0s autopkgtest [10:18:26]: starting date and time: 2025-12-03 10:18:26+0000 0s autopkgtest [10:18:26]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [10:18:26]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j54gnp7z/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults --apt-upgrade insilicoseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/resolute/armhf 22s autopkgtest [10:18:48]: testbed dpkg architecture: armhf 24s autopkgtest [10:18:50]: testbed apt version: 3.1.12 28s autopkgtest [10:18:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [10:18:57]: testbed release detected to be: None 39s autopkgtest [10:19:05]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 42s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 42s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 42s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [25.2 kB] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [147 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [981 kB] 43s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [187 kB] 43s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [678 kB] 43s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [8468 B] 43s Get:11 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [305 kB] 43s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1414 kB] 43s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 46s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1366 kB] 46s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.5 MB] 47s Get:16 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 50s Fetched 42.6 MB in 8s (5277 kB/s) 51s Reading package lists... 57s autopkgtest [10:19:23]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s libpython3-stdlib python3 python3-gdbm python3-minimal 61s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Need to get 72.9 kB of archives. 61s After this operation, 2048 B of additional disk space will be used. 61s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.9-2 [28.1 kB] 61s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.9-2 [23.0 kB] 61s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.9-2 [10.8 kB] 61s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.13.9-2 [11.0 kB] 61s Fetched 72.9 kB in 0s (194 kB/s) 62s (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 ... 65928 files and directories currently installed.) 62s Preparing to unpack .../python3-minimal_3.13.9-2_armhf.deb ... 62s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 62s Setting up python3-minimal (3.13.9-2) ... 62s (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 ... 65928 files and directories currently installed.) 62s Preparing to unpack .../python3_3.13.9-2_armhf.deb ... 62s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 62s Preparing to unpack .../libpython3-stdlib_3.13.9-2_armhf.deb ... 62s Unpacking libpython3-stdlib:armhf (3.13.9-2) over (3.13.7-1) ... 62s Preparing to unpack .../python3-gdbm_3.13.9-2_armhf.deb ... 62s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 62s Setting up python3-gdbm (3.13.9-2) ... 62s Setting up libpython3-stdlib:armhf (3.13.9-2) ... 62s Setting up python3 (3.13.9-2) ... 62s Processing triggers for man-db (2.13.1-1) ... 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Solving dependencies... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [10:19:34]: rebooting testbed after setup commands that affected boot 111s autopkgtest [10:20:17]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 139s autopkgtest [10:20:45]: @@@@@@@@@@@@@@@@@@@@ apt-source insilicoseq 153s Get:1 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (dsc) [2411 B] 153s Get:2 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (tar) [4591 kB] 153s Get:3 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (diff) [5304 B] 153s gpgv: Signature made Wed Apr 24 11:31:14 2024 UTC 153s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 153s gpgv: issuer "emollier@debian.org" 153s gpgv: Can't check signature: No public key 153s dpkg-source: warning: cannot verify inline signature for ./insilicoseq_2.0.1-1.dsc: no acceptable signature found 153s autopkgtest [10:20:59]: testing package insilicoseq version 2.0.1-1 156s autopkgtest [10:21:02]: build not needed 159s autopkgtest [10:21:05]: test run-unit-test: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Solving dependencies... 