0s autopkgtest [14:00:35]: starting date and time: 2025-12-03 14:00:35+0000 0s autopkgtest [14:00:35]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:00:35]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l6_l0ipa/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-4.secgroup --name adt-resolute-i386-insilicoseq-20251203-140035-juju-7f2275-prod-proposed-migration-environment-15-758b5652-2f45-4fd9-bdd1-6883ba51b9f8 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-i386-insilicoseq-20251203-140035-juju-7f2275-prod-proposed-migration-environment-15-758b5652-2f45-4fd9-bdd1-6883ba51b9f8 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 45s autopkgtest [14:01:20]: testbed dpkg architecture: amd64 45s autopkgtest [14:01:20]: testbed apt version: 3.1.12 45s autopkgtest [14:01:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 45s autopkgtest [14:01:20]: testbed release detected to be: None 46s autopkgtest [14:01:21]: updating testbed package index (apt update) 46s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 46s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 46s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 46s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 46s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.5 kB] 46s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [148 kB] 46s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [984 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [156 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [202 kB] 47s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6168 B] 47s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 47s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [745 kB] 47s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [334 kB] 47s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.3 kB] 47s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4780 B] 47s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [10.6 kB] 47s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [828 B] 48s Fetched 2764 kB in 1s (2811 kB/s) 48s Reading package lists... 49s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 49s Reading package lists... 49s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s The following packages will be upgraded: 50s libpython3-stdlib python3 python3-gdbm python3-minimal 50s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s Need to get 72.9 kB of archives. 50s After this operation, 2048 B of additional disk space will be used. 50s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 50s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 50s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 50s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 50s dpkg-preconfigure: unable to re-open stdin: No such file or directory 50s Fetched 72.9 kB in 0s (0 B/s) 50s (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 ... 83538 files and directories currently installed.) 50s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 50s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 50s Setting up python3-minimal (3.13.9-2) ... 50s (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 ... 83538 files and directories currently installed.) 50s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 50s running python pre-rtupdate hooks for python3.13... 50s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 50s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 51s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 51s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 51s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 51s Setting up python3-gdbm (3.13.9-2) ... 51s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 51s Setting up python3 (3.13.9-2) ... 51s running python rtupdate hooks for python3.13... 51s running python post-rtupdate hooks for python3.13... 51s Processing triggers for man-db (2.13.1-1) ... 51s autopkgtest [14:01:26]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 52s Calculating upgrade... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Solving dependencies... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s autopkgtest [14:01:29]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 54s autopkgtest [14:01:29]: @@@@@@@@@@@@@@@@@@@@ apt-source insilicoseq 55s Get:1 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (dsc) [2411 B] 55s Get:2 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (tar) [4591 kB] 55s Get:3 http://ftpmaster.internal/ubuntu resolute/universe insilicoseq 2.0.1-1 (diff) [5304 B] 56s gpgv: Signature made Wed Apr 24 11:31:14 2024 UTC 56s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 56s gpgv: issuer "emollier@debian.org" 56s gpgv: Can't check signature: No public key 56s dpkg-source: warning: cannot verify inline signature for ./insilicoseq_2.0.1-1.dsc: no acceptable signature found 56s autopkgtest [14:01:31]: testing package insilicoseq version 2.0.1-1 56s autopkgtest [14:01:31]: build not needed 56s autopkgtest [14:01:31]: test run-unit-test: preparing testbed 56s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Solving dependencies... 