0s autopkgtest [22:23:50]: starting date and time: 2024-06-28 22:23:50+0000 0s autopkgtest [22:23:50]: git checkout: 85adf9a1 setup-testbed: prevent /tmp from getting a tmpfs mount 0s autopkgtest [22:23:50]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jsxgiu7b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-38.secgroup --name adt-oracular-amd64-python-skbio-20240628-222350-juju-7f2275-prod-proposed-migration-environment-3-c78b82e3-834c-44cc-9730-5dedc6dce205 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 88s autopkgtest [22:25:18]: testbed dpkg architecture: amd64 89s autopkgtest [22:25:19]: testbed apt version: 2.9.5 89s autopkgtest [22:25:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 90s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [52.6 kB] 90s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7052 B] 90s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 90s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [375 kB] 90s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [84.2 kB] 90s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [102 kB] 90s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [28.0 kB] 90s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 90s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [408 kB] 90s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [231 kB] 90s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7968 B] 90s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 90s Fetched 1419 kB in 0s (5024 kB/s) 90s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 95s The following packages will be upgraded: 95s base-files libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 95s motd-news-config 95s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 10.4 MB of archives. 95s After this operation, 35.8 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 motd-news-config all 13.3ubuntu2 [5416 B] 95s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu2 [29.3 kB] 95s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu2 [2120 kB] 95s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu2 [20.4 kB] 95s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.3ubuntu2 [75.3 kB] 95s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu2 [3261 kB] 95s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu2 [680 kB] 95s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu2 [4220 kB] 95s Preconfiguring packages ... 95s Fetched 10.4 MB in 0s (92.0 MB/s) 95s (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.) 95s Preparing to unpack .../motd-news-config_13.3ubuntu2_all.deb ... 95s Unpacking motd-news-config (13.3ubuntu2) over (13.1ubuntu1) ... 96s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu2_amd64.deb ... 96s Unpacking libc-devtools (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 96s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu2_amd64.deb ... 96s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 96s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu2_amd64.deb ... 96s Unpacking libc-dev-bin (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 96s Preparing to unpack .../base-files_13.3ubuntu2_amd64.deb ... 96s Unpacking base-files (13.3ubuntu2) over (13.1ubuntu1) ... 96s Setting up base-files (13.3ubuntu2) ... 96s Updating /etc/profile to current default. 97s motd-news.service is a disabled or a static unit not running, not starting it. 97s (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 ... 74420 files and directories currently installed.) 97s Preparing to unpack .../libc6_2.39-3.1ubuntu2_amd64.deb ... 97s Unpacking libc6:amd64 (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 98s Setting up libc6:amd64 (2.39-3.1ubuntu2) ... 98s (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 ... 74420 files and directories currently installed.) 98s Preparing to unpack .../libc-bin_2.39-3.1ubuntu2_amd64.deb ... 98s Unpacking libc-bin (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 98s Setting up libc-bin (2.39-3.1ubuntu2) ... 98s (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 ... 74420 files and directories currently installed.) 98s Preparing to unpack .../locales_2.39-3.1ubuntu2_all.deb ... 98s Unpacking locales (2.39-3.1ubuntu2) over (2.39-0ubuntu9) ... 99s Setting up motd-news-config (13.3ubuntu2) ... 99s Setting up locales (2.39-3.1ubuntu2) ... 100s Generating locales (this might take a while)... 101s en_US.UTF-8... done 101s Generation complete. 101s Setting up libc-dev-bin (2.39-3.1ubuntu2) ... 101s Setting up libc-devtools (2.39-3.1ubuntu2) ... 101s Setting up libc6-dev:amd64 (2.39-3.1ubuntu2) ... 101s Processing triggers for man-db (2.12.1-2) ... 103s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu7) ... 103s update-initramfs: deferring update (trigger activated) 103s Processing triggers for install-info (7.1-3build2) ... 103s Processing triggers for initramfs-tools (0.142ubuntu28) ... 103s update-initramfs: Generating /boot/initrd.img-6.8.0-31-generic 103s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 115s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 117s Reading package lists... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [22:25:49]: rebooting testbed after setup commands that affected boot 122s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 137s autopkgtest [22:26:07]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 138s autopkgtest [22:26:08]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 140s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (dsc) [2803 B] 140s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (tar) [3559 kB] 140s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (diff) [15.7 kB] 140s gpgv: Signature made Wed Apr 10 15:30:06 2024 UTC 140s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4build1.dsc: no acceptable signature found 140s autopkgtest [22:26:10]: testing package python-skbio version 0.5.9-4build1 140s autopkgtest [22:26:10]: build not needed 140s autopkgtest [22:26:10]: test import-skbio: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 142s The following additional packages will be installed: 142s blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 libgraphite2-3 142s libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjs-jquery 142s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libopenjp2-7 142s libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 142s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 142s python3-appdirs python3-asttokens python3-brotli python3-contourpy 142s python3-cycler python3-dateutil python3-decorator python3-executing 142s python3-fonttools python3-fs python3-h5py python3-h5py-serial 142s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 142s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 142s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 142s python3-packaging python3-pandas python3-pandas-lib python3-parso 142s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 142s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 142s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 142s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 142s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 142s Suggested packages: 142s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 142s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 142s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 142s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 142s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 142s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 142s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 142s python-pexpect-doc python-pil-doc python-scipy-doc python-skbio-doc 142s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 142s Recommended packages: 142s javascript-common python3-bs4 python3-cssselect python3-html5lib 142s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 142s python3-tables python3-numba python3-olefile g++ | c++-compiler 142s isympy-common 143s The following NEW packages will be installed: 143s autopkgtest-satdep blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 143s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 143s libimagequant0 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 143s liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 143s libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 143s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 143s python3-contourpy python3-cycler python3-dateutil python3-decorator 143s python3-executing python3-fonttools python3-fs python3-h5py 143s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 143s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 143s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 143s python3-packaging python3-pandas python3-pandas-lib python3-parso 143s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 143s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 143s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 143s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 143s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 143s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 70.4 MB/70.4 MB of archives. 143s After this operation, 320 MB of additional disk space will be used. 143s Get:1 /tmp/autopkgtest.GeVxOm/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 143s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 143s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 143s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 143s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 143s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 143s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 143s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 143s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 143s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.0-1 [171 kB] 143s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 143s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 143s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 143s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 143s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 143s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 143s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 143s Get:18 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 143s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.1ubuntu4 [56.0 kB] 143s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 143s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 143s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 143s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 