162s The following NEW packages will be installed: 162s fontconfig-config fonts-urw-base35 insilicoseq libblas3 libcairo2 162s libdeflate0 libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 162s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 162s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 162s libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib libqhull-r8.0 162s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 162s libxcb-render0 libxcb-shm0 libxrender1 python3-all python3-biopython 162s python3-cairo python3-charset-normalizer python3-decorator python3-freetype 162s python3-iniconfig python3-numpy python3-numpy-dev python3-pil python3-pluggy 162s python3-pysam python3-pytest python3-reportlab python3-rlpycairo 162s python3-scipy python3.14 python3.14-minimal sgml-base w3c-sgml-lib 162s x11-common xfonts-encodings xfonts-utils xml-core 162s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 59.0 MB of archives. 162s After this operation, 239 MB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 162s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7 [133 kB] 162s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-9ubuntu1 [334 kB] 162s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7 [2091 kB] 163s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 164s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.0-4 [892 kB] 164s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.0-4 [2146 kB] 164s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libfontenc1 armhf 1:1.1.8-1build2 [11.7 kB] 164s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.13.3+dfsg-1build1 [334 kB] 165s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 165s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 165s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 165s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 166s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.15.0-2.3ubuntu1 [38.1 kB] 166s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-charset-normalizer armhf 3.4.4-1 [167 kB] 166s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-9ubuntu1 [129 kB] 166s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 166s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 166s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 166s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.17-1 [139 kB] 166s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libopenjp2-7 armhf 2.5.3-2.1 [174 kB] 166s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 166s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.1.0-1 [512 kB] 166s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libraqm0 armhf 0.10.3-1 [12.7 kB] 166s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 166s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 166s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 166s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 166s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 166s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 166s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 166s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 166s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pil armhf 12.0.0-1ubuntu1 [462 kB] 166s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.15.0-2.3ubuntu1 [114 kB] 166s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 166s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2build1 [15.5 kB] 166s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2build1 [5962 B] 166s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 166s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-1build1 [489 kB] 166s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cairo armhf 1.27.0-2build1 [135 kB] 166s Get:41 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-freetype all 2.5.1-2 [92.2 kB] 166s Get:42 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rlpycairo all 0.3.0-4 [9332 B] 166s Get:43 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-reportlab all 4.4.5-1 [1148 kB] 166s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 166s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19 [20.3 kB] 166s Get:46 http://ftpmaster.internal/ubuntu resolute/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 166s Get:47 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython armhf 1.86+dfsg-1 [1652 kB] 166s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 166s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 166s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pysam armhf 0.23.3+ds-2 [4358 kB] 166s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 166s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-7 [174 kB] 166s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.16.3-1 [18.2 MB] 167s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf insilicoseq all 2.0.1-1 [4247 kB] 167s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.0-4 [2270 kB] 167s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.0-4 [805 kB] 167s Get:57 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.13.9-2 [892 B] 167s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 2.1.0-1 [6840 B] 167s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-1 [21.0 kB] 167s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 8.3.5-2 [252 kB] 168s Fetched 59.0 MB in 6s (10.6 MB/s) 168s Selecting previously unselected package python3-numpy-dev:armhf. 