0s autopkgtest [20:34:14]: starting date and time: 2025-06-05 20:34:14+0000 0s autopkgtest [20:34:14]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [20:34:14]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.itlr6gke/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade idseq-bench --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.4-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@bos03-arm64-16.secgroup --name adt-questing-arm64-idseq-bench-20250605-203414-juju-7f2275-prod-proposed-migration-environment-21-16b0c22f-15b1-44eb-9bdb-c06306f69a56 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 150s autopkgtest [20:36:44]: testbed dpkg architecture: arm64 151s autopkgtest [20:36:45]: testbed apt version: 3.1.0ubuntu3 151s autopkgtest [20:36:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 151s autopkgtest [20:36:45]: testbed release detected to be: None 152s autopkgtest [20:36:46]: updating testbed package index (apt update) 152s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 153s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 153s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 153s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 153s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [13.0 kB] 153s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [55.3 kB] 153s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [438 kB] 153s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/restricted Sources [3168 B] 153s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [71.0 kB] 153s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/restricted arm64 Packages [8092 B] 153s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [377 kB] 153s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [10.8 kB] 153s Fetched 1225 kB in 1s (1272 kB/s) 155s Reading package lists... 155s autopkgtest [20:36:49]: upgrading testbed (apt dist-upgrade and autopurge) 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Calculating upgrade... 157s The following packages will be upgraded: 157s libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib 157s libpython3.12t64 python3 python3-minimal 157s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 5242 kB of archives. 157s After this operation, 291 kB disk space will be freed. 157s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-minimal arm64 3.13.4-1 [27.9 kB] 157s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3 arm64 3.13.4-1 [24.0 kB] 157s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libpython3-stdlib arm64 3.13.4-1 [10.5 kB] 157s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12t64 arm64 3.12.10-1 [2314 kB] 158s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-stdlib arm64 3.12.10-1 [2029 kB] 158s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-minimal arm64 3.12.10-1 [836 kB] 159s Fetched 5242 kB in 1s (3994 kB/s) 160s (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 ... 118214 files and directories currently installed.) 160s Preparing to unpack .../python3-minimal_3.13.4-1_arm64.deb ... 160s Unpacking python3-minimal (3.13.4-1) over (3.13.3-1) ... 160s Setting up python3-minimal (3.13.4-1) ... 160s (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 ... 118214 files and directories currently installed.) 160s Preparing to unpack .../python3_3.13.4-1_arm64.deb ... 160s Unpacking python3 (3.13.4-1) over (3.13.3-1) ... 160s Preparing to unpack .../libpython3-stdlib_3.13.4-1_arm64.deb ... 160s Unpacking libpython3-stdlib:arm64 (3.13.4-1) over (3.13.3-1) ... 160s Preparing to unpack .../libpython3.12t64_3.12.10-1_arm64.deb ... 160s Unpacking libpython3.12t64:arm64 (3.12.10-1) over (3.12.8-3) ... 161s Preparing to unpack .../libpython3.12-stdlib_3.12.10-1_arm64.deb ... 161s Unpacking libpython3.12-stdlib:arm64 (3.12.10-1) over (3.12.8-3) ... 161s Preparing to unpack .../libpython3.12-minimal_3.12.10-1_arm64.deb ... 161s Unpacking libpython3.12-minimal:arm64 (3.12.10-1) over (3.12.8-3) ... 161s Setting up libpython3.12-minimal:arm64 (3.12.10-1) ... 161s Setting up libpython3-stdlib:arm64 (3.13.4-1) ... 161s Setting up libpython3.12-stdlib:arm64 (3.12.10-1) ... 161s Setting up python3 (3.13.4-1) ... 162s Setting up libpython3.12t64:arm64 (3.12.10-1) ... 162s Processing triggers for man-db (2.13.1-1) ... 163s Processing triggers for libc-bin (2.41-6ubuntu2) ... 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Solving dependencies... 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s autopkgtest [20:37:02]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 168s autopkgtest [20:37:02]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench 171s Get:1 http://ftpmaster.internal/ubuntu questing/universe idseq-bench 0.0~git20210602.27fb6dc-2 (dsc) [2356 B] 171s Get:2 http://ftpmaster.internal/ubuntu questing/universe idseq-bench 0.0~git20210602.27fb6dc-2 (tar) [17.3 kB] 171s Get:3 http://ftpmaster.internal/ubuntu questing/universe idseq-bench 0.0~git20210602.27fb6dc-2 (diff) [4472 B] 171s gpgv: Signature made Thu Apr 17 04:41:33 2025 UTC 171s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 171s gpgv: issuer "tille@debian.org" 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-2.dsc: no acceptable signature found 171s autopkgtest [20:37:05]: testing package idseq-bench version 0.0~git20210602.27fb6dc-2 171s autopkgtest [20:37:05]: build not needed 172s autopkgtest [20:37:06]: test run-unit-test: preparing testbed 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Solving dependencies... 