 125s Setting up btrfs-progs (6.6.3-1.2) ... 125s Setting up binutils-common:amd64 (2.42.50.20240625-1ubuntu1) ... 125s Setting up libctf-nobfd0:amd64 (2.42.50.20240625-1ubuntu1) ... 125s Setting up xxd (2:9.1.0496-1ubuntu2) ... 125s Setting up libsframe1:amd64 (2.42.50.20240625-1ubuntu1) ... 125s Setting up vim-common (2:9.1.0496-1ubuntu2) ... 125s Setting up python3-requests (2.32.3+dfsg-1ubuntu1) ... 125s Setting up libbinutils:amd64 (2.42.50.20240625-1ubuntu1) ... 125s Setting up libctf0:amd64 (2.42.50.20240625-1ubuntu1) ... 125s Setting up openssh-sftp-server (1:9.6p1-3ubuntu14) ... 125s Setting up cloud-init (24.2~5g8c396a4b-0ubuntu1) ... 125s 125s Configuration file '/etc/cloud/cloud.cfg' 125s ==> Modified (by you or by a script) since installation. 125s ==> Package distributor has shipped an updated version. 125s ==> Using new file as you requested. 125s Installing new version of config file /etc/cloud/cloud.cfg ... 126s Setting up openssh-server (1:9.6p1-3ubuntu14) ... 127s Replacing config file /etc/ssh/sshd_config with new version 128s Setting up vim-tiny (2:9.1.0496-1ubuntu2) ... 128s Setting up libgprofng0:amd64 (2.42.50.20240625-1ubuntu1) ... 128s Setting up binutils-x86-64-linux-gnu (2.42.50.20240625-1ubuntu1) ... 128s Setting up binutils (2.42.50.20240625-1ubuntu1) ... 128s Processing triggers for initramfs-tools (0.142ubuntu28) ... 128s update-initramfs: Generating /boot/initrd.img-6.8.0-31-generic 128s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 138s Processing triggers for libc-bin (2.39-0ubuntu9) ... 138s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 138s Processing triggers for ufw (0.36.2-6) ... 138s Processing triggers for man-db (2.12.1-2) ... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 142s Reading package lists... 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s autopkgtest [19:13:56]: rebooting testbed after setup commands that affected boot 162s autopkgtest [19:14:13]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 164s autopkgtest [19:14:15]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 165s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (dsc) [2803 B] 165s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (tar) [3559 kB] 165s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (diff) [15.7 kB] 166s gpgv: Signature made Wed Apr 10 15:30:06 2024 UTC 166s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 166s gpgv: Can't check signature: No public key 166s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4build1.dsc: no acceptable signature found 166s autopkgtest [19:14:17]: testing package python-skbio version 0.5.9-4build1 166s autopkgtest [19:14:17]: build not needed 167s autopkgtest [19:14:18]: test import-skbio: preparing testbed 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 171s The following additional packages will be installed: 171s blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 libgraphite2-3 171s libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjs-jquery 171s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libopenjp2-7 171s libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 171s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 171s python3-appdirs python3-asttokens python3-brotli python3-contourpy 171s python3-cycler python3-dateutil python3-decorator python3-executing 171s python3-fonttools python3-fs python3-h5py python3-h5py-serial 171s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 171s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 171s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 171s python3-packaging python3-pandas python3-pandas-lib python3-parso 171s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 171s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 171s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 171s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 171s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 171s Suggested packages: 171s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 171s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 171s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 171s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 171s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 171s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 171s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 171s python-pexpect-doc python-pil-doc python-scipy-doc python-skbio-doc 171s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 171s Recommended packages: 171s javascript-common python3-bs4 python3-cssselect python3-html5lib 171s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 171s python3-tables python3-numba python3-olefile g++ | c++-compiler 171s isympy-common 171s The following NEW packages will be installed: 171s autopkgtest-satdep blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 171s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 171s libimagequant0 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 171s liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 171s libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 171s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 171s python3-contourpy python3-cycler python3-dateutil python3-decorator 171s python3-executing python3-fonttools python3-fs python3-h5py 171s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 171s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 171s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 171s python3-packaging python3-pandas python3-pandas-lib python3-parso 171s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 171s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 171s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 171s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 171s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 171s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 171s Need to get 70.4 MB/70.4 MB of archives. 