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 65928 files and directories currently installed.) 168s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 168s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 168s Selecting previously unselected package libblas3:armhf. 168s Preparing to unpack .../01-libblas3_3.12.1-7_armhf.deb ... 168s Unpacking libblas3:armhf (3.12.1-7) ... 168s Selecting previously unselected package libgfortran5:armhf. 168s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_armhf.deb ... 168s Unpacking libgfortran5:armhf (15.2.0-9ubuntu1) ... 168s Selecting previously unselected package liblapack3:armhf. 168s Preparing to unpack .../03-liblapack3_3.12.1-7_armhf.deb ... 168s Unpacking liblapack3:armhf (3.12.1-7) ... 168s Selecting previously unselected package python3-numpy. 168s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 168s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 168s Selecting previously unselected package libpython3.14-minimal:armhf. 168s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_armhf.deb ... 168s Unpacking libpython3.14-minimal:armhf (3.14.0-4) ... 168s Selecting previously unselected package python3.14-minimal. 168s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_armhf.deb ... 168s Unpacking python3.14-minimal (3.14.0-4) ... 168s Selecting previously unselected package libfontenc1:armhf. 168s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build2_armhf.deb ... 168s Unpacking libfontenc1:armhf (1:1.1.8-1build2) ... 168s Selecting previously unselected package libfreetype6:armhf. 168s Preparing to unpack .../08-libfreetype6_2.13.3+dfsg-1build1_armhf.deb ... 168s Unpacking libfreetype6:armhf (2.13.3+dfsg-1build1) ... 169s Selecting previously unselected package x11-common. 169s Preparing to unpack .../09-x11-common_1%3a7.7+24ubuntu1_all.deb ... 169s Unpacking x11-common (1:7.7+24ubuntu1) ... 169s Selecting previously unselected package xfonts-encodings. 169s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 169s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 169s Selecting previously unselected package xfonts-utils. 169s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_armhf.deb ... 169s Unpacking xfonts-utils (1:7.7+7) ... 169s Selecting previously unselected package fonts-urw-base35. 169s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 169s Unpacking fonts-urw-base35 (20200910-8) ... 169s Selecting previously unselected package fontconfig-config. 169s Preparing to unpack .../13-fontconfig-config_2.15.0-2.3ubuntu1_armhf.deb ... 169s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 169s Selecting previously unselected package python3-charset-normalizer. 169s Preparing to unpack .../14-python3-charset-normalizer_3.4.4-1_armhf.deb ... 169s Unpacking python3-charset-normalizer (3.4.4-1) ... 169s Selecting previously unselected package libgomp1:armhf. 169s Preparing to unpack .../15-libgomp1_15.2.0-9ubuntu1_armhf.deb ... 169s Unpacking libgomp1:armhf (15.2.0-9ubuntu1) ... 169s Selecting previously unselected package libimagequant0:armhf. 169s Preparing to unpack .../16-libimagequant0_2.18.0-1build1_armhf.deb ... 169s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 169s Selecting previously unselected package libjpeg-turbo8:armhf. 169s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 169s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 169s Selecting previously unselected package libjpeg8:armhf. 169s Preparing to unpack .../18-libjpeg8_8c-2ubuntu11_armhf.deb ... 169s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 169s Selecting previously unselected package liblcms2-2:armhf. 169s Preparing to unpack .../19-liblcms2-2_2.17-1_armhf.deb ... 169s Unpacking liblcms2-2:armhf (2.17-1) ... 170s Selecting previously unselected package libopenjp2-7:armhf. 170s Preparing to unpack .../20-libopenjp2-7_2.5.3-2.1_armhf.deb ... 170s Unpacking libopenjp2-7:armhf (2.5.3-2.1) ... 170s Selecting previously unselected package libgraphite2-3:armhf. 170s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 170s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 170s Selecting previously unselected package libharfbuzz0b:armhf. 170s Preparing to unpack .../22-libharfbuzz0b_12.1.0-1_armhf.deb ... 170s Unpacking libharfbuzz0b:armhf (12.1.0-1) ... 170s Selecting previously unselected package libraqm0:armhf. 