0s autopkgtest [14:12:04]: starting date and time: 2026-02-06 14:12:04+0000 0s autopkgtest [14:12:04]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:12:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wezv5fgm/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade python-pyani --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.1-0.1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-25.secgroup --name adt-resolute-amd64-python-pyani-20260206-141203-juju-7f2275-prod-proposed-migration-environment-2-e56e3e30-f977-4fe4-875c-f7562a848274 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-python-pyani-20260206-141203-juju-7f2275-prod-proposed-migration-environment-2-e56e3e30-f977-4fe4-875c-f7562a848274 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 94s autopkgtest [14:13:38]: testbed dpkg architecture: amd64 94s autopkgtest [14:13:38]: testbed apt version: 3.1.14 95s autopkgtest [14:13:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s autopkgtest [14:13:39]: testbed release detected to be: None 95s autopkgtest [14:13:39]: updating testbed package index (apt update) 96s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 96s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9256 B] 96s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1473 kB] 96s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [191 kB] 96s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [30.8 kB] 96s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [249 kB] 96s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [181 kB] 96s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6436 B] 96s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 96s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [68.4 kB] 96s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 96s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [518 kB] 96s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1348 kB] 97s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [35.8 kB] 97s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.7 kB] 97s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 97s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1060 B] 97s Fetched 4271 kB in 1s (3443 kB/s) 98s Reading package lists... 99s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 99s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 99s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 99s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 99s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade... 100s The following packages will be upgraded: 100s amd64-microcode apt busybox-initramfs busybox-static dmsetup findutils less 100s libapt-pkg7.0 libattr1 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 100s libdrm2 libgpm2 libkeyutils1 libmaxminddb0 libnpth0t64 libsensors-config 100s libsensors5 mawk patch pollinate python3-linkify-it python3-markdown-it 100s python3-pkg-resources python3-referencing python3-setuptools sed tar 100s 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 6787 kB of archives. 100s After this operation, 270 kB disk space will be freed. 100s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 100s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 100s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 100s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 100s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 100s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 100s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 100s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 100s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 100s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 100s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 100s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 100s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 100s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 100s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 100s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 100s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 100s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 100s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 100s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 100s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 100s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 100s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 100s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 100s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 100s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 100s Get:27 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 100s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 100s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 100s dpkg-preconfigure: unable to re-open stdin: No such file or directory 100s Fetched 6787 kB in 0s (24.3 MB/s) 100s (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 ... 83957 files and directories currently installed.) 100s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 100s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 100s Setting up findutils (4.10.0-3build2) ... 100s (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 ... 83957 files and directories currently installed.) 100s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 100s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 100s Setting up sed (4.9-2build3) ... 100s (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 ... 83957 files and directories currently installed.) 100s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 100s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 101s Setting up tar (1.35+dfsg-3.1build2) ... 101s (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 ... 83957 files and directories currently installed.) 101s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 101s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 101s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 101s (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 ... 83957 files and directories currently installed.) 101s Preparing to unpack .../00-mawk_1.3.4.20260129-1_amd64.deb ... 101s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 101s Preparing to unpack .../01-libapt-pkg7.0_3.1.15_amd64.deb ... 101s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ... 101s Preparing to unpack .../02-apt_3.1.15_amd64.deb ... 101s Unpacking apt (3.1.15) over (3.1.14) ... 101s Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ... 101s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 101s Preparing to unpack .../04-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ... 101s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 101s Preparing to unpack .../05-less_668-1build1_amd64.deb ... 101s Unpacking less (668-1build1) over (668-1) ... 101s Preparing to unpack .../06-libkeyutils1_1.6.3-6ubuntu3_amd64.deb ... 101s Unpacking libkeyutils1:amd64 (1.6.3-6ubuntu3) over (1.6.3-6ubuntu2) ... 101s Preparing to unpack .../07-python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 101s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 101s Preparing to unpack .../08-python3-markdown-it_3.0.0-3build1_all.deb ... 101s Unpacking python3-markdown-it (3.0.0-3build1) over (3.0.0-3) ... 101s Preparing to unpack .../09-busybox-static_1%3a1.37.0-7ubuntu1_amd64.deb ... 101s Unpacking busybox-static (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 101s Preparing to unpack .../10-libdrm-common_2.4.131-1_all.deb ... 101s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 101s Preparing to unpack .../11-libdrm2_2.4.131-1_amd64.deb ... 101s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ... 101s Preparing to unpack .../12-libgpm2_1.20.7-12build1_amd64.deb ... 101s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ... 101s Preparing to unpack .../13-libmaxminddb0_1.12.2-1build2_amd64.deb ... 101s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ... 101s Preparing to unpack .../14-libsensors-config_1%3a3.6.2-2build1_all.deb ... 101s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ... 101s Preparing to unpack .../15-libsensors5_1%3a3.6.2-2build1_amd64.deb ... 101s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ... 101s Preparing to unpack .../16-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ... 101s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 101s Preparing to unpack .../17-libdrm-amdgpu1_2.4.131-1_amd64.deb ... 101s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ... 101s Preparing to unpack .../18-libnpth0t64_1.8-3build1_amd64.deb ... 101s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ... 101s Preparing to unpack .../19-patch_2.8-2build1_amd64.deb ... 101s Unpacking patch (2.8-2build1) over (2.8-2) ... 102s Preparing to unpack .../20-pollinate_4.33-4ubuntu5_all.deb ... 102s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 102s Preparing to unpack .../21-python3-pkg-resources_78.1.1-0.1build1_all.deb ... 102s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 102s Preparing to unpack .../22-python3-setuptools_78.1.1-0.1build1_all.deb ... 102s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 102s Preparing to unpack .../23-python3-referencing_0.36.2-1ubuntu2_all.deb ... 102s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 102s Preparing to unpack .../24-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ... 102s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ... 102s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 102s Setting up libnpth0t64:amd64 (1.8-3build1) ... 102s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 102s Setting up libgpm2:amd64 (1.20.7-12build1) ... 102s Setting up python3-setuptools (78.1.1-0.1build1) ... 103s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 103s Setting up libsensors-config (1:3.6.2-2build1) ... 103s Setting up less (668-1build1) ... 103s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 103s amd64-microcode: microcode will be updated at next boot 103s Setting up pollinate (4.33-4ubuntu5) ... 113s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 113s Setting up patch (2.8-2build1) ... 