171s After this operation, 320 MB of additional disk space will be used. 171s Get:1 /tmp/autopkgtest.LqFDXE/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 171s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 171s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 171s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 171s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 171s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 171s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 171s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 171s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 171s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.0-1 [171 kB] 171s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 171s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 171s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 171s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 171s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 171s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 171s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 171s Get:18 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 171s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.1ubuntu4 [56.0 kB] 171s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 171s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 171s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 171s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 171s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 171s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 171s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 171s Get:27 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 171s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 171s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libssw0 amd64 1.1-14build1 [22.1 kB] 171s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 171s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 171s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 171s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 171s Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 171s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 171s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 171s Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 171s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB] 171s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 171s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 171s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 171s Get:42 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 171s Get:43 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.12.0-2 [16.5 MB] 171s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 171s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 171s Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB] 171s Get:47 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 171s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB] 171s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 171s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 171s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 171s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 171s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu3 [906 kB] 171s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 171s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-hdmedians amd64 0.14.2-5.1build1 [124 kB] 171s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 171s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 171s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 171s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 171s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 171s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 171s Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 171s Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 171s Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 171s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-prompt-toolkit all 3.0.47-1 [256 kB] 171s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pure-eval all 0.2.2-2 [11.1 kB] 171s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 171s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 171s Get:69 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 171s Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB] 171s Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.3.0-2 [457 kB] 171s Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB] 171s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.3.0-2 [9224 B] 171s Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 171s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB] 171s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 171s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB] 171s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 172s Get:79 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 172s Get:80 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 172s Get:81 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-skbio amd64 0.5.9-4build1 [750 kB] 172s Fetched 70.4 MB in 1s (96.1 MB/s) 172s Selecting previously unselected package libtcl8.6:amd64. 