170s Preparing to unpack .../23-libraqm0_0.10.3-1_armhf.deb ... 170s Unpacking libraqm0:armhf (0.10.3-1) ... 170s Selecting previously unselected package libdeflate0:armhf. 170s Preparing to unpack .../24-libdeflate0_1.23-2_armhf.deb ... 170s Unpacking libdeflate0:armhf (1.23-2) ... 170s Selecting previously unselected package libjbig0:armhf. 170s Preparing to unpack .../25-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 170s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 170s Selecting previously unselected package liblerc4:armhf. 170s Preparing to unpack .../26-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 170s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 170s Selecting previously unselected package libsharpyuv0:armhf. 170s Preparing to unpack .../27-libsharpyuv0_1.5.0-0.1_armhf.deb ... 170s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 170s Selecting previously unselected package libwebp7:armhf. 170s Preparing to unpack .../28-libwebp7_1.5.0-0.1_armhf.deb ... 170s Unpacking libwebp7:armhf (1.5.0-0.1) ... 170s Selecting previously unselected package libtiff6:armhf. 170s Preparing to unpack .../29-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 170s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 170s Selecting previously unselected package libwebpdemux2:armhf. 170s Preparing to unpack .../30-libwebpdemux2_1.5.0-0.1_armhf.deb ... 170s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 170s Selecting previously unselected package libwebpmux3:armhf. 170s Preparing to unpack .../31-libwebpmux3_1.5.0-0.1_armhf.deb ... 170s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 170s Selecting previously unselected package python3-pil:armhf. 170s Preparing to unpack .../32-python3-pil_12.0.0-1ubuntu1_armhf.deb ... 170s Unpacking python3-pil:armhf (12.0.0-1ubuntu1) ... 170s Selecting previously unselected package libfontconfig1:armhf. 170s Preparing to unpack .../33-libfontconfig1_2.15.0-2.3ubuntu1_armhf.deb ... 170s Unpacking libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 170s Selecting previously unselected package libpixman-1-0:armhf. 170s Preparing to unpack .../34-libpixman-1-0_0.46.4-1_armhf.deb ... 170s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 170s Selecting previously unselected package libxcb-render0:armhf. 170s Preparing to unpack .../35-libxcb-render0_1.17.0-2build1_armhf.deb ... 170s Unpacking libxcb-render0:armhf (1.17.0-2build1) ... 170s Selecting previously unselected package libxcb-shm0:armhf. 170s Preparing to unpack .../36-libxcb-shm0_1.17.0-2build1_armhf.deb ... 170s Unpacking libxcb-shm0:armhf (1.17.0-2build1) ... 170s Selecting previously unselected package libxrender1:armhf. 170s Preparing to unpack .../37-libxrender1_1%3a0.9.12-1_armhf.deb ... 170s Unpacking libxrender1:armhf (1:0.9.12-1) ... 170s Selecting previously unselected package libcairo2:armhf. 170s Preparing to unpack .../38-libcairo2_1.18.4-1build1_armhf.deb ... 170s Unpacking libcairo2:armhf (1.18.4-1build1) ... 170s Selecting previously unselected package python3-cairo. 170s Preparing to unpack .../39-python3-cairo_1.27.0-2build1_armhf.deb ... 170s Unpacking python3-cairo (1.27.0-2build1) ... 170s Selecting previously unselected package python3-freetype. 170s Preparing to unpack .../40-python3-freetype_2.5.1-2_all.deb ... 170s Unpacking python3-freetype (2.5.1-2) ... 170s Selecting previously unselected package python3-rlpycairo. 170s Preparing to unpack .../41-python3-rlpycairo_0.3.0-4_all.deb ... 170s Unpacking python3-rlpycairo (0.3.0-4) ... 170s Selecting previously unselected package python3-reportlab. 170s Preparing to unpack .../42-python3-reportlab_4.4.5-1_all.deb ... 170s Unpacking python3-reportlab (4.4.5-1) ... 170s Selecting previously unselected package sgml-base. 170s Preparing to unpack .../43-sgml-base_1.31+nmu1_all.deb ... 170s Unpacking sgml-base (1.31+nmu1) ... 170s Selecting previously unselected package xml-core. 170s Preparing to unpack .../44-xml-core_0.19_all.deb ... 170s Unpacking xml-core (0.19) ... 171s Selecting previously unselected package w3c-sgml-lib. 171s Preparing to unpack .../45-w3c-sgml-lib_1.3-3_all.deb ... 171s Unpacking w3c-sgml-lib (1.3-3) ... 171s Selecting previously unselected package python3-biopython. 171s Preparing to unpack .../46-python3-biopython_1.86+dfsg-1_armhf.deb ... 171s Unpacking python3-biopython (1.86+dfsg-1) ... 171s Selecting previously unselected package libhtscodecs2:armhf. 171s Preparing to unpack .../47-libhtscodecs2_1.6.1-2_armhf.deb ... 171s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 171s Selecting previously unselected package libhts3t64:armhf. 171s Preparing to unpack .../48-libhts3t64_1.22.1+ds2-1_armhf.deb ... 