143s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 143s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 143s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 143s Get:27 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 143s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 143s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libssw0 amd64 1.1-14build1 [22.1 kB] 143s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 143s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 143s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 143s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 143s Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 143s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 143s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 143s Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 143s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB] 143s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 143s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 143s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 143s Get:42 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 143s Get:43 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.12.0-2 [16.5 MB] 143s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 143s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 143s Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB] 143s Get:47 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 143s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB] 143s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 143s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 143s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 143s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 143s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu3 [906 kB] 143s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 143s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-hdmedians amd64 0.14.2-5.1build1 [124 kB] 143s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 143s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 143s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 143s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 143s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 143s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 143s Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 143s Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 143s Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 143s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-prompt-toolkit all 3.0.47-1 [256 kB] 143s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pure-eval all 0.2.2-2 [11.1 kB] 143s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 143s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 143s Get:69 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 143s Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB] 143s Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.3.0-2 [457 kB] 143s Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB] 143s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.3.0-2 [9224 B] 143s Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 143s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB] 143s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 143s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB] 143s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 143s Get:79 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 143s Get:80 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 143s Get:81 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-skbio amd64 0.5.9-4build1 [750 kB] 144s Fetched 70.4 MB in 1s (97.3 MB/s) 144s Selecting previously unselected package libtcl8.6:amd64. 144s (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 ... 74420 files and directories currently installed.) 144s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 144s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 144s Selecting previously unselected package libxrender1:amd64. 144s Preparing to unpack .../01-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 144s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 144s Selecting previously unselected package libxft2:amd64. 144s Preparing to unpack .../02-libxft2_2.3.6-1build1_amd64.deb ... 144s Unpacking libxft2:amd64 (2.3.6-1build1) ... 144s Selecting previously unselected package x11-common. 144s Preparing to unpack .../03-x11-common_1%3a7.7+23ubuntu3_all.deb ... 144s Unpacking x11-common (1:7.7+23ubuntu3) ... 145s Selecting previously unselected package libxss1:amd64. 145s Preparing to unpack .../04-libxss1_1%3a1.2.3-1build3_amd64.deb ... 145s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 145s Selecting previously unselected package libtk8.6:amd64. 145s Preparing to unpack .../05-libtk8.6_8.6.14-1build1_amd64.deb ... 145s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 145s Selecting previously unselected package tk8.6-blt2.5. 145s Preparing to unpack .../06-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 145s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 145s Selecting previously unselected package blt. 145s Preparing to unpack .../07-blt_2.5.3+dfsg-7build1_amd64.deb ... 145s Unpacking blt (2.5.3+dfsg-7build1) ... 