172s (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 ... 74416 files and directories currently installed.) 172s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 172s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 172s Selecting previously unselected package libxrender1:amd64. 172s Preparing to unpack .../01-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 172s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 172s Selecting previously unselected package libxft2:amd64. 172s Preparing to unpack .../02-libxft2_2.3.6-1build1_amd64.deb ... 172s Unpacking libxft2:amd64 (2.3.6-1build1) ... 172s Selecting previously unselected package x11-common. 172s Preparing to unpack .../03-x11-common_1%3a7.7+23ubuntu3_all.deb ... 172s Unpacking x11-common (1:7.7+23ubuntu3) ... 172s Selecting previously unselected package libxss1:amd64. 172s Preparing to unpack .../04-libxss1_1%3a1.2.3-1build3_amd64.deb ... 172s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 172s Selecting previously unselected package libtk8.6:amd64. 172s Preparing to unpack .../05-libtk8.6_8.6.14-1build1_amd64.deb ... 172s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 172s Selecting previously unselected package tk8.6-blt2.5. 173s Preparing to unpack .../06-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 173s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 173s Selecting previously unselected package blt. 173s Preparing to unpack .../07-blt_2.5.3+dfsg-7build1_amd64.deb ... 173s Unpacking blt (2.5.3+dfsg-7build1) ... 173s Selecting previously unselected package fonts-lyx. 173s Preparing to unpack .../08-fonts-lyx_2.4.0-1_all.deb ... 173s Unpacking fonts-lyx (2.4.0-1) ... 173s Selecting previously unselected package libaec0:amd64. 173s Preparing to unpack .../09-libaec0_1.1.3-1_amd64.deb ... 173s Unpacking libaec0:amd64 (1.1.3-1) ... 173s Selecting previously unselected package libblas3:amd64. 173s Preparing to unpack .../10-libblas3_3.12.0-3build1_amd64.deb ... 173s Unpacking libblas3:amd64 (3.12.0-3build1) ... 173s Selecting previously unselected package libgfortran5:amd64. 173s Preparing to unpack .../11-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 173s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 173s Selecting previously unselected package libgomp1:amd64. 173s Preparing to unpack .../12-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 173s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 173s Selecting previously unselected package libgraphite2-3:amd64. 173s Preparing to unpack .../13-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 173s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 173s Selecting previously unselected package libharfbuzz0b:amd64. 173s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 173s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 173s Selecting previously unselected package libsz2:amd64. 173s Preparing to unpack .../15-libsz2_1.1.3-1_amd64.deb ... 173s Unpacking libsz2:amd64 (1.1.3-1) ... 173s Selecting previously unselected package libhdf5-103-1t64:amd64. 173s Preparing to unpack .../16-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 173s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 173s Selecting previously unselected package libhdf5-hl-100t64:amd64. 173s Preparing to unpack .../17-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 173s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 173s Selecting previously unselected package libimagequant0:amd64. 173s Preparing to unpack .../18-libimagequant0_2.18.0-1build1_amd64.deb ... 173s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 173s Selecting previously unselected package libjs-jquery. 173s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 173s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 173s Selecting previously unselected package libjs-jquery-ui. 173s Preparing to unpack .../20-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 173s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 173s Selecting previously unselected package liblapack3:amd64. 173s Preparing to unpack .../21-liblapack3_3.12.0-3build1_amd64.deb ... 173s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 173s Selecting previously unselected package liblbfgsb0:amd64. 173s Preparing to unpack .../22-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 173s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 173s Selecting previously unselected package liblcms2-2:amd64. 173s Preparing to unpack .../23-liblcms2-2_2.14-2build1_amd64.deb ... 173s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 173s Selecting previously unselected package liblzf1:amd64. 173s Preparing to unpack .../24-liblzf1_3.6-4_amd64.deb ... 173s Unpacking liblzf1:amd64 (3.6-4) ... 173s Selecting previously unselected package libqhull-r8.0:amd64. 173s Preparing to unpack .../25-libqhull-r8.0_2020.2-6build1_amd64.deb ... 