171s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 171s Selecting previously unselected package python3-pysam. 171s Preparing to unpack .../49-python3-pysam_0.23.3+ds-2_armhf.deb ... 171s Unpacking python3-pysam (0.23.3+ds-2) ... 171s Selecting previously unselected package python3-decorator. 171s Preparing to unpack .../50-python3-decorator_5.2.1-2_all.deb ... 171s Unpacking python3-decorator (5.2.1-2) ... 171s Selecting previously unselected package libqhull-r8.0:armhf. 171s Preparing to unpack .../51-libqhull-r8.0_2020.2-7_armhf.deb ... 171s Unpacking libqhull-r8.0:armhf (2020.2-7) ... 171s Selecting previously unselected package python3-scipy. 171s Preparing to unpack .../52-python3-scipy_1.16.3-1_armhf.deb ... 171s Unpacking python3-scipy (1.16.3-1) ... 172s Selecting previously unselected package insilicoseq. 172s Preparing to unpack .../53-insilicoseq_2.0.1-1_all.deb ... 172s Unpacking insilicoseq (2.0.1-1) ... 172s Selecting previously unselected package libpython3.14-stdlib:armhf. 172s Preparing to unpack .../54-libpython3.14-stdlib_3.14.0-4_armhf.deb ... 172s Unpacking libpython3.14-stdlib:armhf (3.14.0-4) ... 172s Selecting previously unselected package python3.14. 172s Preparing to unpack .../55-python3.14_3.14.0-4_armhf.deb ... 172s Unpacking python3.14 (3.14.0-4) ... 172s Selecting previously unselected package python3-all. 172s Preparing to unpack .../56-python3-all_3.13.9-2_armhf.deb ... 172s Unpacking python3-all (3.13.9-2) ... 172s Selecting previously unselected package python3-iniconfig. 172s Preparing to unpack .../57-python3-iniconfig_2.1.0-1_all.deb ... 172s Unpacking python3-iniconfig (2.1.0-1) ... 172s Selecting previously unselected package python3-pluggy. 172s Preparing to unpack .../58-python3-pluggy_1.6.0-1_all.deb ... 172s Unpacking python3-pluggy (1.6.0-1) ... 172s Selecting previously unselected package python3-pytest. 172s Preparing to unpack .../59-python3-pytest_8.3.5-2_all.deb ... 172s Unpacking python3-pytest (8.3.5-2) ... 172s Setting up libhtscodecs2:armhf (1.6.1-2) ... 172s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 172s Setting up liblcms2-2:armhf (2.17-1) ... 172s Setting up python3-iniconfig (2.1.0-1) ... 173s Setting up libpixman-1-0:armhf (0.46.4-1) ... 173s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 173s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 173s Setting up libxrender1:armhf (1:0.9.12-1) ... 173s Setting up libxcb-render0:armhf (1.17.0-2build1) ... 173s Setting up python3-charset-normalizer (3.4.4-1) ... 173s Setting up libpython3.14-minimal:armhf (3.14.0-4) ... 173s Setting up x11-common (1:7.7+24ubuntu1) ... 173s Setting up libdeflate0:armhf (1.23-2) ... 173s Setting up libqhull-r8.0:armhf (2020.2-7) ... 173s Setting up libxcb-shm0:armhf (1.17.0-2build1) ... 173s Setting up libgomp1:armhf (15.2.0-9ubuntu1) ... 173s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 173s Setting up python3-decorator (5.2.1-2) ... 173s Setting up libfontenc1:armhf (1:1.1.8-1build2) ... 173s Setting up libblas3:armhf (3.12.1-7) ... 173s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 173s Setting up libfreetype6:armhf (2.13.3+dfsg-1build1) ... 173s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 173s Setting up libimagequant0:armhf (2.18.0-1build1) ... 173s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 173s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 173s Setting up libgfortran5:armhf (15.2.0-9ubuntu1) ... 173s Setting up python3-pluggy (1.6.0-1) ... 174s Setting up libwebp7:armhf (1.5.0-0.1) ... 174s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 174s Setting up libopenjp2-7:armhf (2.5.3-2.1) ... 174s Setting up libharfbuzz0b:armhf (12.1.0-1) ... 174s Setting up sgml-base (1.31+nmu1) ... 174s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 174s Setting up python3.14-minimal (3.14.0-4) ... 175s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 175s Setting up liblapack3:armhf (3.12.1-7) ... 175s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 175s Setting up python3-pysam (0.23.3+ds-2) ... 175s Setting up libpython3.14-stdlib:armhf (3.14.0-4) ... 175s Setting up python3-pytest (8.3.5-2) ... 176s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 176s Setting up python3-freetype (2.5.1-2) ... 176s Setting up xfonts-utils (1:7.7+7) ... 176s Setting up libraqm0:armhf (0.10.3-1) ... 176s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 180s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 180s Setting up xml-core (0.19) ... 180s Setting up python3.14 (3.14.0-4) ... 181s Setting up python3-scipy (1.16.3-1) ... 190s Setting up python3-all (3.13.9-2) ... 190s Setting up fonts-urw-base35 (20200910-8) ... 