57s The following NEW packages will be installed: 57s fontconfig-config fonts-urw-base35 insilicoseq libblas3 libcairo2 57s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 57s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 57s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 57s libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib libqhull-r8.0 57s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 57s libxcb-render0 libxcb-shm0 libxrender1 python3-all python3-biopython 57s python3-cairo python3-charset-normalizer python3-decorator python3-freetype 57s python3-iniconfig python3-numpy python3-numpy-dev python3-pil python3-pluggy 57s python3-pysam python3-pytest python3-reportlab python3-rlpycairo 57s python3-scipy python3.14 python3.14-minimal sgml-base w3c-sgml-lib 57s x11-common xfonts-encodings xfonts-utils xml-core 57s 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 64.0 MB of archives. 57s After this operation, 279 MB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.0-4 [906 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.0-4 [2559 kB] 57s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 57s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 58s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 58s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 58s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 58s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 58s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-1 [175 kB] 58s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 58s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 58s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 58s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 58s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 58s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 58s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 58s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 58s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 58s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 58s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 58s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 58s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 58s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 58s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 58s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 58s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 58s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 58s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 58s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 58s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 58s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 58s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 58s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 58s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 58s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 58s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 58s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.5-1 [1148 kB] 58s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 58s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 58s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 58s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 58s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 58s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 58s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 58s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 58s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 58s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-1 [18.8 MB] 58s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 insilicoseq all 2.0.1-1 [4247 kB] 58s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.0-4 [2397 kB] 58s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.0-4 [805 kB] 58s Get:56 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.9-2 [892 B] 58s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-1 [6840 B] 58s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 58s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 59s Fetched 64.0 MB in 2s (40.6 MB/s) 59s Selecting previously unselected package python3-numpy-dev:amd64. 59s (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 ... 