173s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 173s Selecting previously unselected package libraqm0:amd64. 173s Preparing to unpack .../26-libraqm0_0.10.1-1build1_amd64.deb ... 173s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 173s Selecting previously unselected package libssw0:amd64. 173s Preparing to unpack .../27-libssw0_1.1-14build1_amd64.deb ... 173s Unpacking libssw0:amd64 (1.1-14build1) ... 173s Selecting previously unselected package libwebpdemux2:amd64. 173s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_amd64.deb ... 173s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 173s Selecting previously unselected package libwebpmux3:amd64. 173s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_amd64.deb ... 173s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 173s Selecting previously unselected package libxslt1.1:amd64. 173s Preparing to unpack .../30-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 173s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 173s Selecting previously unselected package python-matplotlib-data. 173s Preparing to unpack .../31-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 173s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 173s Selecting previously unselected package python3-appdirs. 173s Preparing to unpack .../32-python3-appdirs_1.4.4-4_all.deb ... 173s Unpacking python3-appdirs (1.4.4-4) ... 173s Selecting previously unselected package python3-asttokens. 173s Preparing to unpack .../33-python3-asttokens_2.4.1-1_all.deb ... 173s Unpacking python3-asttokens (2.4.1-1) ... 174s Selecting previously unselected package python3-brotli. 174s Preparing to unpack .../34-python3-brotli_1.1.0-2build2_amd64.deb ... 174s Unpacking python3-brotli (1.1.0-2build2) ... 174s Selecting previously unselected package python3-numpy. 174s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 174s Unpacking python3-numpy (1:1.26.4+ds-10) ... 174s Selecting previously unselected package python3-contourpy. 174s Preparing to unpack .../36-python3-contourpy_1.0.7-3_amd64.deb ... 174s Unpacking python3-contourpy (1.0.7-3) ... 174s Selecting previously unselected package python3-cycler. 174s Preparing to unpack .../37-python3-cycler_0.12.1-1_all.deb ... 174s Unpacking python3-cycler (0.12.1-1) ... 174s Selecting previously unselected package python3-dateutil. 174s Preparing to unpack .../38-python3-dateutil_2.9.0-2_all.deb ... 174s Unpacking python3-dateutil (2.9.0-2) ... 174s Selecting previously unselected package python3-decorator. 174s Preparing to unpack .../39-python3-decorator_5.1.1-5_all.deb ... 174s Unpacking python3-decorator (5.1.1-5) ... 174s Selecting previously unselected package python3-executing. 174s Preparing to unpack .../40-python3-executing_2.0.1-0.1_all.deb ... 174s Unpacking python3-executing (2.0.1-0.1) ... 174s Selecting previously unselected package python3-scipy. 174s Preparing to unpack .../41-python3-scipy_1.12.0-2_amd64.deb ... 174s Unpacking python3-scipy (1.12.0-2) ... 175s Selecting previously unselected package python3-ufolib2. 175s Preparing to unpack .../42-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 175s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 175s Selecting previously unselected package python3-mpmath. 175s Preparing to unpack .../43-python3-mpmath_1.3.0-1_all.deb ... 175s Unpacking python3-mpmath (1.3.0-1) ... 175s Selecting previously unselected package python3-sympy. 175s Preparing to unpack .../44-python3-sympy_1.12-8_all.deb ... 175s Unpacking python3-sympy (1.12-8) ... 175s Selecting previously unselected package python3-fs. 175s Preparing to unpack .../45-python3-fs_2.4.16-4_all.deb ... 175s Unpacking python3-fs (2.4.16-4) ... 175s Selecting previously unselected package python3-lxml:amd64. 175s Preparing to unpack .../46-python3-lxml_5.2.1-1_amd64.deb ... 175s Unpacking python3-lxml:amd64 (5.2.1-1) ... 175s Selecting previously unselected package python3-lz4. 175s Preparing to unpack .../47-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 175s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 175s Selecting previously unselected package python3-unicodedata2. 175s Preparing to unpack .../48-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 175s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 175s Selecting previously unselected package unicode-data. 175s Preparing to unpack .../49-unicode-data_15.1.0-1_all.deb ... 175s Unpacking unicode-data (15.1.0-1) ... 175s Selecting previously unselected package python3-fonttools. 175s Preparing to unpack .../50-python3-fonttools_4.46.0-1build2_amd64.deb ... 175s Unpacking python3-fonttools (4.46.0-1build2) ... 175s Selecting previously unselected package python3-h5py-serial. 175s Preparing to unpack .../51-python3-h5py-serial_3.10.0-1ubuntu3_amd64.deb ... 175s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 175s Selecting previously unselected package python3-h5py. 175s Preparing to unpack .../52-python3-h5py_3.10.0-1ubuntu3_all.deb ... 175s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 176s Selecting previously unselected package python3-hdmedians. 176s Preparing to unpack .../53-python3-hdmedians_0.14.2-5.1build1_amd64.deb ... 176s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 176s Selecting previously unselected package python3-iniconfig. 176s Preparing to unpack .../54-python3-iniconfig_1.1.1-2_all.deb ... 