174s The following NEW packages will be installed: 174s fontconfig-config fonts-urw-base35 idseq-bench insilicoseq libblas3 174s libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 174s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 174s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 174s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 174s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download 174s python3-all python3-biopython python3-cairo python3-decorator 174s python3-freetype python3-joblib python3-numpy python3-numpy-dev python3-pil 174s python3-pysam python3-reportlab python3-rlpycairo python3-scipy 174s python3-sklearn python3-sklearn-lib python3-smart-open python3-threadpoolctl 174s python3-wrapt sgml-base w3c-sgml-lib x11-common xfonts-encodings 174s xfonts-utils xml-core 174s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 56.5 MB of archives. 174s After this operation, 234 MB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1 [146 kB] 174s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2build1 [160 kB] 174s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15.1.0-5ubuntu1 [447 kB] 175s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2build1 [2308 kB] 175s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.4+ds-1 [3990 kB] 175s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 175s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 176s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 176s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 176s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 177s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 177s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15.1.0-5ubuntu1 [147 kB] 177s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 177s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 177s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 177s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 177s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 177s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 177s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 177s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 177s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 177s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 177s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 177s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 177s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 177s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 177s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 177s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 177s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 177s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 177s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 177s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 177s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 177s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 177s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 177s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 177s Get:37 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 177s Get:38 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 177s Get:39 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 178s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 178s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 178s Get:42 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 178s Get:43 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB] 178s Get:44 http://ftpmaster.internal/ubuntu questing/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 178s Get:45 http://ftpmaster.internal/ubuntu questing/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 178s Get:46 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 179s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 179s Get:48 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-scipy arm64 1.15.3-1 [15.8 MB] 183s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 insilicoseq all 2.0.1-1 [4247 kB] 184s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-acc-download all 0.2.8-3 [13.3 kB] 184s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-joblib all 1.4.2-4 [205 kB] 184s Get:52 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 184s Get:53 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 185s Get:54 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 185s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 python3-wrapt arm64 1.15.0-4build1 [34.2 kB] 185s Get:56 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-smart-open all 7.1.0-1 [89.9 kB] 185s Get:57 http://ftpmaster.internal/ubuntu questing/universe arm64 idseq-bench all 0.0~git20210602.27fb6dc-2 [24.4 kB] 185s Get:58 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-all arm64 3.13.4-1 [880 B] 186s Fetched 56.5 MB in 11s (5076 kB/s) 186s Selecting previously unselected package python3-numpy-dev:arm64. 186s (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 ... 118214 files and directories currently installed.) 186s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1_arm64.deb ... 186s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1) ... 186s Selecting previously unselected package libblas3:arm64. 186s Preparing to unpack .../01-libblas3_3.12.1-2build1_arm64.deb ... 186s Unpacking libblas3:arm64 (3.12.1-2build1) ... 186s Selecting previously unselected package libgfortran5:arm64. 