83538 files and directories currently installed.) 59s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 59s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 59s Selecting previously unselected package libblas3:amd64. 59s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 59s Unpacking libblas3:amd64 (3.12.1-7) ... 59s Selecting previously unselected package libgfortran5:amd64. 59s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 59s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 59s Selecting previously unselected package liblapack3:amd64. 59s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 59s Unpacking liblapack3:amd64 (3.12.1-7) ... 59s Selecting previously unselected package python3-numpy. 59s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 59s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 59s Selecting previously unselected package libpython3.14-minimal:amd64. 59s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_amd64.deb ... 59s Unpacking libpython3.14-minimal:amd64 (3.14.0-4) ... 59s Selecting previously unselected package python3.14-minimal. 59s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_amd64.deb ... 59s Unpacking python3.14-minimal (3.14.0-4) ... 59s Selecting previously unselected package libfontenc1:amd64. 59s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 59s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 59s Selecting previously unselected package x11-common. 59s Preparing to unpack .../08-x11-common_1%3a7.7+24ubuntu1_all.deb ... 59s Unpacking x11-common (1:7.7+24ubuntu1) ... 59s Selecting previously unselected package xfonts-encodings. 59s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 59s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 59s Selecting previously unselected package xfonts-utils. 59s Preparing to unpack .../10-xfonts-utils_1%3a7.7+7_amd64.deb ... 59s Unpacking xfonts-utils (1:7.7+7) ... 59s Selecting previously unselected package fonts-urw-base35. 59s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ... 59s Unpacking fonts-urw-base35 (20200910-8) ... 59s Selecting previously unselected package fontconfig-config. 59s Preparing to unpack .../12-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 59s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 59s Selecting previously unselected package python3-charset-normalizer. 59s Preparing to unpack .../13-python3-charset-normalizer_3.4.4-1_amd64.deb ... 59s Unpacking python3-charset-normalizer (3.4.4-1) ... 59s Selecting previously unselected package libgomp1:amd64. 59s Preparing to unpack .../14-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 59s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 59s Selecting previously unselected package libimagequant0:amd64. 59s Preparing to unpack .../15-libimagequant0_2.18.0-1build1_amd64.deb ... 59s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 59s Selecting previously unselected package libjpeg-turbo8:amd64. 59s Preparing to unpack .../16-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 59s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 59s Selecting previously unselected package libjpeg8:amd64. 59s Preparing to unpack .../17-libjpeg8_8c-2ubuntu11_amd64.deb ... 59s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 59s Selecting previously unselected package liblcms2-2:amd64. 59s Preparing to unpack .../18-liblcms2-2_2.17-1_amd64.deb ... 59s Unpacking liblcms2-2:amd64 (2.17-1) ... 59s Selecting previously unselected package libopenjp2-7:amd64. 59s Preparing to unpack .../19-libopenjp2-7_2.5.3-2.1_amd64.deb ... 59s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 59s Selecting previously unselected package libgraphite2-3:amd64. 59s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 59s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 59s Selecting previously unselected package libharfbuzz0b:amd64. 59s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_amd64.deb ... 59s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 59s Selecting previously unselected package libraqm0:amd64. 59s Preparing to unpack .../22-libraqm0_0.10.3-1_amd64.deb ... 59s Unpacking libraqm0:amd64 (0.10.3-1) ... 59s Selecting previously unselected package libdeflate0:amd64. 59s Preparing to unpack .../23-libdeflate0_1.23-2_amd64.deb ... 59s Unpacking libdeflate0:amd64 (1.23-2) ... 59s Selecting previously unselected package libjbig0:amd64. 59s Preparing to unpack .../24-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 59s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 59s Selecting previously unselected package liblerc4:amd64. 