113s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 113s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 113s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 113s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 113s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 113s Setting up mawk (1.3.4.20260129-1) ... 113s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 113s Setting up libdrm-common (2.4.131-1) ... 113s Setting up python3-referencing (0.36.2-1ubuntu2) ... 113s Setting up apt (3.1.15) ... 114s Setting up python3-markdown-it (3.0.0-3build1) ... 114s Setting up libdrm2:amd64 (2.4.131-1) ... 114s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 114s Processing triggers for libc-bin (2.42-2ubuntu4) ... 114s Processing triggers for man-db (2.13.1-1) ... 115s Processing triggers for install-info (7.2-5) ... 115s Processing triggers for initramfs-tools (0.150ubuntu7) ... 115s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 120s autopkgtest [14:14:04]: upgrading testbed (apt dist-upgrade and autopurge) 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [14:14:05]: rebooting testbed after setup commands that affected boot 150s autopkgtest [14:14:34]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 152s autopkgtest [14:14:36]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pyani 155s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-pyani 0.2.13-1 (dsc) [1798 B] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-pyani 0.2.13-1 (tar) [49.0 MB] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-pyani 0.2.13-1 (diff) [11.2 kB] 155s gpgv: Signature made Tue Mar 18 07:26:50 2025 UTC 155s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 155s gpgv: issuer "nilesh@debian.org" 155s gpgv: Can't check signature: No public key 155s dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.13-1.dsc: no acceptable signature found 156s autopkgtest [14:14:40]: testing package python-pyani version 0.2.13-1 157s autopkgtest [14:14:41]: build not needed 164s autopkgtest [14:14:48]: test run-unit-test: preparing testbed 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Solving dependencies... 165s The following NEW packages will be installed: 165s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 165s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 165s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 165s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 165s liblerc4 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 165s libopenjp2-7 libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib 165s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 165s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 165s libxslt1.1 libxss1 libzopfli1 mummer ncbi-blast+ ncbi-data ncbi-vdb-data 165s python-matplotlib-data python3-all python3-biopython python3-brotli 165s python3-cairo python3-charset-normalizer python3-contourpy python3-cycler 165s python3-decorator python3-fonttools python3-freetype python3-iniconfig 165s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 165s python3-mpmath python3-numpy python3-numpy-dev python3-pandas 165s python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy 165s python3-pyani python3-pytest python3-pytz python3-reportlab 165s python3-rlpycairo python3-scipy python3-seaborn python3-sympy python3-tk 165s python3-ufolib2 python3-zopfli python3.13-tk python3.14 python3.14-minimal 165s python3.14-tk sgml-base unicode-data w3c-sgml-lib x11-common 165s xfonts-encodings xfonts-utils xml-core 165s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 135 MB of archives. 165s After this operation, 583 MB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-12ubuntu1 [939 kB] 165s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 166s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 166s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 166s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 167s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 167s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 167s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 167s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 167s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 167s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7build1 [97.1 kB] 167s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 167s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 167s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 167s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.5.0~RC2-3 [171 kB] 167s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 167s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 167s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 167s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 167s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 167s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 167s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 167s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-12ubuntu1 [151 kB] 167s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 167s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 167s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 167s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 167s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 167s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 167s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 167s Get:33 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.5-0.1ubuntu2 [259 kB] 167s Get:34 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.5-0.1ubuntu2 [35.4 kB] 167s Get:35 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.5-0.1ubuntu2 [130 kB] 167s Get:36 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2build1 [81.4 kB] 167s Get:37 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2build1 [1242 kB] 167s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 167s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-8 [197 kB] 167s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1build1 [15.5 kB] 167s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 167s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 167s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 167s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 167s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 167s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 167s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 167s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 167s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1build1 [12.8 kB] 167s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1build1 [26.4 kB] 167s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 167s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3build1 [114 kB] 167s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 mummer amd64 3.23+dfsg-8build1 [690 kB] 167s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 168s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] 168s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 168s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 168s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.9-3 [890 B] 168s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-2 [173 kB] 168s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.11-1 [108 kB] 168s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.2-1 [109 kB] 168s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-3 [11.2 kB] 168s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 168s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.4-1 [188 kB] 168s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 168s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 168s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 168s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 168s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.9-1 [1149 kB] 168s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1build1 [11.2 kB] 168s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 168s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3build1 [278 kB] 168s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 168s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 168s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 168s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 168s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 168s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 168s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.5+dfsg-1 [27.7 kB] 168s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-4 [19.0 MB] 169s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 169s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 169s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 169s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 169s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1build1 [9543 kB] 169s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.61.1-3 [1742 kB] 169s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 169s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 169s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 169s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 169s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 170s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 170s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 170s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-seaborn all 0.13.2-6 [225 kB] 170s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyani amd64 0.2.13-1 [46.7 kB] 170s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 170s Fetched 135 MB in 5s (28.7 MB/s) 170s Selecting previously unselected package python3-numpy-dev:amd64. 170s (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 ... 83962 files and directories currently installed.) 170s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 170s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 170s Selecting previously unselected package libblas3:amd64. 170s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_amd64.deb ... 