186s Preparing to unpack .../02-libgfortran5_15.1.0-5ubuntu1_arm64.deb ... 186s Unpacking libgfortran5:arm64 (15.1.0-5ubuntu1) ... 186s Selecting previously unselected package liblapack3:arm64. 186s Preparing to unpack .../03-liblapack3_3.12.1-2build1_arm64.deb ... 186s Unpacking liblapack3:arm64 (3.12.1-2build1) ... 186s Selecting previously unselected package python3-numpy. 186s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1_arm64.deb ... 186s Unpacking python3-numpy (1:2.2.4+ds-1) ... 187s Selecting previously unselected package libfontenc1:arm64. 187s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 187s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 187s Selecting previously unselected package x11-common. 187s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu4_all.deb ... 187s Unpacking x11-common (1:7.7+23ubuntu4) ... 187s Selecting previously unselected package xfonts-encodings. 187s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 187s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 187s Selecting previously unselected package xfonts-utils. 187s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ... 187s Unpacking xfonts-utils (1:7.7+7) ... 187s Selecting previously unselected package fonts-urw-base35. 187s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 187s Unpacking fonts-urw-base35 (20200910-8) ... 187s Selecting previously unselected package fontconfig-config. 187s Preparing to unpack .../10-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 188s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 188s Selecting previously unselected package libgomp1:arm64. 188s Preparing to unpack .../11-libgomp1_15.1.0-5ubuntu1_arm64.deb ... 188s Unpacking libgomp1:arm64 (15.1.0-5ubuntu1) ... 188s Selecting previously unselected package libimagequant0:arm64. 188s Preparing to unpack .../12-libimagequant0_2.18.0-1build1_arm64.deb ... 188s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 188s Selecting previously unselected package libjpeg-turbo8:arm64. 188s Preparing to unpack .../13-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 188s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 188s Selecting previously unselected package libjpeg8:arm64. 188s Preparing to unpack .../14-libjpeg8_8c-2ubuntu11_arm64.deb ... 188s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 188s Selecting previously unselected package liblcms2-2:arm64. 188s Preparing to unpack .../15-liblcms2-2_2.16-2_arm64.deb ... 188s Unpacking liblcms2-2:arm64 (2.16-2) ... 188s Selecting previously unselected package libopenjp2-7:arm64. 188s Preparing to unpack .../16-libopenjp2-7_2.5.3-2_arm64.deb ... 188s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 188s Selecting previously unselected package libgraphite2-3:arm64. 188s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 188s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 188s Selecting previously unselected package libharfbuzz0b:arm64. 188s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_arm64.deb ... 188s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 188s Selecting previously unselected package libraqm0:arm64. 188s Preparing to unpack .../19-libraqm0_0.10.2-1_arm64.deb ... 188s Unpacking libraqm0:arm64 (0.10.2-1) ... 188s Selecting previously unselected package libdeflate0:arm64. 188s Preparing to unpack .../20-libdeflate0_1.23-2_arm64.deb ... 188s Unpacking libdeflate0:arm64 (1.23-2) ... 188s Selecting previously unselected package libjbig0:arm64. 188s Preparing to unpack .../21-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 188s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 188s Selecting previously unselected package liblerc4:arm64. 189s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 189s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 189s Selecting previously unselected package libsharpyuv0:arm64. 189s Preparing to unpack .../23-libsharpyuv0_1.5.0-0.1_arm64.deb ... 189s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 189s Selecting previously unselected package libwebp7:arm64. 189s Preparing to unpack .../24-libwebp7_1.5.0-0.1_arm64.deb ... 189s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 189s Selecting previously unselected package libtiff6:arm64. 189s Preparing to unpack .../25-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 189s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 189s Selecting previously unselected package libwebpdemux2:arm64. 189s Preparing to unpack .../26-libwebpdemux2_1.5.0-0.1_arm64.deb ... 189s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 189s Selecting previously unselected package libwebpmux3:arm64. 189s Preparing to unpack .../27-libwebpmux3_1.5.0-0.1_arm64.deb ... 189s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 189s Selecting previously unselected package python3-pil:arm64. 189s Preparing to unpack .../28-python3-pil_11.1.0-5build1_arm64.deb ... 189s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 189s Selecting previously unselected package libfontconfig1:arm64. 189s Preparing to unpack .../29-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 189s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 189s Selecting previously unselected package libpixman-1-0:arm64. 189s Preparing to unpack .../30-libpixman-1-0_0.44.0-3_arm64.deb ... 189s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 189s Selecting previously unselected package libxcb-render0:arm64. 189s Preparing to unpack .../31-libxcb-render0_1.17.0-2_arm64.deb ... 