59s Preparing to unpack .../25-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 59s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 59s Selecting previously unselected package libsharpyuv0:amd64. 59s Preparing to unpack .../26-libsharpyuv0_1.5.0-0.1_amd64.deb ... 59s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libwebp7:amd64. 59s Preparing to unpack .../27-libwebp7_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libtiff6:amd64. 59s Preparing to unpack .../28-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 59s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 59s Selecting previously unselected package libwebpdemux2:amd64. 59s Preparing to unpack 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Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 59s Selecting previously unselected package libxcb-shm0:amd64. 59s Preparing to unpack .../35-libxcb-shm0_1.17.0-2build1_amd64.deb ... 59s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 59s Selecting previously unselected package libxrender1:amd64. 59s Preparing to unpack .../36-libxrender1_1%3a0.9.12-1_amd64.deb ... 59s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 59s Selecting previously unselected package libcairo2:amd64. 59s Preparing to unpack .../37-libcairo2_1.18.4-1build1_amd64.deb ... 59s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 59s Selecting previously unselected package python3-cairo. 59s Preparing to unpack .../38-python3-cairo_1.27.0-2build1_amd64.deb ... 59s Unpacking python3-cairo (1.27.0-2build1) ... 59s Selecting previously unselected package python3-freetype. 60s Preparing to unpack .../39-python3-freetype_2.5.1-2_all.deb ... 60s Unpacking python3-freetype (2.5.1-2) ... 60s Selecting previously unselected package python3-rlpycairo. 60s Preparing to unpack .../40-python3-rlpycairo_0.3.0-4_all.deb ... 60s Unpacking python3-rlpycairo (0.3.0-4) ... 60s Selecting previously unselected package python3-reportlab. 60s Preparing to unpack .../41-python3-reportlab_4.4.5-1_all.deb ... 60s Unpacking python3-reportlab (4.4.5-1) ... 60s Selecting previously unselected package sgml-base. 60s Preparing to unpack .../42-sgml-base_1.31+nmu1_all.deb ... 60s Unpacking sgml-base (1.31+nmu1) ... 60s Selecting previously unselected package xml-core. 60s Preparing to unpack .../43-xml-core_0.19_all.deb ... 60s Unpacking xml-core (0.19) ... 60s Selecting previously unselected package w3c-sgml-lib. 60s Preparing to unpack .../44-w3c-sgml-lib_1.3-3_all.deb ... 60s Unpacking w3c-sgml-lib (1.3-3) ... 60s Selecting previously unselected package python3-biopython. 60s Preparing to unpack .../45-python3-biopython_1.86+dfsg-1_amd64.deb ... 60s Unpacking python3-biopython (1.86+dfsg-1) ... 60s Selecting previously unselected package libhtscodecs2:amd64. 60s Preparing to unpack .../46-libhtscodecs2_1.6.1-2_amd64.deb ... 60s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 60s Selecting previously unselected package libhts3t64:amd64. 60s Preparing to unpack .../47-libhts3t64_1.22.1+ds2-1_amd64.deb ... 60s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 60s Selecting previously unselected package python3-pysam. 60s Preparing to unpack .../48-python3-pysam_0.23.3+ds-2_amd64.deb ... 60s Unpacking python3-pysam (0.23.3+ds-2) ... 60s Selecting previously unselected package python3-decorator. 60s Preparing to unpack .../49-python3-decorator_5.2.1-2_all.deb ... 60s Unpacking python3-decorator (5.2.1-2) ... 60s Selecting previously unselected package libqhull-r8.0:amd64. 60s Preparing to unpack .../50-libqhull-r8.0_2020.2-7_amd64.deb ... 60s Unpacking libqhull-r8.0:amd64 (2020.2-7) ... 60s Selecting previously unselected package python3-scipy. 60s Preparing to unpack .../51-python3-scipy_1.16.3-1_amd64.deb ... 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libxcb-shm0:amd64 (1.17.0-2build1) ... 61s Setting up libgomp1:amd64 (15.2.0-9ubuntu1) ... 61s Setting up python3-freetype (2.5.1-2) ... 61s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 61s Setting up python3-decorator (5.2.1-2) ... 61s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 61s Setting up libblas3:amd64 (3.12.1-7) ... 61s 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 61s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 61s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 61s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 61s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 61s Setting up libgfortran5:amd64 (15.2.0-9ubuntu1) ... 61s Setting up python3-pluggy (1.6.0-1) ... 61s Setting up libwebp7:amd64 (1.5.0-0.1) ... 61s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 61s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 61s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 61s Setting up sgml-base (1.31+nmu1) ... 