145s Selecting previously unselected package fonts-lyx. 145s Preparing to unpack .../08-fonts-lyx_2.4.0-1_all.deb ... 145s Unpacking fonts-lyx (2.4.0-1) ... 145s Selecting previously unselected package libaec0:amd64. 145s Preparing to unpack .../09-libaec0_1.1.3-1_amd64.deb ... 145s Unpacking libaec0:amd64 (1.1.3-1) ... 145s Selecting previously unselected package libblas3:amd64. 145s Preparing to unpack .../10-libblas3_3.12.0-3build1_amd64.deb ... 145s Unpacking libblas3:amd64 (3.12.0-3build1) ... 145s Selecting previously unselected package libgfortran5:amd64. 145s Preparing to unpack .../11-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 145s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 145s Selecting previously unselected package libgomp1:amd64. 145s Preparing to unpack .../12-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 145s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 145s Selecting previously unselected package libgraphite2-3:amd64. 145s Preparing to unpack .../13-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 145s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 145s Selecting previously unselected package libharfbuzz0b:amd64. 145s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 145s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 145s Selecting previously unselected package libsz2:amd64. 145s Preparing to unpack .../15-libsz2_1.1.3-1_amd64.deb ... 145s Unpacking libsz2:amd64 (1.1.3-1) ... 145s Selecting previously unselected package libhdf5-103-1t64:amd64. 145s Preparing to unpack .../16-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 145s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 145s Selecting previously unselected package libhdf5-hl-100t64:amd64. 145s Preparing to unpack .../17-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 145s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 145s Selecting previously unselected package libimagequant0:amd64. 145s Preparing to unpack .../18-libimagequant0_2.18.0-1build1_amd64.deb ... 145s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 145s Selecting previously unselected package libjs-jquery. 145s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 145s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 145s Selecting previously unselected package libjs-jquery-ui. 145s Preparing to unpack .../20-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 145s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 145s Selecting previously unselected package liblapack3:amd64. 145s Preparing to unpack .../21-liblapack3_3.12.0-3build1_amd64.deb ... 145s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 145s Selecting previously unselected package liblbfgsb0:amd64. 145s Preparing to unpack .../22-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 145s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 145s Selecting previously unselected package liblcms2-2:amd64. 145s Preparing to unpack .../23-liblcms2-2_2.14-2build1_amd64.deb ... 145s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 145s Selecting previously unselected package liblzf1:amd64. 145s Preparing to unpack .../24-liblzf1_3.6-4_amd64.deb ... 145s Unpacking liblzf1:amd64 (3.6-4) ... 145s Selecting previously unselected package libqhull-r8.0:amd64. 145s Preparing to unpack .../25-libqhull-r8.0_2020.2-6build1_amd64.deb ... 145s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 145s Selecting previously unselected package libraqm0:amd64. 145s Preparing to unpack .../26-libraqm0_0.10.1-1build1_amd64.deb ... 145s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 146s Selecting previously unselected package libssw0:amd64. 146s Preparing to unpack .../27-libssw0_1.1-14build1_amd64.deb ... 146s Unpacking libssw0:amd64 (1.1-14build1) ... 146s Selecting previously unselected package libwebpdemux2:amd64. 146s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_amd64.deb ... 146s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 146s Selecting previously unselected package libwebpmux3:amd64. 146s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_amd64.deb ... 146s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 146s Selecting previously unselected package libxslt1.1:amd64. 146s Preparing to unpack .../30-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 146s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 146s Selecting previously unselected package python-matplotlib-data. 146s Preparing to unpack .../31-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 146s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 146s Selecting previously unselected package python3-appdirs. 146s Preparing to unpack .../32-python3-appdirs_1.4.4-4_all.deb ... 146s Unpacking python3-appdirs (1.4.4-4) ... 146s Selecting previously unselected package python3-asttokens. 146s Preparing to unpack .../33-python3-asttokens_2.4.1-1_all.deb ... 146s Unpacking python3-asttokens (2.4.1-1) ... 146s Selecting previously unselected package python3-brotli. 146s Preparing to unpack .../34-python3-brotli_1.1.0-2build2_amd64.deb ... 146s Unpacking python3-brotli (1.1.0-2build2) ... 146s Selecting previously unselected package python3-numpy. 146s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 146s Unpacking python3-numpy (1:1.26.4+ds-10) ... 146s Selecting previously unselected package python3-contourpy. 