170s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 170s Selecting previously unselected package libgfortran5:amd64. 170s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_amd64.deb ... 170s Unpacking libgfortran5:amd64 (15.2.0-12ubuntu1) ... 170s Selecting previously unselected package liblapack3:amd64. 170s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 170s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 170s Selecting previously unselected package python3-numpy. 170s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 170s Unpacking python3-numpy (1:2.3.5+ds-3) ... 170s Selecting previously unselected package libpython3.14-minimal:amd64. 170s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_amd64.deb ... 170s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 171s Selecting previously unselected package python3.14-minimal. 171s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_amd64.deb ... 171s Unpacking python3.14-minimal (3.14.2-1) ... 171s Selecting previously unselected package fonts-dejavu-mono. 171s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8build1_all.deb ... 171s Unpacking fonts-dejavu-mono (2.37-8build1) ... 171s Selecting previously unselected package fonts-dejavu-core. 171s Preparing to unpack .../08-fonts-dejavu-core_2.37-8build1_all.deb ... 171s Unpacking fonts-dejavu-core (2.37-8build1) ... 171s Selecting previously unselected package libfontenc1:amd64. 171s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 171s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 171s Selecting previously unselected package x11-common. 171s Preparing to unpack .../10-x11-common_1%3a7.7+24ubuntu1_all.deb ... 171s Unpacking x11-common (1:7.7+24ubuntu1) ... 171s Selecting previously unselected package xfonts-encodings. 171s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 171s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 171s Selecting previously unselected package xfonts-utils. 171s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7build1_amd64.deb ... 171s Unpacking xfonts-utils (1:7.7+7build1) ... 171s Selecting previously unselected package fonts-urw-base35. 171s Preparing to unpack .../13-fonts-urw-base35_20200910-8build1_all.deb ... 171s Unpacking fonts-urw-base35 (20200910-8build1) ... 171s Selecting previously unselected package fontconfig-config. 171s Preparing to unpack .../14-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 171s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 171s Selecting previously unselected package fonts-dejavu-extra. 171s Preparing to unpack .../15-fonts-dejavu-extra_2.37-8build1_all.deb ... 171s Unpacking fonts-dejavu-extra (2.37-8build1) ... 171s Selecting previously unselected package fonts-lyx. 171s Preparing to unpack .../16-fonts-lyx_2.5.0~RC2-3_all.deb ... 171s Unpacking fonts-lyx (2.5.0~RC2-3) ... 171s Selecting previously unselected package libfontconfig1:amd64. 171s Preparing to unpack .../17-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 171s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 171s Selecting previously unselected package libpixman-1-0:amd64. 171s Preparing to unpack .../18-libpixman-1-0_0.46.4-1_amd64.deb ... 171s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 171s Selecting previously unselected package libxcb-render0:amd64. 171s Preparing to unpack .../19-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 171s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 171s Selecting previously unselected package libxcb-shm0:amd64. 171s Preparing to unpack .../20-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 171s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 171s Selecting previously unselected package libxrender1:amd64. 171s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_amd64.deb ... 171s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 171s Selecting previously unselected package libcairo2:amd64. 171s Preparing to unpack .../22-libcairo2_1.18.4-3_amd64.deb ... 171s Unpacking libcairo2:amd64 (1.18.4-3) ... 171s Selecting previously unselected package libdeflate0:amd64. 171s Preparing to unpack .../23-libdeflate0_1.23-2_amd64.deb ... 171s Unpacking libdeflate0:amd64 (1.23-2) ... 171s Selecting previously unselected package libgomp1:amd64. 171s Preparing to unpack .../24-libgomp1_15.2.0-12ubuntu1_amd64.deb ... 171s Unpacking libgomp1:amd64 (15.2.0-12ubuntu1) ... 171s Selecting previously unselected package libgraphite2-3:amd64. 171s Preparing to unpack .../25-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 171s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 171s Selecting previously unselected package libharfbuzz0b:amd64. 171s Preparing to unpack .../26-libharfbuzz0b_12.3.2-1_amd64.deb ... 171s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 171s Selecting previously unselected package libimagequant0:amd64. 171s Preparing to unpack .../27-libimagequant0_2.18.0-1build1_amd64.deb ... 171s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 171s Selecting previously unselected package libjpeg-turbo8:amd64. 171s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 171s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 171s Selecting previously unselected package libjpeg8:amd64. 171s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_amd64.deb ... 171s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 171s Selecting previously unselected package liblcms2-2:amd64. 171s Preparing to unpack .../30-liblcms2-2_2.17-1_amd64.deb ... 171s Unpacking liblcms2-2:amd64 (2.17-1) ... 171s Selecting previously unselected package liblerc4:amd64. 171s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 171s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 171s Selecting previously unselected package libmbedcrypto16:amd64. 171s Preparing to unpack .../32-libmbedcrypto16_3.6.5-0.1ubuntu2_amd64.deb ... 171s Unpacking libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 171s Selecting previously unselected package libmbedx509-7:amd64. 171s Preparing to unpack .../33-libmbedx509-7_3.6.5-0.1ubuntu2_amd64.deb ... 171s Unpacking libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 171s Selecting previously unselected package libmbedtls21:amd64. 171s Preparing to unpack .../34-libmbedtls21_3.6.5-0.1ubuntu2_amd64.deb ... 171s Unpacking libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 171s Selecting previously unselected package ncbi-vdb-data. 171s Preparing to unpack .../35-ncbi-vdb-data_3.2.1+dfsg-2build1_all.deb ... 171s Unpacking ncbi-vdb-data (3.2.1+dfsg-2build1) ... 171s Selecting previously unselected package libncbi-vdb3:amd64. 171s Preparing to unpack .../36-libncbi-vdb3_3.2.1+dfsg-2build1_amd64.deb ... 171s Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2build1) ... 171s Selecting previously unselected package libpython3.14-stdlib:amd64. 171s Preparing to unpack .../37-libpython3.14-stdlib_3.14.2-1_amd64.deb ... 171s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 171s Selecting previously unselected package libqhull-r8.0:amd64. 171s Preparing to unpack .../38-libqhull-r8.0_2020.2-8_amd64.deb ... 171s Unpacking libqhull-r8.0:amd64 (2020.2-8) ... 171s Selecting previously unselected package libraqm0:amd64. 171s Preparing to unpack .../39-libraqm0_0.10.3-1build1_amd64.deb ... 171s Unpacking libraqm0:amd64 (0.10.3-1build1) ... 171s Selecting previously unselected package libsharpyuv0:amd64. 171s Preparing to unpack .../40-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 171s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 171s Selecting previously unselected package libtcl8.6:amd64. 171s Preparing to unpack .../41-libtcl8.6_8.6.17+dfsg-1build1_amd64.deb ... 171s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 171s Selecting previously unselected package libjbig0:amd64. 171s Preparing to unpack .../42-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 171s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 171s Selecting previously unselected package libwebp7:amd64. 171s Preparing to unpack .../43-libwebp7_1.5.0-0.1build1_amd64.deb ... 171s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 171s Selecting previously unselected package libtiff6:amd64. 171s Preparing to unpack .../44-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 171s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 171s Selecting previously unselected package libxft2:amd64. 171s Preparing to unpack .../45-libxft2_2.3.6-1build2_amd64.deb ... 171s Unpacking libxft2:amd64 (2.3.6-1build2) ... 171s Selecting previously unselected package libxss1:amd64. 171s Preparing to unpack .../46-libxss1_1%3a1.2.3-1build4_amd64.deb ... 171s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 171s Selecting previously unselected package libtk8.6:amd64. 171s Preparing to unpack .../47-libtk8.6_8.6.17-1_amd64.deb ... 171s Unpacking libtk8.6:amd64 (8.6.17-1) ... 171s Selecting previously unselected package libwebpdemux2:amd64. 171s Preparing to unpack .../48-libwebpdemux2_1.5.0-0.1build1_amd64.deb ... 171s Unpacking libwebpdemux2:amd64 (1.5.0-0.1build1) ... 171s Selecting previously unselected package libwebpmux3:amd64. 172s Preparing to unpack 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previously unselected package python-matplotlib-data. 172s Preparing to unpack .../55-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 172s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 172s Selecting previously unselected package python3.14. 172s Preparing to unpack .../56-python3.14_3.14.2-1_amd64.deb ... 172s Unpacking python3.14 (3.14.2-1) ... 172s Selecting previously unselected package python3-all. 172s Preparing to unpack .../57-python3-all_3.13.9-3_amd64.deb ... 172s Unpacking python3-all (3.13.9-3) ... 172s Selecting previously unselected package python3-charset-normalizer. 172s Preparing to unpack .../58-python3-charset-normalizer_3.4.4-2_amd64.deb ... 172s Unpacking python3-charset-normalizer (3.4.4-2) ... 172s Selecting previously unselected package python3.13-tk. 172s Preparing to unpack .../59-python3.13-tk_3.13.11-1_amd64.deb ... 172s Unpacking python3.13-tk (3.13.11-1) ... 