190s Setting up python3-pil:armhf (12.0.0-1ubuntu1) ... 191s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 191s Setting up libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 191s Setting up libcairo2:armhf (1.18.4-1build1) ... 191s Setting up python3-cairo (1.27.0-2build1) ... 191s Setting up python3-rlpycairo (0.3.0-4) ... 191s Setting up python3-reportlab (4.4.5-1) ... 193s Processing triggers for libc-bin (2.42-2ubuntu2) ... 193s Processing triggers for systemd (257.9-0ubuntu2) ... 193s Processing triggers for man-db (2.13.1-1) ... 194s Processing triggers for sgml-base (1.31+nmu1) ... 194s Setting up w3c-sgml-lib (1.3-3) ... 221s Setting up python3-biopython (1.86+dfsg-1) ... 224s Setting up insilicoseq (2.0.1-1) ... 233s autopkgtest [10:22:19]: test run-unit-test: [----------------------- 235s Testing with python3.14 in /tmp/autopkgtest.wbDqCU/autopkgtest_tmp: 235s ============================= test session starts ============================== 235s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 235s cachedir: .pytest_cache 235s rootdir: /tmp/autopkgtest.wbDqCU/autopkgtest_tmp 235s plugins: typeguard-4.4.2 236s collecting ... collected 46 items 236s 236s test/test_abundance.py::test_parsing PASSED [ 2%] 236s test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] 236s test/test_abundance.py::test_parsing_empty PASSED [ 6%] 236s test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] 236s test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] 236s test/test_abundance.py::test_cov_calc PASSED [ 13%] 236s test/test_abundance.py::test_distributions PASSED [ 15%] 236s test/test_abundance.py::test_abunance_draft PASSED [ 17%] 236s test/test_abundance.py::test_coverage_scaling PASSED [ 19%] 236s test/test_bam.py::test_read_fail PASSED [ 21%] 236s test/test_bam.py::test_to_model PASSED [ 23%] 236s test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] 236s test/test_error_model.py::test_perfect_phred PASSED [ 28%] 236s test/test_error_model.py::test_basic_phred PASSED [ 30%] 236s test/test_error_model.py::test_kde_phred PASSED [ 32%] 236s test/test_error_model.py::test_introduce_errors PASSED [ 34%] 236s test/test_error_model.py::test_mut_sequence PASSED [ 36%] 236s test/test_error_model.py::test_introduce_indels PASSED [ 39%] 236s test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] 236s test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] 236s test/test_error_model.py::test_bad_err_mod PASSED [ 45%] 236s test/test_generator.py::test_cleanup_fail PASSED [ 47%] 238s test/test_generator.py::test_simulate_and_save PASSED [ 50%] 240s test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] 240s test/test_generator.py::test_small_input PASSED [ 54%] 240s test/test_generator.py::test_basic PASSED [ 56%] 240s test/test_generator.py::test_kde PASSED [ 58%] 240s test/test_generator.py::test_kde_short PASSED [ 60%] 240s test/test_generator.py::test_amp PASSED [ 63%] 240s test/test_modeller.py::test_kde_qualities PASSED [ 65%] 240s test/test_modeller.py::test_substitutions PASSED [ 67%] 240s test/test_modeller.py::test_indels PASSED [ 69%] 240s test/test_util.py::test_phred_conversions PASSED [ 71%] 240s test/test_util.py::test_rev_comp PASSED [ 73%] 240s test/test_util.py::test_count_records PASSED [ 76%] 240s test/test_util.py::test_count_records_empty PASSED [ 78%] 240s test/test_util.py::test_split_list PASSED [ 80%] 240s test/test_util.py::test_convert_n_reads PASSED [ 82%] 240s test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] 240s test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] 240s test/test_util.py::test_genome_file_exists PASSED [ 89%] 240s test/test_util.py::test_reservoir PASSED [ 91%] 240s test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] 240s test/test_util.py::test_concatenate PASSED [ 95%] 240s test/test_util.py::test_concatenate_read_only PASSED [ 97%] 240s test/test_util.py::test_compress PASSED [100%] 240s 240s =============================== warnings summary =============================== 240s test/test_bam.py: 60 warnings 240s /usr/lib/python3/dist-packages/iss/modeller.py:90: DeprecationWarning: The numpy.linalg.linalg has been made private and renamed to numpy.linalg._linalg. All public functions exported by it are available from numpy.linalg. Please use numpy.linalg.LinAlgError instead. 240s cdfs_list = raw_qualities_to_histogram(quals) 240s 240s test/test_modeller.py::test_kde_qualities 240s test/test_modeller.py::test_kde_qualities 240s /tmp/autopkgtest.wbDqCU/autopkgtest_tmp/test/test_modeller.py:14: DeprecationWarning: The numpy.linalg.linalg has been made private and renamed to numpy.linalg._linalg. All public functions exported by it are available from numpy.linalg. Please use numpy.linalg.LinAlgError instead. 