146s Preparing to unpack .../36-python3-contourpy_1.0.7-3_amd64.deb ... 146s Unpacking python3-contourpy (1.0.7-3) ... 146s Selecting previously unselected package python3-cycler. 146s Preparing to unpack .../37-python3-cycler_0.12.1-1_all.deb ... 146s Unpacking python3-cycler (0.12.1-1) ... 146s Selecting previously unselected package python3-dateutil. 146s Preparing to unpack .../38-python3-dateutil_2.9.0-2_all.deb ... 146s Unpacking python3-dateutil (2.9.0-2) ... 146s Selecting previously unselected package python3-decorator. 146s Preparing to unpack .../39-python3-decorator_5.1.1-5_all.deb ... 146s Unpacking python3-decorator (5.1.1-5) ... 146s Selecting previously unselected package python3-executing. 146s Preparing to unpack .../40-python3-executing_2.0.1-0.1_all.deb ... 146s Unpacking python3-executing (2.0.1-0.1) ... 146s Selecting previously unselected package python3-scipy. 146s Preparing to unpack .../41-python3-scipy_1.12.0-2_amd64.deb ... 146s Unpacking python3-scipy (1.12.0-2) ... 147s Selecting previously unselected package python3-ufolib2. 147s Preparing to unpack .../42-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 147s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 147s Selecting previously unselected package python3-mpmath. 147s Preparing to unpack .../43-python3-mpmath_1.3.0-1_all.deb ... 147s Unpacking python3-mpmath (1.3.0-1) ... 147s Selecting previously unselected package python3-sympy. 147s Preparing to unpack .../44-python3-sympy_1.12-8_all.deb ... 147s Unpacking python3-sympy (1.12-8) ... 147s Selecting previously unselected package python3-fs. 147s Preparing to unpack .../45-python3-fs_2.4.16-4_all.deb ... 147s Unpacking python3-fs (2.4.16-4) ... 147s Selecting previously unselected package python3-lxml:amd64. 147s Preparing to unpack .../46-python3-lxml_5.2.1-1_amd64.deb ... 147s Unpacking python3-lxml:amd64 (5.2.1-1) ... 147s Selecting previously unselected package python3-lz4. 147s Preparing to unpack .../47-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 147s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 147s Selecting previously unselected package python3-unicodedata2. 147s Preparing to unpack .../48-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 147s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 147s Selecting previously unselected package unicode-data. 147s Preparing to unpack .../49-unicode-data_15.1.0-1_all.deb ... 147s Unpacking unicode-data (15.1.0-1) ... 148s Selecting previously unselected package python3-fonttools. 148s Preparing to unpack .../50-python3-fonttools_4.46.0-1build2_amd64.deb ... 148s Unpacking python3-fonttools (4.46.0-1build2) ... 148s Selecting previously unselected package python3-h5py-serial. 148s Preparing to unpack .../51-python3-h5py-serial_3.10.0-1ubuntu3_amd64.deb ... 148s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 148s Selecting previously unselected package python3-h5py. 148s Preparing to unpack .../52-python3-h5py_3.10.0-1ubuntu3_all.deb ... 148s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 148s Selecting previously unselected package python3-hdmedians. 148s Preparing to unpack .../53-python3-hdmedians_0.14.2-5.1build1_amd64.deb ... 148s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 148s Selecting previously unselected package python3-iniconfig. 148s Preparing to unpack .../54-python3-iniconfig_1.1.1-2_all.deb ... 148s Unpacking python3-iniconfig (1.1.1-2) ... 148s Selecting previously unselected package python3-parso. 148s Preparing to unpack .../55-python3-parso_0.8.3-1_all.deb ... 148s Unpacking python3-parso (0.8.3-1) ... 148s Selecting previously unselected package python3-typeshed. 148s Preparing to unpack .../56-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 148s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 149s Selecting previously unselected package python3-jedi. 149s Preparing to unpack .../57-python3-jedi_0.19.1+ds1-1_all.deb ... 149s Unpacking python3-jedi (0.19.1+ds1-1) ... 149s Selecting previously unselected package python3-traitlets. 149s Preparing to unpack .../58-python3-traitlets_5.5.0-2_all.deb ... 149s Unpacking python3-traitlets (5.5.0-2) ... 149s Selecting previously unselected package python3-matplotlib-inline. 149s Preparing to unpack .../59-python3-matplotlib-inline_0.1.6-2_all.deb ... 149s Unpacking python3-matplotlib-inline (0.1.6-2) ... 149s Selecting previously unselected package python3-ptyprocess. 149s Preparing to unpack .../60-python3-ptyprocess_0.7.0-5_all.deb ... 149s Unpacking python3-ptyprocess (0.7.0-5) ... 149s Selecting previously unselected package python3-pexpect. 149s Preparing to unpack .../61-python3-pexpect_4.9-2_all.deb ... 149s Unpacking python3-pexpect (4.9-2) ... 149s Selecting previously unselected package python3-wcwidth. 149s Preparing to unpack .../62-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 149s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 149s Selecting previously unselected package python3-prompt-toolkit. 149s Preparing to unpack .../63-python3-prompt-toolkit_3.0.47-1_all.deb ... 149s Unpacking python3-prompt-toolkit (3.0.47-1) ... 149s Selecting previously unselected package python3-pure-eval. 149s Preparing to unpack .../64-python3-pure-eval_0.2.2-2_all.deb ... 149s Unpacking python3-pure-eval (0.2.2-2) ... 