172s Selecting previously unselected package python3.14-tk. 172s Preparing to unpack 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... 175s Setting up sgml-base (1.31+nmu1build1) ... 175s Setting up libxss1:amd64 (1:1.2.3-1build4) ... 175s Setting up libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 175s Setting up python3-mpmath (1.3.0-2) ... 176s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 176s Setting up libwebpmux3:amd64 (1.5.0-0.1build1) ... 176s Setting up python3.14-minimal (3.14.2-1) ... 176s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 176s Setting up python3-sympy (1.14.0-2) ... 183s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 183s return p.returncode 184s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 184s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 184s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 184s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 184s Setting up python3-pytest (9.0.2-2) ... 184s Setting up libwebpdemux2:amd64 (1.5.0-0.1build1) ... 184s Setting up xfonts-utils (1:7.7+7build1) ... 184s Setting up python3-zopfli (0.4.0-1) ... 184s Setting up libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 184s Setting up libraqm0:amd64 (0.10.3-1build1) ... 184s Setting up python3-numpy (1:2.3.5+ds-3) ... 187s Setting up libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 187s Setting up python3-lxml:amd64 (6.0.2-1) ... 187s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 187s Setting up xml-core (0.19build1) ... 187s Setting up python3-contourpy (1.3.3-1) ... 187s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 187s Setting up python3.14 (3.14.2-1) ... 188s Setting up libxft2:amd64 (2.3.6-1build2) ... 188s Setting up python3-scipy (1.16.3-4) ... 192s Setting up libtk8.6:amd64 (8.6.17-1) ... 192s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 192s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2build1) ... 192s Setting up python3-all (3.13.9-3) ... 192s Setting up fonts-urw-base35 (20200910-8build1) ... 193s Setting up libcairo2:amd64 (1.18.4-3) ... 193s Setting up python3.13-tk (3.13.11-1) ... 193s Setting up ncbi-blast+ (2.16.0+ds-7) ... 193s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 193s Setting up python3-pandas (2.3.3+dfsg-3) ... 199s Setting up python3.14-tk (3.14.2-1) ... 199s Setting up python3-cairo (1.27.0-2build1) ... 199s Setting up python3-tk (3.13.9-3) ... 199s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 199s Setting up python3-rlpycairo (0.3.0-4) ... 199s Setting up python3-reportlab (4.4.9-1) ... 200s Setting up python3-fonttools (4.61.1-3) ... 201s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 201s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 203s Setting up python3-seaborn (0.13.2-6) ... 204s Processing triggers for systemd (259-1ubuntu3) ... 204s Processing triggers for man-db (2.13.1-1) ... 205s Processing triggers for libc-bin (2.42-2ubuntu4) ... 205s Processing triggers for sgml-base (1.31+nmu1build1) ... 205s Setting up w3c-sgml-lib (1.3-3build1) ... 221s Setting up python3-biopython (1.86+dfsg-1) ... 222s Setting up python3-pyani (0.2.13-1) ... 223s autopkgtest [14:15:47]: test run-unit-test: [----------------------- 223s Testing with python3.14 in /tmp/autopkgtest.iFzLSA/build.ml5/src: 223s ============================= test session starts ============================== 223s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3 223s cachedir: .pytest_cache 223s rootdir: /tmp/autopkgtest.iFzLSA/build.ml5/src 223s plugins: typeguard-4.4.4 225s collecting ... collected 56 items 225s 225s tests/test_anib.py::TestBLASTCmdline::test_blastall_dbjobdict SKIPPED [ 1%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastall_generation SKIPPED [ 3%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastall_graph SKIPPED (l...) [ 5%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastdb_commands PASSED [ 7%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastn_commands PASSED [ 8%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastn_dbjobdict PASSED [ 10%] 225s tests/test_anib.py::TestBLASTCmdline::test_blastn_generation PASSED [ 12%] 226s tests/test_anib.py::TestBLASTCmdline::test_blastn_graph PASSED [ 14%] 226s tests/test_anib.py::TestBLASTCmdline::test_formatdb_generation SKIPPED [ 16%] 226s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastdb_commands SKIPPED [ 17%] 226s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastn_commands SKIPPED [ 19%] 226s tests/test_anib.py::TestBLASTCmdline::test_makeblastdb_generation PASSED [ 21%] 227s tests/test_anib.py::TestFragments::test_fragment_files PASSED [ 23%] 227s tests/test_anib.py::TestParsing::test_blastdir_processing PASSED [ 25%] 227s tests/test_anib.py::TestParsing::test_legacy_blastdir_processing SKIPPED [ 26%] 227s tests/test_anib.py::TestParsing::test_parse_blasttab SKIPPED (legacy...) [ 28%] 227s tests/test_anim.py::TestNUCmerCmdline::test_maxmatch_cmd_generation PASSED [ 30%] 227s tests/test_anim.py::TestNUCmerCmdline::test_multi_cmd_generation PASSED [ 32%] 227s tests/test_anim.py::TestNUCmerCmdline::test_nucmer_job_generation PASSED [ 33%] 227s tests/test_anim.py::TestNUCmerCmdline::test_single_cmd_generation PASSED [ 35%] 227s tests/test_anim.py::TestDeltafileProcessing::test_deltafile_import PASSED [ 37%] 228s tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir PASSED [ 39%] 239s tests/test_concordance.py::TestConcordance::test_anib_concordance PASSED [ 41%] 239s tests/test_concordance.py::TestConcordance::test_aniblastall_concordance SKIPPED [ 42%] 247s tests/test_concordance.py::TestConcordance::test_anim_concordance PASSED [ 44%] 254s tests/test_concordance.py::TestConcordance::test_tetra_concordance PASSED [ 46%] 254s tests/test_dependencies.py::test_import_biopython PASSED [ 48%] 254s tests/test_dependencies.py::test_import_matplotlib PASSED [ 50%] 254s tests/test_dependencies.py::test_import_numpy PASSED [ 51%] 254s tests/test_dependencies.py::test_import_pandas PASSED [ 53%] 254s tests/test_dependencies.py::test_import_scipy PASSED [ 55%] 254s tests/test_dependencies.py::test_run_blast PASSED [ 57%] 254s tests/test_dependencies.py::test_run_blastall SKIPPED (unconditional...) [ 58%] 254s tests/test_dependencies.py::test_run_nucmer PASSED [ 60%] 255s tests/test_graphics.py::test_png_mpl PASSED [ 62%] 255s tests/test_graphics.py::test_svg_mpl PASSED [ 64%] 255s tests/test_graphics.py::test_pdf_mpl PASSED [ 66%] 255s tests/test_graphics.py::test_png_seaborn PASSED [ 67%] 255s tests/test_graphics.py::test_svg_seaborn PASSED [ 69%] 255s tests/test_graphics.py::test_pdf_seaborn PASSED [ 71%] 255s tests/test_jobs.py::TestJob::test_add_dependency PASSED [ 73%] 255s tests/test_jobs.py::TestJob::test_create_job PASSED [ 75%] 255s tests/test_jobs.py::TestJob::test_create_job_with_command PASSED [ 76%] 255s tests/test_jobs.py::TestJob::test_remove_dependency PASSED [ 78%] 256s tests/test_jobs.py::TestJobGroup::test_1d_jobgroup PASSED [ 80%] 256s tests/test_jobs.py::TestJobGroup::test_2d_jobgroup PASSED [ 82%] 256s tests/test_jobs.py::TestJobGroup::test_add_dependency PASSED [ 83%] 256s tests/test_jobs.py::TestJobGroup::test_create_jobgroup PASSED [ 85%] 256s tests/test_jobs.py::TestJobGroup::test_remove_dependency PASSED [ 87%] 256s tests/test_multiprocessing.py::TestMultiprocessing::test_cmdsets PASSED [ 89%] 296s tests/test_multiprocessing.py::TestMultiprocessing::test_dependency_graph_run PASSED [ 91%] 296s tests/test_multiprocessing.py::TestMultiprocessing::test_multiprocessing_run PASSED [ 92%] 296s tests/test_parsing.py::test_anim_delta PASSED [ 94%] 304s tests/test_tetra.py::TestTETRA::test_correlations PASSED [ 96%] 304s tests/test_tetra.py::TestTETRA::test_tetraclean PASSED [ 98%] 307s tests/test_tetra.py::TestTETRA::test_zscore PASSED [100%] 307s 307s =============================== warnings summary =============================== 307s tests/test_anib.py::TestParsing::test_blastdir_processing 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s /usr/lib/python3/dist-packages/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 307s results.alignment_lengths[org][org] = length 307s 307s tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s /usr/lib/python3/dist-packages/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 307s results.alignment_lengths[org][org] = length 307s 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 307s data[columns[idx]][row] = 1.0 307s 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 307s data[columns[idx]][row] = float(val) 307s 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_anim_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 307s data[columns[idx]][row] = 100.0 307s 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 307s lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) 307s 307s tests/test_concordance.py::TestConcordance::test_anib_concordance 307s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 307s hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) 307s 307s tests/test_concordance.py::TestConcordance::test_tetra_concordance 307s tests/test_tetra.py::TestTETRA::test_correlations 307s /usr/lib/python3/dist-packages/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 307s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 307s A typical example is when you are setting values in a column of a DataFrame, like: 307s 307s df["col"][row_indexer] = value 307s 307s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 307s 307s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 307s 308s correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) 308s 308s tests/test_concordance.py::TestConcordance::test_tetra_concordance 308s tests/test_tetra.py::TestTETRA::test_correlations 308s /usr/lib/python3/dist-packages/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 308s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 308s A typical example is when you are setting values in a column of a DataFrame, like: 308s 308s df["col"][row_indexer] = value 308s 308s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 308s 308s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 