240s cdf_list = modeller.raw_qualities_to_histogram(quality_distribution) 240s 240s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 240s ================== 45 passed, 1 skipped, 62 warnings in 4.69s ================== 240s Testing with python3.13 in /tmp/autopkgtest.wbDqCU/autopkgtest_tmp: 240s ============================= test session starts ============================== 240s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 240s cachedir: .pytest_cache 240s rootdir: /tmp/autopkgtest.wbDqCU/autopkgtest_tmp 240s plugins: typeguard-4.4.2 241s collecting ... collected 46 items 241s 241s test/test_abundance.py::test_parsing PASSED [ 2%] 241s test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] 241s test/test_abundance.py::test_parsing_empty PASSED [ 6%] 241s test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] 241s test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] 241s test/test_abundance.py::test_cov_calc PASSED [ 13%] 241s test/test_abundance.py::test_distributions PASSED [ 15%] 241s test/test_abundance.py::test_abunance_draft PASSED [ 17%] 241s test/test_abundance.py::test_coverage_scaling PASSED [ 19%] 241s test/test_bam.py::test_read_fail PASSED [ 21%] 241s test/test_bam.py::test_to_model PASSED [ 23%] 241s test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] 241s test/test_error_model.py::test_perfect_phred PASSED [ 28%] 241s test/test_error_model.py::test_basic_phred PASSED [ 30%] 241s test/test_error_model.py::test_kde_phred PASSED [ 32%] 241s test/test_error_model.py::test_introduce_errors PASSED [ 34%] 241s test/test_error_model.py::test_mut_sequence PASSED [ 36%] 241s test/test_error_model.py::test_introduce_indels PASSED [ 39%] 241s test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] 241s test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] 241s test/test_error_model.py::test_bad_err_mod PASSED [ 45%] 241s test/test_generator.py::test_cleanup_fail PASSED [ 47%] 243s test/test_generator.py::test_simulate_and_save PASSED [ 50%] 245s test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] 245s test/test_generator.py::test_small_input PASSED [ 54%] 245s test/test_generator.py::test_basic PASSED [ 56%] 245s test/test_generator.py::test_kde PASSED [ 58%] 245s test/test_generator.py::test_kde_short PASSED [ 60%] 245s test/test_generator.py::test_amp PASSED [ 63%] 245s test/test_modeller.py::test_kde_qualities PASSED [ 65%] 245s test/test_modeller.py::test_substitutions PASSED [ 67%] 245s test/test_modeller.py::test_indels PASSED [ 69%] 245s test/test_util.py::test_phred_conversions PASSED [ 71%] 245s test/test_util.py::test_rev_comp PASSED [ 73%] 245s test/test_util.py::test_count_records PASSED [ 76%] 245s test/test_util.py::test_count_records_empty PASSED [ 78%] 245s test/test_util.py::test_split_list PASSED [ 80%] 245s test/test_util.py::test_convert_n_reads PASSED [ 82%] 245s test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] 245s test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] 245s test/test_util.py::test_genome_file_exists PASSED [ 89%] 245s test/test_util.py::test_reservoir PASSED [ 91%] 245s test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] 245s test/test_util.py::test_concatenate PASSED [ 95%] 245s test/test_util.py::test_concatenate_read_only PASSED [ 97%] 245s test/test_util.py::test_compress PASSED [100%] 245s 245s =============================== warnings summary =============================== 245s test/test_bam.py: 60 warnings 245s /usr/lib/python3/dist-packages/iss/modeller.py:90: DeprecationWarning: The numpy.linalg.linalg has been made private and renamed to numpy.linalg._linalg. All public functions exported by it are available from numpy.linalg. Please use numpy.linalg.LinAlgError instead. 245s cdfs_list = raw_qualities_to_histogram(quals) 245s 245s test/test_modeller.py::test_kde_qualities 245s test/test_modeller.py::test_kde_qualities 245s /tmp/autopkgtest.wbDqCU/autopkgtest_tmp/test/test_modeller.py:14: DeprecationWarning: The numpy.linalg.linalg has been made private and renamed to numpy.linalg._linalg. All public functions exported by it are available from numpy.linalg. Please use numpy.linalg.LinAlgError instead. 245s cdf_list = modeller.raw_qualities_to_histogram(quality_distribution) 245s 245s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 245s ================== 45 passed, 1 skipped, 62 warnings in 4.56s ================== 245s autopkgtest [10:22:31]: test run-unit-test: -----------------------] 251s autopkgtest [10:22:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 251s run-unit-test PASS 255s autopkgtest [10:22:41]: @@@@@@@@@@@@@@@@@@@@ summary 255s run-unit-test PASS