61s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 61s Setting up python3.14-minimal (3.14.0-4) ... 62s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 62s Setting up liblapack3:amd64 (3.12.1-7) ... 62s 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 62s Setting up python3-pysam (0.23.3+ds-2) ... 62s Setting up libpython3.14-stdlib:amd64 (3.14.0-4) ... 62s Setting up python3-pytest (8.3.5-2) ... 62s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 62s Setting up xfonts-utils (1:7.7+7) ... 62s Setting up libraqm0:amd64 (0.10.3-1) ... 62s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 65s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 65s Setting up xml-core (0.19) ... 65s Setting up python3.14 (3.14.0-4) ... 66s Setting up python3-scipy (1.16.3-1) ... 70s Setting up python3-all (3.13.9-2) ... 70s Setting up fonts-urw-base35 (20200910-8) ... 71s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 71s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 71s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 71s Setting up libcairo2:amd64 (1.18.4-1build1) ... 71s Setting up python3-cairo (1.27.0-2build1) ... 71s Setting up python3-rlpycairo (0.3.0-4) ... 71s Setting up python3-reportlab (4.4.5-1) ... 72s Processing triggers for libc-bin (2.42-2ubuntu2) ... 72s Processing triggers for systemd (257.9-0ubuntu2) ... 72s Processing triggers for man-db (2.13.1-1) ... 73s Processing triggers for sgml-base (1.31+nmu1) ... 73s Setting up w3c-sgml-lib (1.3-3) ... 90s Setting up python3-biopython (1.86+dfsg-1) ... 92s Setting up insilicoseq (2.0.1-1) ... 93s autopkgtest [14:02:08]: test environment configured for cross building 93s autopkgtest [14:02:08]: test run-unit-test: [----------------------- 93s Testing with python3.14 in /tmp/autopkgtest.Wn1j4A/autopkgtest_tmp: 93s ============================= test session starts ============================== 93s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 93s cachedir: .pytest_cache 93s rootdir: /tmp/autopkgtest.Wn1j4A/autopkgtest_tmp 93s plugins: typeguard-4.4.2 94s collecting ... collected 46 items 94s 94s test/test_abundance.py::test_parsing PASSED [ 2%] 94s test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] 94s test/test_abundance.py::test_parsing_empty PASSED [ 6%] 94s test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] 94s test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] 94s test/test_abundance.py::test_cov_calc PASSED [ 13%] 94s test/test_abundance.py::test_distributions PASSED [ 15%] 94s test/test_abundance.py::test_abunance_draft PASSED [ 17%] 94s test/test_abundance.py::test_coverage_scaling PASSED [ 19%] 94s test/test_bam.py::test_read_fail PASSED [ 21%] 94s test/test_bam.py::test_to_model PASSED [ 23%] 94s test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] 94s test/test_error_model.py::test_perfect_phred PASSED [ 28%] 94s test/test_error_model.py::test_basic_phred PASSED [ 30%] 94s test/test_error_model.py::test_kde_phred PASSED [ 32%] 94s test/test_error_model.py::test_introduce_errors PASSED [ 34%] 94s test/test_error_model.py::test_mut_sequence PASSED [ 36%] 94s test/test_error_model.py::test_introduce_indels PASSED [ 39%] 94s test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] 94s test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] 94s test/test_error_model.py::test_bad_err_mod PASSED [ 45%] 94s test/test_generator.py::test_cleanup_fail PASSED [ 47%] 95s test/test_generator.py::test_simulate_and_save PASSED [ 50%] 96s test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] 96s test/test_generator.py::test_small_input PASSED [ 54%] 96s test/test_generator.py::test_basic PASSED [ 56%] 96s test/test_generator.py::test_kde PASSED [ 58%] 96s test/test_generator.py::test_kde_short PASSED [ 60%] 96s test/test_generator.py::test_amp PASSED [ 63%] 96s test/test_modeller.py::test_kde_qualities PASSED [ 65%] 96s test/test_modeller.py::test_substitutions PASSED [ 67%] 96s test/test_modeller.py::test_indels PASSED [ 69%] 96s test/test_util.py::test_phred_conversions PASSED [ 71%] 96s test/test_util.py::test_rev_comp PASSED [ 73%] 96s test/test_util.py::test_count_records PASSED [ 76%] 96s test/test_util.py::test_count_records_empty PASSED [ 78%] 96s test/test_util.py::test_split_list PASSED [ 80%] 96s test/test_util.py::test_convert_n_reads PASSED [ 82%] 96s test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] 96s test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] 96s test/test_util.py::test_genome_file_exists PASSED [ 89%] 96s test/test_util.py::test_reservoir PASSED [ 91%] 96s test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] 96s test/test_util.py::test_concatenate PASSED [ 95%] 96s test/test_util.py::test_concatenate_read_only PASSED [ 97%] 96s test/test_util.py::test_compress PASSED [100%] 96s 96s =============================== warnings summary =============================== 96s test/test_bam.py: 60 warnings 96s /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. 