308s 308s correlations[org2][org1] = correlations[org1][org2] 308s 308s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 308s ============ 46 passed, 10 skipped, 28 warnings in 83.75s (0:01:23) ============ 308s Testing with python3.13 in /tmp/autopkgtest.iFzLSA/build.ml5/src: 308s ============================= test session starts ============================== 308s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3 308s cachedir: .pytest_cache 308s rootdir: /tmp/autopkgtest.iFzLSA/build.ml5/src 308s plugins: typeguard-4.4.4 309s collecting ... collected 56 items 309s 309s tests/test_anib.py::TestBLASTCmdline::test_blastall_dbjobdict SKIPPED [ 1%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastall_generation SKIPPED [ 3%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastall_graph SKIPPED (l...) [ 5%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastdb_commands PASSED [ 7%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastn_commands PASSED [ 8%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastn_dbjobdict PASSED [ 10%] 309s tests/test_anib.py::TestBLASTCmdline::test_blastn_generation PASSED [ 12%] 310s tests/test_anib.py::TestBLASTCmdline::test_blastn_graph PASSED [ 14%] 310s tests/test_anib.py::TestBLASTCmdline::test_formatdb_generation SKIPPED [ 16%] 310s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastdb_commands SKIPPED [ 17%] 310s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastn_commands SKIPPED [ 19%] 310s tests/test_anib.py::TestBLASTCmdline::test_makeblastdb_generation PASSED [ 21%] 311s tests/test_anib.py::TestFragments::test_fragment_files PASSED [ 23%] 311s tests/test_anib.py::TestParsing::test_blastdir_processing PASSED [ 25%] 311s tests/test_anib.py::TestParsing::test_legacy_blastdir_processing SKIPPED [ 26%] 311s tests/test_anib.py::TestParsing::test_parse_blasttab SKIPPED (legacy...) [ 28%] 311s tests/test_anim.py::TestNUCmerCmdline::test_maxmatch_cmd_generation PASSED [ 30%] 311s tests/test_anim.py::TestNUCmerCmdline::test_multi_cmd_generation PASSED [ 32%] 311s tests/test_anim.py::TestNUCmerCmdline::test_nucmer_job_generation PASSED [ 33%] 311s tests/test_anim.py::TestNUCmerCmdline::test_single_cmd_generation PASSED [ 35%] 311s tests/test_anim.py::TestDeltafileProcessing::test_deltafile_import PASSED [ 37%] 311s tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir PASSED [ 39%] 323s tests/test_concordance.py::TestConcordance::test_anib_concordance PASSED [ 41%] 323s tests/test_concordance.py::TestConcordance::test_aniblastall_concordance SKIPPED [ 42%] 332s tests/test_concordance.py::TestConcordance::test_anim_concordance PASSED [ 44%] 339s tests/test_concordance.py::TestConcordance::test_tetra_concordance PASSED [ 46%] 339s tests/test_dependencies.py::test_import_biopython PASSED [ 48%] 339s tests/test_dependencies.py::test_import_matplotlib PASSED [ 50%] 339s tests/test_dependencies.py::test_import_numpy PASSED [ 51%] 339s tests/test_dependencies.py::test_import_pandas PASSED [ 53%] 339s tests/test_dependencies.py::test_import_scipy PASSED [ 55%] 339s tests/test_dependencies.py::test_run_blast PASSED [ 57%] 339s tests/test_dependencies.py::test_run_blastall SKIPPED (unconditional...) [ 58%] 339s tests/test_dependencies.py::test_run_nucmer PASSED [ 60%] 339s tests/test_graphics.py::test_png_mpl PASSED [ 62%] 339s tests/test_graphics.py::test_svg_mpl PASSED [ 64%] 340s tests/test_graphics.py::test_pdf_mpl PASSED [ 66%] 340s tests/test_graphics.py::test_png_seaborn PASSED [ 67%] 340s tests/test_graphics.py::test_svg_seaborn PASSED [ 69%] 340s tests/test_graphics.py::test_pdf_seaborn PASSED [ 71%] 340s tests/test_jobs.py::TestJob::test_add_dependency PASSED [ 73%] 340s tests/test_jobs.py::TestJob::test_create_job PASSED [ 75%] 340s tests/test_jobs.py::TestJob::test_create_job_with_command PASSED [ 76%] 340s tests/test_jobs.py::TestJob::test_remove_dependency PASSED [ 78%] 340s tests/test_jobs.py::TestJobGroup::test_1d_jobgroup PASSED [ 80%] 340s tests/test_jobs.py::TestJobGroup::test_2d_jobgroup PASSED [ 82%] 340s tests/test_jobs.py::TestJobGroup::test_add_dependency PASSED [ 83%] 340s tests/test_jobs.py::TestJobGroup::test_create_jobgroup PASSED [ 85%] 340s tests/test_jobs.py::TestJobGroup::test_remove_dependency PASSED [ 87%] 340s tests/test_multiprocessing.py::TestMultiprocessing::test_cmdsets PASSED [ 89%] 379s tests/test_multiprocessing.py::TestMultiprocessing::test_dependency_graph_run PASSED [ 91%] 379s tests/test_multiprocessing.py::TestMultiprocessing::test_multiprocessing_run PASSED [ 92%] 379s tests/test_parsing.py::test_anim_delta PASSED [ 94%] 387s tests/test_tetra.py::TestTETRA::test_correlations PASSED [ 96%] 387s tests/test_tetra.py::TestTETRA::test_tetraclean PASSED [ 98%] 390s tests/test_tetra.py::TestTETRA::test_zscore PASSED [100%] 390s 390s =============================== warnings summary =============================== 390s tests/test_anib.py::TestParsing::test_blastdir_processing 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s /usr/lib/python3/dist-packages/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s results.alignment_lengths[org][org] = length 390s 390s tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s /usr/lib/python3/dist-packages/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s results.alignment_lengths[org][org] = length 390s 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s data[columns[idx]][row] = 1.0 390s 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s data[columns[idx]][row] = float(val) 390s 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_anim_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s data[columns[idx]][row] = 100.0 390s 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 390s lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) 390s 390s tests/test_concordance.py::TestConcordance::test_anib_concordance 390s /tmp/autopkgtest.iFzLSA/build.ml5/src/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 390s hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) 390s 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s tests/test_tetra.py::TestTETRA::test_correlations 390s /usr/lib/python3/dist-packages/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) 390s 390s tests/test_concordance.py::TestConcordance::test_tetra_concordance 390s tests/test_tetra.py::TestTETRA::test_correlations 390s /usr/lib/python3/dist-packages/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! 390s You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. 390s A typical example is when you are setting values in a column of a DataFrame, like: 390s 390s df["col"][row_indexer] = value 390s 390s Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. 390s 390s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 390s 390s correlations[org2][org1] = correlations[org1][org2] 390s 390s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 390s ============ 46 passed, 10 skipped, 28 warnings in 82.05s (0:01:22) ============ 391s autopkgtest [14:18:35]: test run-unit-test: -----------------------] 392s autopkgtest [14:18:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 392s run-unit-test PASS 392s autopkgtest [14:18:36]: test autodep8-python3: preparing testbed 411s Creating nova instance adt-resolute-amd64-python-pyani-20260206-141203-juju-7f2275-prod-proposed-migration-environment-2-e56e3e30-f977-4fe4-875c-f7562a848274 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 521s autopkgtest [14:20:45]: testbed dpkg architecture: amd64 521s autopkgtest [14:20:45]: testbed apt version: 3.1.14 521s autopkgtest [14:20:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 521s autopkgtest [14:20:45]: testbed release detected to be: resolute 522s autopkgtest [14:20:46]: updating testbed package index (apt update) 522s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 522s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 522s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 522s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 522s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [30.8 kB] 522s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1473 kB] 522s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9256 B] 522s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [191 kB] 522s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [181 kB] 523s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [249 kB] 523s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6436 B] 523s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [68.4 kB] 523s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 523s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 523s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1348 kB] 523s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [518 kB] 523s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [35.8 kB] 523s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.7 kB] 523s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 523s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1060 B] 524s Fetched 4271 kB in 1s (5653 kB/s) 524s Reading package lists... 525s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 525s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 525s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 525s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 525s Reading package lists... 525s Reading package lists... 526s Building dependency tree... 526s Reading state information... 526s Calculating upgrade... 526s The following packages will be upgraded: 526s amd64-microcode apt busybox-initramfs busybox-static dmsetup findutils less 526s libapt-pkg7.0 libattr1 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 526s libdrm2 libgpm2 libkeyutils1 libmaxminddb0 libnpth0t64 libsensors-config 526s libsensors5 mawk patch pollinate python3-linkify-it python3-markdown-it 526s python3-pkg-resources python3-referencing python3-setuptools sed tar 526s 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 526s Need to get 6787 kB of archives. 526s After this operation, 270 kB disk space will be freed. 