176s Unpacking python3-iniconfig (1.1.1-2) ... 176s Selecting previously unselected package python3-parso. 176s Preparing to unpack .../55-python3-parso_0.8.3-1_all.deb ... 176s Unpacking python3-parso (0.8.3-1) ... 176s Selecting previously unselected package python3-typeshed. 176s Preparing to unpack .../56-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 176s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 176s Selecting previously unselected package python3-jedi. 176s Preparing to unpack .../57-python3-jedi_0.19.1+ds1-1_all.deb ... 176s Unpacking python3-jedi (0.19.1+ds1-1) ... 177s Selecting previously unselected package python3-traitlets. 177s Preparing to unpack .../58-python3-traitlets_5.5.0-2_all.deb ... 177s Unpacking python3-traitlets (5.5.0-2) ... 177s Selecting previously unselected package python3-matplotlib-inline. 177s Preparing to unpack .../59-python3-matplotlib-inline_0.1.6-2_all.deb ... 177s Unpacking python3-matplotlib-inline (0.1.6-2) ... 177s Selecting previously unselected package python3-ptyprocess. 177s Preparing to unpack .../60-python3-ptyprocess_0.7.0-5_all.deb ... 177s Unpacking python3-ptyprocess (0.7.0-5) ... 177s Selecting previously unselected package python3-pexpect. 177s Preparing to unpack .../61-python3-pexpect_4.9-2_all.deb ... 177s Unpacking python3-pexpect (4.9-2) ... 177s Selecting previously unselected package python3-wcwidth. 177s Preparing to unpack .../62-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 177s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 177s Selecting previously unselected package python3-prompt-toolkit. 177s Preparing to unpack .../63-python3-prompt-toolkit_3.0.47-1_all.deb ... 177s Unpacking python3-prompt-toolkit (3.0.47-1) ... 177s Selecting previously unselected package python3-pure-eval. 177s Preparing to unpack .../64-python3-pure-eval_0.2.2-2_all.deb ... 177s Unpacking python3-pure-eval (0.2.2-2) ... 177s Selecting previously unselected package python3-stack-data. 177s Preparing to unpack .../65-python3-stack-data_0.6.3-1_all.deb ... 177s Unpacking python3-stack-data (0.6.3-1) ... 177s Selecting previously unselected package python3-ipython. 177s Preparing to unpack .../66-python3-ipython_8.20.0-1ubuntu1_all.deb ... 177s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 177s Selecting previously unselected package python3-kiwisolver. 177s Preparing to unpack .../67-python3-kiwisolver_1.4.5-1_amd64.deb ... 177s Unpacking python3-kiwisolver (1.4.5-1) ... 177s Selecting previously unselected package libopenjp2-7:amd64. 177s Preparing to unpack .../68-libopenjp2-7_2.5.0-2build3_amd64.deb ... 177s Unpacking libopenjp2-7:amd64 (2.5.0-2build3) ... 177s Selecting previously unselected package python3-pil:amd64. 177s Preparing to unpack .../69-python3-pil_10.3.0-2_amd64.deb ... 177s Unpacking python3-pil:amd64 (10.3.0-2) ... 177s Selecting previously unselected package python3-tk:amd64. 177s Preparing to unpack .../70-python3-tk_3.12.3-0ubuntu1_amd64.deb ... 177s Unpacking python3-tk:amd64 (3.12.3-0ubuntu1) ... 177s Selecting previously unselected package python3-pil.imagetk:amd64. 177s Preparing to unpack .../71-python3-pil.imagetk_10.3.0-2_amd64.deb ... 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Note that the correlation/,/After permuting host : parasite interactions, we find that the observed/d {} ; 280s + 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 {} ; 280s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 284s ============================= test session starts ============================== 286s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 286s rootdir: /tmp/autopkgtest.LqFDXE/autopkgtest_tmp 286s collected 2390 items 286s 286s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 286s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 286s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 286s ........................................................................ 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[ 93%] 344s skbio/tree/tests/test_nj.py ........... [ 93%] 344s skbio/tree/tests/test_tree.py .......................................... [ 95%] 344s ................................................... [ 97%] 344s skbio/util/tests/test_decorator.py ....................... [ 98%] 344s skbio/util/tests/test_misc.py .................... [ 99%] 344s skbio/util/tests/test_testing.py ............... [100%] 344s 344s =============================== warnings summary =============================== 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 344s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 344s /tmp/autopkgtest.LqFDXE/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 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 344s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 344s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 344s /tmp/autopkgtest.LqFDXE/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]` 344s df['bar'][0].append(42) 344s 344s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 344s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 344s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 344s /tmp/autopkgtest.LqFDXE/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]` 344s df['bar'][0].append(42) 344s 344s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 344s gap_freqs /= length 344s 344s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 344s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 344s 344s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 344s freqs = counts / counts.sum() 344s 344s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 344s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 344s 344s skbio/diversity/tests/test_block.py: 3 warnings 344s skbio/diversity/tests/test_driver.py: 9 warnings 344s /tmp/autopkgtest.LqFDXE/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. 