149s Selecting previously unselected package python3-stack-data. 149s Preparing to unpack .../65-python3-stack-data_0.6.3-1_all.deb ... 149s Unpacking python3-stack-data (0.6.3-1) ... 149s Selecting previously unselected package python3-ipython. 149s Preparing to unpack .../66-python3-ipython_8.20.0-1ubuntu1_all.deb ... 149s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 149s Selecting previously unselected package python3-kiwisolver. 149s Preparing to unpack .../67-python3-kiwisolver_1.4.5-1_amd64.deb ... 149s Unpacking python3-kiwisolver (1.4.5-1) ... 149s Selecting previously unselected package libopenjp2-7:amd64. 149s Preparing to unpack .../68-libopenjp2-7_2.5.0-2build3_amd64.deb ... 149s Unpacking libopenjp2-7:amd64 (2.5.0-2build3) ... 149s Selecting previously unselected package python3-pil:amd64. 149s Preparing to unpack .../69-python3-pil_10.3.0-2_amd64.deb ... 149s Unpacking python3-pil:amd64 (10.3.0-2) ... 149s Selecting previously unselected package python3-tk:amd64. 149s Preparing to unpack .../70-python3-tk_3.12.3-0ubuntu1_amd64.deb ... 149s Unpacking python3-tk:amd64 (3.12.3-0ubuntu1) ... 149s Selecting previously unselected package python3-pil.imagetk:amd64. 149s Preparing to unpack .../71-python3-pil.imagetk_10.3.0-2_amd64.deb ... 149s Unpacking python3-pil.imagetk:amd64 (10.3.0-2) ... 150s Selecting previously unselected package python3-packaging. 150s Preparing to unpack .../72-python3-packaging_24.0-1_all.deb ... 150s Unpacking python3-packaging (24.0-1) ... 150s Selecting previously unselected package python3-matplotlib. 150s Preparing to unpack .../73-python3-matplotlib_3.6.3-2ubuntu1_amd64.deb ... 150s Unpacking python3-matplotlib (3.6.3-2ubuntu1) ... 150s Selecting previously unselected package python3-natsort. 150s Preparing to unpack .../74-python3-natsort_8.0.2-2_all.deb ... 150s Unpacking python3-natsort (8.0.2-2) ... 150s Selecting previously unselected package python3-pandas-lib:amd64. 150s Preparing to unpack .../75-python3-pandas-lib_2.1.4+dfsg-8_amd64.deb ... 150s Unpacking python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... 150s Selecting previously unselected package python3-pandas. 150s Preparing to unpack .../76-python3-pandas_2.1.4+dfsg-8_all.deb ... 150s Unpacking python3-pandas (2.1.4+dfsg-8) ... 150s Selecting previously unselected package python3-pluggy. 150s Preparing to unpack .../77-python3-pluggy_1.5.0-1_all.deb ... 150s Unpacking python3-pluggy (1.5.0-1) ... 150s Selecting previously unselected package python3-pytest. 150s Preparing to unpack .../78-python3-pytest_7.4.4-1_all.deb ... 150s Unpacking python3-pytest (7.4.4-1) ... 150s Selecting previously unselected package python3-skbio. 150s Preparing to unpack .../79-python3-skbio_0.5.9-4build1_amd64.deb ... 150s Unpacking python3-skbio (0.5.9-4build1) ... 151s Selecting previously unselected package autopkgtest-satdep. 151s Preparing to unpack .../80-1-autopkgtest-satdep.deb ... 151s Unpacking autopkgtest-satdep (0) ... 151s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 151s Setting up liblcms2-2:amd64 (2.14-2build1) ... 151s Setting up python3-iniconfig (1.1.1-2) ... 151s Setting up python3-pure-eval (0.2.2-2) ... 151s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 151s Setting up python3-parso (0.8.3-1) 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Note that the correlation/,/After permuting host : parasite interactions, we find that the observed/d {} ; 229s + 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 {} ; 229s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 232s ============================= test session starts ============================== 232s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 232s rootdir: /tmp/autopkgtest.GeVxOm/autopkgtest_tmp 232s collected 2390 items 232s 233s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 233s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 233s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 233s ........................................................................ 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[ 93%] 302s skbio/tree/tests/test_nj.py ........... [ 93%] 302s skbio/tree/tests/test_tree.py .......................................... [ 95%] 303s ................................................... [ 97%] 303s skbio/util/tests/test_decorator.py ....................... [ 98%] 303s skbio/util/tests/test_misc.py .................... [ 99%] 303s skbio/util/tests/test_testing.py ............... [100%] 303s 303s =============================== warnings summary =============================== 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 303s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 303s /tmp/autopkgtest.GeVxOm/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 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 303s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 303s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 303s /tmp/autopkgtest.GeVxOm/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]` 303s df['bar'][0].append(42) 303s 303s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 303s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 303s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 303s /tmp/autopkgtest.GeVxOm/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]` 303s df['bar'][0].append(42) 303s 303s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 303s gap_freqs /= length 303s 303s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 303s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 303s 303s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 303s freqs = counts / counts.sum() 303s 303s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 303s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 303s 303s skbio/diversity/tests/test_block.py: 3 warnings 303s skbio/diversity/tests/test_driver.py: 9 warnings 303s /tmp/autopkgtest.GeVxOm/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. 