526s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 526s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 526s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 526s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 526s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 526s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 526s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 526s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 526s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 526s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 526s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 526s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 526s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 526s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 526s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 526s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 526s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 526s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 526s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 526s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 526s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 526s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 526s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 526s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 526s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 526s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 526s Get:27 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 526s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 526s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 527s dpkg-preconfigure: unable to re-open stdin: No such file or directory 527s Fetched 6787 kB in 0s (20.6 MB/s) 527s 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up busybox-initramfs (1:1.37.0-7ubuntu1) ... 540s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 540s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 540s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 540s Setting up mawk (1.3.4.20260129-1) ... 540s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 540s Setting up libdrm-common (2.4.131-1) ... 540s Setting up python3-referencing (0.36.2-1ubuntu2) ... 540s Setting up apt (3.1.15) ... 540s Setting up python3-markdown-it (3.0.0-3build1) ... 541s Setting up libdrm2:amd64 (2.4.131-1) ... 541s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 541s Processing triggers for libc-bin (2.42-2ubuntu4) ... 541s Processing triggers for man-db (2.13.1-1) ... 542s Processing triggers for install-info (7.2-5) ... 542s Processing triggers for initramfs-tools (0.150ubuntu7) ... 542s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 547s autopkgtest [14:21:11]: upgrading testbed (apt dist-upgrade and autopurge) 547s Reading package lists... 547s Building dependency tree... 547s Reading state information... 547s Calculating upgrade... 548s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 548s Reading package lists... 548s Building dependency tree... 548s Reading state information... 548s Solving dependencies... 548s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 548s autopkgtest [14:21:12]: rebooting testbed after setup commands that affected boot 578s Reading package lists... 579s Building dependency tree... 579s Reading state information... 579s Solving dependencies... 579s The following NEW packages will be installed: 579s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 579s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 579s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 579s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 579s liblerc4 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 579s libopenjp2-7 libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib 579s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 579s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 579s libxslt1.1 libxss1 libzopfli1 mummer ncbi-blast+ ncbi-data ncbi-vdb-data 579s python-matplotlib-data python3-all python3-biopython python3-brotli 579s python3-cairo python3-charset-normalizer python3-contourpy python3-cycler 579s python3-decorator python3-fonttools python3-freetype python3-kiwisolver 579s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 579s python3-numpy-dev python3-pandas python3-pandas-lib python3-pil 579s python3-pil.imagetk python3-pyani python3-pytz python3-reportlab 579s python3-rlpycairo python3-scipy python3-seaborn python3-sympy python3-tk 579s python3-ufolib2 python3-zopfli python3.13-tk python3.14 python3.14-minimal 579s python3.14-tk sgml-base unicode-data w3c-sgml-lib x11-common 579s xfonts-encodings xfonts-utils xml-core 579s 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. 579s Need to get 135 MB of archives. 579s After this operation, 582 MB of additional disk space will be used. 579s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 579s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 579s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-12ubuntu1 [939 kB] 579s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 579s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 579s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 579s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 579s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 579s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 579s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 579s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 579s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 579s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7build1 [97.1 kB] 579s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 580s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 580s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 580s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.5.0~RC2-3 [171 kB] 580s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 580s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 580s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 580s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 580s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 580s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 580s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 580s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-12ubuntu1 [151 kB] 580s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 580s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 580s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 580s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 580s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 580s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 580s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 580s Get:33 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.5-0.1ubuntu2 [259 kB] 580s Get:34 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.5-0.1ubuntu2 [35.4 kB] 580s Get:35 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.5-0.1ubuntu2 [130 kB] 580s Get:36 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2build1 [81.4 kB] 580s Get:37 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2build1 [1242 kB] 580s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 580s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-8 [197 kB] 580s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1build1 [15.5 kB] 580s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 580s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 580s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 580s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 580s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 580s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 580s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 580s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 580s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1build1 [12.8 kB] 580s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1build1 [26.4 kB] 580s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 580s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3build1 [114 kB] 580s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 mummer amd64 3.23+dfsg-8build1 [690 kB] 580s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 580s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] 580s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 580s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 580s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.9-3 [890 B] 580s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-2 [173 kB] 580s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.11-1 [108 kB] 580s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.2-1 [109 kB] 580s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-3 [11.2 kB] 580s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 580s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.4-1 [188 kB] 580s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 580s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 580s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 580s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 580s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.9-1 [1149 kB] 581s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1build1 [11.2 kB] 581s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 581s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3build1 [278 kB] 581s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 581s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 581s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 581s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 581s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 581s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 581s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.5+dfsg-1 [27.7 kB] 581s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-4 [19.0 MB] 581s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 581s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 581s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 581s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 581s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1build1 [9543 kB] 581s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.61.1-3 [1742 kB] 581s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 581s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 582s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 582s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 582s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 582s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-seaborn all 0.13.2-6 [225 kB] 582s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyani amd64 0.2.13-1 [46.7 kB] 582s Fetched 135 MB in 3s (46.3 MB/s) 582s Selecting previously unselected package python3-numpy-dev:amd64. 