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 344s /tmp/autopkgtest.LqFDXE/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 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 344s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 344s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 344s /tmp/autopkgtest.LqFDXE/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 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 344s /tmp/autopkgtest.LqFDXE/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 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 344s obs_counts = obs_counts / len(self) 344s 344s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 344s warnings.warn(ConstantInputWarning()) 344s 344s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 344s warnings.warn(ConstantInputWarning()) 344s 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 344s /tmp/autopkgtest.LqFDXE/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 -13.54184654426961 and the largest is 16.5872013747859. 344s warn( 344s 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 344s /tmp/autopkgtest.LqFDXE/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 -15.629533932395208 and the largest is 20.90315427793891. 344s warn( 344s 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 344s proportion_explained = eigvals / sum_eigenvalues 344s 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/distance/_permdisp.py:290: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 344s stat, _ = f_oneway(*groups) 344s 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 344s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 344s /tmp/autopkgtest.LqFDXE/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 -0.007758325147780521 and the largest is 2.7077929489469237. 344s warn( 344s 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 344s /tmp/autopkgtest.LqFDXE/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. 344s fig.tight_layout() 344s 344s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 344s plot = scatter_fn(c=point_colors, cmap=cmap) 344s 344s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 344s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 344s return self.run(*args, **kwds) 344s 344s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 344s /tmp/autopkgtest.LqFDXE/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]` 344s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 344s 344s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 344s /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. 344s res = hypotest_fun_out(*samples, **kwds) 344s 344s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/composition.py:1589: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 344s return significance_test(*[x[cats == k] for k in cs]) 344s 344s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 344s X_log = np.log(mat) 344s 344s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 344s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 344s X -= avg[:, None] 344s 344s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 344s /tmp/autopkgtest.LqFDXE/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 344s x = np.log(x) 344s 344s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 344s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 344s x = asanyarray(arr - arrmean) 344s 344s skbio/stats/tests/test_gradient.py: 13 warnings 344s /tmp/autopkgtest.LqFDXE/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]` 344s np.abs((w_vector[i] - w_vector[i-1])) 344s 344s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 344s /tmp/autopkgtest.LqFDXE/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. 344s trajectories.loc[idx] = ( 344s 344s skbio/stats/tests/test_power.py: 27 warnings 344s /tmp/autopkgtest.LqFDXE/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.) 344s pwr[id2] = _calculate_power(ps, a) 344s 344s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 344s /tmp/autopkgtest.LqFDXE/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(). 344s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 344s 344s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 344s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 119 warnings in 63.71s (0:01:03) = 345s autopkgtest [19:17:16]: test testsuite: -----------------------] 352s autopkgtest [19:17:23]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 352s testsuite PASS 353s autopkgtest [19:17:24]: @@@@@@@@@@@@@@@@@@@@ summary 353s import-skbio PASS 353s testsuite PASS 382s nova [W] Skipping flock for amd64 382s Creating nova instance adt-oracular-amd64-python-skbio-20240627-191131-juju-7f2275-prod-proposed-migration-environment-2-e41c312b-a95e-4b54-a51c-986bf6dd5922 from image adt/ubuntu-oracular-amd64-server-20240627.img (UUID 98622ec5-0b73-44f6-a62f-8532d7a12d37)...