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 303s /tmp/autopkgtest.GeVxOm/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 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 303s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 303s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 303s /tmp/autopkgtest.GeVxOm/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 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 303s /tmp/autopkgtest.GeVxOm/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 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 303s obs_counts = obs_counts / len(self) 303s 303s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 303s warnings.warn(ConstantInputWarning()) 303s 303s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 303s warnings.warn(ConstantInputWarning()) 303s 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 303s /tmp/autopkgtest.GeVxOm/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. 303s warn( 303s 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 303s /tmp/autopkgtest.GeVxOm/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. 303s warn( 303s 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 303s proportion_explained = eigvals / sum_eigenvalues 303s 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/distance/_permdisp.py:290: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 303s stat, _ = f_oneway(*groups) 303s 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 303s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 303s /tmp/autopkgtest.GeVxOm/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. 303s warn( 303s 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 303s /tmp/autopkgtest.GeVxOm/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. 303s fig.tight_layout() 303s 303s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 303s plot = scatter_fn(c=point_colors, cmap=cmap) 303s 303s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 303s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 303s return self.run(*args, **kwds) 303s 303s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 303s /tmp/autopkgtest.GeVxOm/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]` 303s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 303s 303s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 303s /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. 303s res = hypotest_fun_out(*samples, **kwds) 303s 303s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/composition.py:1589: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 303s return significance_test(*[x[cats == k] for k in cs]) 303s 303s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 303s X_log = np.log(mat) 303s 303s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 303s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 303s X -= avg[:, None] 303s 303s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 303s /tmp/autopkgtest.GeVxOm/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 303s x = np.log(x) 303s 303s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 303s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 303s x = asanyarray(arr - arrmean) 303s 303s skbio/stats/tests/test_gradient.py: 13 warnings 303s /tmp/autopkgtest.GeVxOm/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]` 303s np.abs((w_vector[i] - w_vector[i-1])) 303s 303s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 303s /tmp/autopkgtest.GeVxOm/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. 303s trajectories.loc[idx] = ( 303s 303s skbio/stats/tests/test_power.py: 27 warnings 303s /tmp/autopkgtest.GeVxOm/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.) 303s pwr[id2] = _calculate_power(ps, a) 303s 303s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 303s /tmp/autopkgtest.GeVxOm/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(). 303s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 303s 303s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 303s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 119 warnings in 73.93s (0:01:13) = 304s autopkgtest [22:28:54]: test testsuite: -----------------------] 304s autopkgtest [22:28:54]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 304s testsuite PASS 304s autopkgtest [22:28:54]: @@@@@@@@@@@@@@@@@@@@ summary 304s import-skbio PASS 304s testsuite PASS 361s nova [W] Skipping flock for amd64 361s Creating nova instance adt-oracular-amd64-python-skbio-20240628-222350-juju-7f2275-prod-proposed-migration-environment-3-c78b82e3-834c-44cc-9730-5dedc6dce205 from image adt/ubuntu-oracular-amd64-server-20240628.img (UUID 9d02b460-22c0-49a4-a380-3bb68f865fe5)...