582s (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 ... 83962 files and directories currently installed.) 582s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 582s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 582s Selecting previously unselected package libblas3:amd64. 582s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_amd64.deb ... 582s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 582s Selecting previously unselected package libgfortran5:amd64. 582s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_amd64.deb ... 582s Unpacking libgfortran5:amd64 (15.2.0-12ubuntu1) ... 582s Selecting previously unselected package liblapack3:amd64. 582s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 582s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 582s Selecting previously unselected package python3-numpy. 582s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 582s Unpacking python3-numpy (1:2.3.5+ds-3) ... 582s Selecting previously unselected package libpython3.14-minimal:amd64. 582s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_amd64.deb ... 582s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 582s Selecting previously unselected package python3.14-minimal. 582s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_amd64.deb ... 582s Unpacking python3.14-minimal (3.14.2-1) ... 582s Selecting previously unselected package fonts-dejavu-mono. 582s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8build1_all.deb ... 582s Unpacking fonts-dejavu-mono (2.37-8build1) ... 582s Selecting previously unselected package fonts-dejavu-core. 582s Preparing to unpack .../08-fonts-dejavu-core_2.37-8build1_all.deb ... 582s Unpacking fonts-dejavu-core (2.37-8build1) ... 583s Selecting previously unselected package libfontenc1:amd64. 583s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 583s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 583s Selecting previously unselected package x11-common. 583s Preparing to unpack .../10-x11-common_1%3a7.7+24ubuntu1_all.deb ... 583s Unpacking x11-common (1:7.7+24ubuntu1) ... 583s Selecting previously unselected package xfonts-encodings. 583s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 583s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 583s Selecting previously unselected package xfonts-utils. 583s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7build1_amd64.deb ... 583s Unpacking xfonts-utils (1:7.7+7build1) ... 583s Selecting previously unselected package fonts-urw-base35. 583s Preparing to unpack .../13-fonts-urw-base35_20200910-8build1_all.deb ... 583s Unpacking fonts-urw-base35 (20200910-8build1) ... 583s Selecting previously unselected package fontconfig-config. 583s Preparing to unpack .../14-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 583s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 583s Selecting previously unselected package fonts-dejavu-extra. 583s Preparing to unpack .../15-fonts-dejavu-extra_2.37-8build1_all.deb ... 583s Unpacking fonts-dejavu-extra (2.37-8build1) ... 583s Selecting previously unselected package fonts-lyx. 583s Preparing to unpack .../16-fonts-lyx_2.5.0~RC2-3_all.deb ... 583s Unpacking fonts-lyx (2.5.0~RC2-3) ... 583s Selecting previously unselected package libfontconfig1:amd64. 583s Preparing to unpack .../17-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 583s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 583s Selecting previously unselected package libpixman-1-0:amd64. 583s Preparing to unpack .../18-libpixman-1-0_0.46.4-1_amd64.deb ... 583s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 583s Selecting previously unselected package libxcb-render0:amd64. 583s Preparing to unpack .../19-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 583s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 583s Selecting previously unselected package libxcb-shm0:amd64. 583s Preparing to unpack .../20-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 583s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 583s Selecting previously unselected package libxrender1:amd64. 583s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_amd64.deb ... 583s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 583s Selecting previously unselected package libcairo2:amd64. 583s Preparing to unpack .../22-libcairo2_1.18.4-3_amd64.deb ... 583s Unpacking libcairo2:amd64 (1.18.4-3) ... 583s Selecting previously unselected package libdeflate0:amd64. 583s Preparing to unpack .../23-libdeflate0_1.23-2_amd64.deb ... 583s Unpacking libdeflate0:amd64 (1.23-2) ... 583s Selecting previously unselected package libgomp1:amd64. 583s Preparing to unpack .../24-libgomp1_15.2.0-12ubuntu1_amd64.deb ... 583s Unpacking libgomp1:amd64 (15.2.0-12ubuntu1) ... 583s Selecting previously unselected package libgraphite2-3:amd64. 583s Preparing to unpack .../25-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 583s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 583s Selecting previously unselected package libharfbuzz0b:amd64. 583s Preparing to unpack .../26-libharfbuzz0b_12.3.2-1_amd64.deb ... 583s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 583s Selecting previously unselected package libimagequant0:amd64. 583s Preparing to unpack .../27-libimagequant0_2.18.0-1build1_amd64.deb ... 583s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 583s Selecting previously unselected package libjpeg-turbo8:amd64. 583s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 583s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 583s Selecting previously unselected package libjpeg8:amd64. 583s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_amd64.deb ... 583s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 583s Selecting previously unselected package liblcms2-2:amd64. 583s Preparing to unpack .../30-liblcms2-2_2.17-1_amd64.deb ... 583s Unpacking liblcms2-2:amd64 (2.17-1) ... 583s Selecting previously unselected package liblerc4:amd64. 583s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 583s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 583s Selecting previously unselected package libmbedcrypto16:amd64. 583s Preparing to unpack .../32-libmbedcrypto16_3.6.5-0.1ubuntu2_amd64.deb ... 583s Unpacking libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 583s Selecting previously unselected package libmbedx509-7:amd64. 583s Preparing to unpack .../33-libmbedx509-7_3.6.5-0.1ubuntu2_amd64.deb ... 583s Unpacking libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 583s Selecting previously unselected package libmbedtls21:amd64. 583s Preparing to unpack .../34-libmbedtls21_3.6.5-0.1ubuntu2_amd64.deb ... 583s Unpacking libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 583s Selecting previously unselected package ncbi-vdb-data. 583s Preparing to unpack .../35-ncbi-vdb-data_3.2.1+dfsg-2build1_all.deb ... 583s Unpacking ncbi-vdb-data (3.2.1+dfsg-2build1) ... 583s Selecting previously unselected package libncbi-vdb3:amd64. 583s Preparing to unpack .../36-libncbi-vdb3_3.2.1+dfsg-2build1_amd64.deb ... 583s Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2build1) ... 583s Selecting previously unselected package libpython3.14-stdlib:amd64. 583s Preparing to unpack .../37-libpython3.14-stdlib_3.14.2-1_amd64.deb ... 583s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 583s Selecting previously unselected package libqhull-r8.0:amd64. 583s Preparing to unpack .../38-libqhull-r8.0_2020.2-8_amd64.deb ... 583s Unpacking libqhull-r8.0:amd64 (2020.2-8) ... 583s Selecting previously unselected package libraqm0:amd64. 583s Preparing to unpack .../39-libraqm0_0.10.3-1build1_amd64.deb ... 583s Unpacking libraqm0:amd64 (0.10.3-1build1) ... 583s Selecting previously unselected package libsharpyuv0:amd64. 583s Preparing to unpack .../40-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 583s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 583s Selecting previously unselected package libtcl8.6:amd64. 583s Preparing to unpack .../41-libtcl8.6_8.6.17+dfsg-1build1_amd64.deb ... 583s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 583s Selecting previously unselected package libjbig0:amd64. 583s Preparing to unpack .../42-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 583s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 583s Selecting previously unselected package libwebp7:amd64. 583s Preparing to unpack .../43-libwebp7_1.5.0-0.1build1_amd64.deb ... 583s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 583s Selecting previously unselected package libtiff6:amd64. 583s Preparing to unpack .../44-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 583s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 583s Selecting previously unselected package libxft2:amd64. 583s Preparing to unpack .../45-libxft2_2.3.6-1build2_amd64.deb ... 583s Unpacking libxft2:amd64 (2.3.6-1build2) ... 583s Selecting previously unselected package libxss1:amd64. 583s Preparing to unpack .../46-libxss1_1%3a1.2.3-1build4_amd64.deb ... 583s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 583s Selecting previously unselected package libtk8.6:amd64. 583s Preparing to unpack .../47-libtk8.6_8.6.17-1_amd64.deb ... 583s Unpacking libtk8.6:amd64 (8.6.17-1) ... 583s Selecting previously unselected package libwebpdemux2:amd64. 583s Preparing to unpack .../48-libwebpdemux2_1.5.0-0.1build1_amd64.deb ... 