96s cdfs_list = raw_qualities_to_histogram(quals) 96s 96s test/test_modeller.py::test_kde_qualities 96s test/test_modeller.py::test_kde_qualities 96s /tmp/autopkgtest.Wn1j4A/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. 96s cdf_list = modeller.raw_qualities_to_histogram(quality_distribution) 96s 96s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 96s ================== 45 passed, 1 skipped, 62 warnings in 2.50s ================== 96s Testing with python3.13 in /tmp/autopkgtest.Wn1j4A/autopkgtest_tmp: 96s ============================= test session starts ============================== 96s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3 96s cachedir: .pytest_cache 96s rootdir: /tmp/autopkgtest.Wn1j4A/autopkgtest_tmp 96s plugins: typeguard-4.4.2 96s collecting ... collected 46 items 96s 96s test/test_abundance.py::test_parsing PASSED [ 2%] 96s test/test_abundance.py::test_parsing_readcounts PASSED [ 4%] 96s test/test_abundance.py::test_parsing_empty PASSED [ 6%] 96s test/test_abundance.py::test_parsing_no_exists PASSED [ 8%] 96s test/test_abundance.py::test_parsing_bad_abundance PASSED [ 10%] 96s test/test_abundance.py::test_cov_calc PASSED [ 13%] 96s test/test_abundance.py::test_distributions PASSED [ 15%] 96s test/test_abundance.py::test_abunance_draft PASSED [ 17%] 96s test/test_abundance.py::test_coverage_scaling PASSED [ 19%] 96s test/test_bam.py::test_read_fail PASSED [ 21%] 96s test/test_bam.py::test_to_model PASSED [ 23%] 96s test/test_download.py::test_ncbi SKIPPED (Test requires Internet.) [ 26%] 96s test/test_error_model.py::test_perfect_phred PASSED [ 28%] 96s test/test_error_model.py::test_basic_phred PASSED [ 30%] 96s test/test_error_model.py::test_kde_phred PASSED [ 32%] 96s test/test_error_model.py::test_introduce_errors PASSED [ 34%] 96s test/test_error_model.py::test_mut_sequence PASSED [ 36%] 96s test/test_error_model.py::test_introduce_indels PASSED [ 39%] 96s test/test_error_model.py::test_adjust_seq_length_extend PASSED [ 41%] 96s test/test_error_model.py::test_introduce_indels_rev PASSED [ 43%] 96s test/test_error_model.py::test_bad_err_mod PASSED [ 45%] 96s test/test_generator.py::test_cleanup_fail PASSED [ 47%] 97s test/test_generator.py::test_simulate_and_save PASSED [ 50%] 98s test/test_generator.py::test_simulate_and_save_short PASSED [ 52%] 98s test/test_generator.py::test_small_input PASSED [ 54%] 98s test/test_generator.py::test_basic PASSED [ 56%] 98s test/test_generator.py::test_kde PASSED [ 58%] 98s test/test_generator.py::test_kde_short PASSED [ 60%] 98s test/test_generator.py::test_amp PASSED [ 63%] 98s test/test_modeller.py::test_kde_qualities PASSED [ 65%] 98s test/test_modeller.py::test_substitutions PASSED [ 67%] 98s test/test_modeller.py::test_indels PASSED [ 69%] 98s test/test_util.py::test_phred_conversions PASSED [ 71%] 98s test/test_util.py::test_rev_comp PASSED [ 73%] 98s test/test_util.py::test_count_records PASSED [ 76%] 98s test/test_util.py::test_count_records_empty PASSED [ 78%] 98s test/test_util.py::test_split_list PASSED [ 80%] 98s test/test_util.py::test_convert_n_reads PASSED [ 82%] 98s test/test_util.py::test_convert_n_reads_bad_not_a_number PASSED [ 84%] 98s test/test_util.py::test_convert_n_reads_bad_suffix PASSED [ 86%] 98s test/test_util.py::test_genome_file_exists PASSED [ 89%] 98s test/test_util.py::test_reservoir PASSED [ 91%] 98s test/test_util.py::test_reservoir_invalid_input PASSED [ 93%] 98s test/test_util.py::test_concatenate PASSED [ 95%] 98s test/test_util.py::test_concatenate_read_only PASSED [ 97%] 98s test/test_util.py::test_compress PASSED [100%] 98s 98s =============================== warnings summary =============================== 98s test/test_bam.py: 60 warnings 98s /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. 98s cdfs_list = raw_qualities_to_histogram(quals) 98s 98s test/test_modeller.py::test_kde_qualities 98s test/test_modeller.py::test_kde_qualities 98s /tmp/autopkgtest.Wn1j4A/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. 98s cdf_list = modeller.raw_qualities_to_histogram(quality_distribution) 98s 98s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 98s ================== 45 passed, 1 skipped, 62 warnings in 2.32s ================== 99s autopkgtest [14:02:14]: test run-unit-test: -----------------------] 99s run-unit-test PASS 99s autopkgtest [14:02:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s autopkgtest [14:02:14]: @@@@@@@@@@@@@@@@@@@@ summary 99s run-unit-test PASS