583s Unpacking libwebpdemux2:amd64 (1.5.0-0.1build1) ... 583s Selecting previously unselected package libwebpmux3:amd64. 583s Preparing to unpack .../49-libwebpmux3_1.5.0-0.1build1_amd64.deb ... 583s Unpacking libwebpmux3:amd64 (1.5.0-0.1build1) ... 583s Selecting previously unselected package libxslt1.1:amd64. 583s Preparing to unpack .../50-libxslt1.1_1.1.43-0.3_amd64.deb ... 583s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 583s Selecting previously unselected package libzopfli1. 583s Preparing to unpack .../51-libzopfli1_1.0.3-3build1_amd64.deb ... 583s Unpacking libzopfli1 (1.0.3-3build1) ... 583s Selecting previously unselected package mummer. 583s Preparing to unpack .../52-mummer_3.23+dfsg-8build1_amd64.deb ... 583s Unpacking mummer (3.23+dfsg-8build1) ... 583s Selecting previously unselected package ncbi-data. 583s Preparing to unpack .../53-ncbi-data_6.1.20170106+dfsg2-7_all.deb ... 583s Unpacking ncbi-data (6.1.20170106+dfsg2-7) ... 583s Selecting previously unselected package ncbi-blast+. 583s Preparing to unpack .../54-ncbi-blast+_2.16.0+ds-7_amd64.deb ... 583s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 584s Selecting previously unselected package python-matplotlib-data. 584s Preparing to unpack .../55-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 584s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 584s Selecting previously unselected package python3.14. 584s Preparing to unpack .../56-python3.14_3.14.2-1_amd64.deb ... 584s Unpacking python3.14 (3.14.2-1) ... 584s Selecting previously unselected package python3-all. 584s Preparing to unpack .../57-python3-all_3.13.9-3_amd64.deb ... 584s Unpacking python3-all (3.13.9-3) ... 584s Selecting previously unselected package python3-charset-normalizer. 584s Preparing to unpack .../58-python3-charset-normalizer_3.4.4-2_amd64.deb ... 584s Unpacking python3-charset-normalizer (3.4.4-2) ... 584s Selecting previously unselected package python3.13-tk. 584s Preparing to unpack .../59-python3.13-tk_3.13.11-1_amd64.deb ... 584s Unpacking python3.13-tk (3.13.11-1) ... 584s Selecting previously unselected package python3.14-tk. 584s Preparing to unpack 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python3-cairo (1.27.0-2build1) ... 584s Selecting previously unselected package python3-freetype. 584s Preparing to unpack .../66-python3-freetype_2.5.1-2_all.deb ... 584s Unpacking python3-freetype (2.5.1-2) ... 584s Selecting previously unselected package python3-rlpycairo. 584s Preparing to unpack .../67-python3-rlpycairo_0.3.0-4_all.deb ... 584s Unpacking python3-rlpycairo (0.3.0-4) ... 584s Selecting previously unselected package python3-reportlab. 584s Preparing to unpack .../68-python3-reportlab_4.4.9-1_all.deb ... 584s Unpacking python3-reportlab (4.4.9-1) ... 584s Selecting previously unselected package sgml-base. 584s Preparing to unpack .../69-sgml-base_1.31+nmu1build1_all.deb ... 584s Unpacking sgml-base (1.31+nmu1build1) ... 584s Selecting previously unselected package xml-core. 584s Preparing to unpack .../70-xml-core_0.19build1_all.deb ... 584s Unpacking xml-core (0.19build1) ... 584s Selecting previously unselected package w3c-sgml-lib. 584s Preparing to unpack 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python3-matplotlib (3.10.7+dfsg1-1) ... 585s Selecting previously unselected package python3-pytz. 585s Preparing to unpack .../88-python3-pytz_2025.2-5_all.deb ... 585s Unpacking python3-pytz (2025.2-5) ... 585s Selecting previously unselected package python3-pandas-lib:amd64. 585s Preparing to unpack .../89-python3-pandas-lib_2.3.3+dfsg-3_amd64.deb ... 585s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 585s Selecting previously unselected package python3-pandas. 585s Preparing to unpack .../90-python3-pandas_2.3.3+dfsg-3_all.deb ... 585s Unpacking python3-pandas (2.3.3+dfsg-3) ... 585s Selecting previously unselected package python3-seaborn. 585s Preparing to unpack .../91-python3-seaborn_0.13.2-6_all.deb ... 585s Unpacking python3-seaborn (0.13.2-6) ... 585s Selecting previously unselected package python3-pyani. 585s Preparing to unpack .../92-python3-pyani_0.2.13-1_amd64.deb ... 585s Unpacking python3-pyani (0.2.13-1) ... 585s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 585s Setting up liblcms2-2:amd64 (2.17-1) ... 585s Setting up ncbi-data (6.1.20170106+dfsg2-7) ... 585s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 585s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 585s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 585s Setting up libxrender1:amd64 (1:0.9.12-1) ... 585s Setting up python3-lz4 (4.4.5+dfsg-1) ... 585s Setting up libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 585s Setting up python3-charset-normalizer (3.4.4-2) ... 585s Setting up fonts-lyx (2.5.0~RC2-3) ... 585s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 585s Setting up x11-common (1:7.7+24ubuntu1) ... 586s Setting up libdeflate0:amd64 (1.23-2) ... 586s Setting up libqhull-r8.0:amd64 (2020.2-8) ... 586s Setting up python3-pytz (2025.2-5) ... 586s Setting up libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 586s Setting up libgomp1:amd64 (15.2.0-12ubuntu1) ... 586s Setting up python3-freetype (2.5.1-2) ... 586s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 586s Setting up unicode-data (16.0.0-1build1) ... 586s Setting up python3-decorator (5.2.1-2) ... 586s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 586s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 586s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 586s Setting up libzopfli1 (1.0.3-3build1) ... 586s Setting up python3-brotli (1.1.0-2build6) ... 586s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 586s Setting up python3-cycler (0.12.1-2) ... 586s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 586s Setting up fonts-dejavu-mono (2.37-8build1) ... 586s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 586s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 586s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 586s Setting up fonts-dejavu-core (2.37-8build1) ... 586s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 586s Setting up libgfortran5:amd64 (15.2.0-12ubuntu1) ... 586s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 586s Setting up fonts-dejavu-extra (2.37-8build1) ... 586s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 586s Setting up mummer (3.23+dfsg-8build1) ... 586s Setting up libopenjp2-7:amd64 (2.5.4-1) ... 586s Setting up libharfbuzz0b:amd64 (12.3.2-1) ... 586s Setting up ncbi-vdb-data (3.2.1+dfsg-2build1) ... 586s Setting up sgml-base (1.31+nmu1build1) ... 587s Setting up libxss1:amd64 (1:1.2.3-1build4) ... 587s Setting up libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 587s Setting up python3-mpmath (1.3.0-2) ... 587s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 587s Setting up libwebpmux3:amd64 (1.5.0-0.1build1) ... 587s Setting up python3.14-minimal (3.14.2-1) ... 588s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 588s Setting up python3-sympy (1.14.0-2) ... 595s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 595s return p.returncode 595s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 595s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 595s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 595s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 595s Setting up libwebpdemux2:amd64 (1.5.0-0.1build1) ... 595s Setting up xfonts-utils (1:7.7+7build1) ... 595s Setting up python3-zopfli (0.4.0-1) ... 595s Setting up libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 595s Setting up libraqm0:amd64 (0.10.3-1build1) ... 595s Setting up python3-numpy (1:2.3.5+ds-3) ... 597s Setting up libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 597s Setting up python3-lxml:amd64 (6.0.2-1) ... 597s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 597s Setting up xml-core (0.19build1) ... 597s Setting up python3-contourpy (1.3.3-1) ... 598s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 598s Setting up python3.14 (3.14.2-1) ... 598s Setting up libxft2:amd64 (2.3.6-1build2) ... 598s Setting up python3-scipy (1.16.3-4) ... 603s Setting up libtk8.6:amd64 (8.6.17-1) ... 603s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 603s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2build1) ... 603s Setting up python3-all (3.13.9-3) ... 603s Setting up fonts-urw-base35 (20200910-8build1) ... 603s Setting up libcairo2:amd64 (1.18.4-3) ... 603s Setting up python3.13-tk (3.13.11-1) ... 603s Setting up ncbi-blast+ (2.16.0+ds-7) ... 603s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 603s Setting up python3-pandas (2.3.3+dfsg-3) ... 609s Setting up python3.14-tk (3.14.2-1) ... 609s Setting up python3-cairo (1.27.0-2build1) ... 609s Setting up python3-tk (3.13.9-3) ... 609s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 609s Setting up python3-rlpycairo (0.3.0-4) ... 609s Setting up python3-reportlab (4.4.9-1) ... 610s Setting up python3-fonttools (4.61.1-3) ... 611s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 611s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 613s Setting up python3-seaborn (0.13.2-6) ... 613s Processing triggers for systemd (259-1ubuntu3) ... 613s Processing triggers for man-db (2.13.1-1) ... 614s Processing triggers for libc-bin (2.42-2ubuntu4) ... 614s Processing triggers for sgml-base (1.31+nmu1build1) ... 614s Setting up w3c-sgml-lib (1.3-3build1) ... 630s Setting up python3-biopython (1.86+dfsg-1) ... 632s Setting up python3-pyani (0.2.13-1) ... 638s autopkgtest [14:22:42]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyani; print(pyani)" ; done 638s autopkgtest [14:22:42]: test autodep8-python3: [----------------------- 638s Testing with python3.14: 638s 638s Testing with python3.13: 638s 638s autopkgtest [14:22:42]: test autodep8-python3: -----------------------] 639s autopkgtest [14:22:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 639s autodep8-python3 PASS (superficial) 639s autopkgtest [14:22:43]: @@@@@@@@@@@@@@@@@@@@ summary 639s run-unit-test PASS 639s autodep8-python3 PASS (superficial)