189s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 189s Selecting previously unselected package libxcb-shm0:arm64. 189s Preparing to unpack .../32-libxcb-shm0_1.17.0-2_arm64.deb ... 189s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 189s Selecting previously unselected package libxrender1:arm64. 189s Preparing to unpack .../33-libxrender1_1%3a0.9.12-1_arm64.deb ... 189s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 189s Selecting previously unselected package libcairo2:arm64. 189s Preparing to unpack .../34-libcairo2_1.18.4-1_arm64.deb ... 189s Unpacking libcairo2:arm64 (1.18.4-1) ... 189s Selecting previously unselected package python3-cairo. 189s Preparing to unpack .../35-python3-cairo_1.27.0-2_arm64.deb ... 189s Unpacking python3-cairo (1.27.0-2) ... 190s Selecting previously unselected package python3-freetype. 190s Preparing to unpack .../36-python3-freetype_2.5.1-1_all.deb ... 190s Unpacking python3-freetype (2.5.1-1) ... 190s Selecting previously unselected package python3-rlpycairo. 190s Preparing to unpack .../37-python3-rlpycairo_0.3.0-3_all.deb ... 190s Unpacking python3-rlpycairo (0.3.0-3) ... 190s Selecting previously unselected package python3-reportlab. 190s Preparing to unpack .../38-python3-reportlab_4.3.1-1_all.deb ... 190s Unpacking python3-reportlab (4.3.1-1) ... 190s Selecting previously unselected package sgml-base. 190s Preparing to unpack .../39-sgml-base_1.31+nmu1_all.deb ... 190s Unpacking sgml-base (1.31+nmu1) ... 190s Selecting previously unselected package xml-core. 190s Preparing to unpack .../40-xml-core_0.19_all.deb ... 190s Unpacking xml-core (0.19) ... 190s Selecting previously unselected package w3c-sgml-lib. 190s Preparing to unpack .../41-w3c-sgml-lib_1.3-3_all.deb ... 190s Unpacking w3c-sgml-lib (1.3-3) ... 190s Selecting previously unselected package python3-biopython. 190s Preparing to unpack .../42-python3-biopython_1.85+dfsg-4_arm64.deb ... 190s Unpacking python3-biopython (1.85+dfsg-4) ... 190s Selecting previously unselected package libhtscodecs2:arm64. 190s Preparing to unpack .../43-libhtscodecs2_1.6.1-2_arm64.deb ... 190s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 190s Selecting previously unselected package libhts3t64:arm64. 190s Preparing to unpack .../44-libhts3t64_1.21+ds-1_arm64.deb ... 190s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 190s Selecting previously unselected package python3-pysam. 190s Preparing to unpack .../45-python3-pysam_0.23.0+ds-1build1_arm64.deb ... 190s Unpacking python3-pysam (0.23.0+ds-1build1) ... 191s Selecting previously unselected package python3-decorator. 191s Preparing to unpack .../46-python3-decorator_5.2.1-2_all.deb ... 191s Unpacking python3-decorator (5.2.1-2) ... 191s Selecting previously unselected package python3-scipy. 191s Preparing to unpack .../47-python3-scipy_1.15.3-1_arm64.deb ... 191s Unpacking python3-scipy (1.15.3-1) ... 191s Selecting previously unselected package insilicoseq. 191s Preparing to unpack .../48-insilicoseq_2.0.1-1_all.deb ... 191s Unpacking insilicoseq (2.0.1-1) ... 192s Selecting previously unselected package ncbi-acc-download. 192s Preparing to unpack .../49-ncbi-acc-download_0.2.8-3_all.deb ... 192s Unpacking ncbi-acc-download (0.2.8-3) ... 192s Selecting previously unselected package python3-joblib. 192s Preparing to unpack .../50-python3-joblib_1.4.2-4_all.deb ... 192s Unpacking python3-joblib (1.4.2-4) ... 192s Selecting previously unselected package python3-threadpoolctl. 192s Preparing to unpack .../51-python3-threadpoolctl_3.1.0-1_all.deb ... 192s Unpacking python3-threadpoolctl (3.1.0-1) ... 192s Selecting previously unselected package python3-sklearn-lib:arm64. 192s Preparing to unpack .../52-python3-sklearn-lib_1.4.2+dfsg-8_arm64.deb ... 192s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 192s Selecting previously unselected package python3-sklearn. 192s Preparing to unpack .../53-python3-sklearn_1.4.2+dfsg-8_all.deb ... 192s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 192s Selecting previously unselected package python3-wrapt. 192s Preparing to unpack .../54-python3-wrapt_1.15.0-4build1_arm64.deb ... 192s Unpacking python3-wrapt (1.15.0-4build1) ... 192s Selecting previously unselected package python3-smart-open. 192s Preparing to unpack .../55-python3-smart-open_7.1.0-1_all.deb ... 192s Unpacking python3-smart-open (7.1.0-1) ... 192s Selecting previously unselected package idseq-bench. 192s Preparing to unpack .../56-idseq-bench_0.0~git20210602.27fb6dc-2_all.deb ... 192s Unpacking idseq-bench (0.0~git20210602.27fb6dc-2) ... 192s Selecting previously unselected package python3-all. 193s Preparing to unpack .../57-python3-all_3.13.4-1_arm64.deb ... 193s Unpacking python3-all (3.13.4-1) ... 193s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 193s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 193s Setting up liblcms2-2:arm64 (2.16-2) ... 193s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 193s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 193s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 193s Setting up libxrender1:arm64 (1:0.9.12-1) ... 193s Setting up python3-joblib (1.4.2-4) ... 193s Setting up libxcb-render0:arm64 (1.17.0-2) ... 193s Setting up python3-threadpoolctl (3.1.0-1) ... 193s Setting up x11-common (1:7.7+23ubuntu4) ... 194s Setting up libdeflate0:arm64 (1.23-2) ... 194s Setting up python3-all (3.13.4-1) ... 194s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 194s Setting up libgomp1:arm64 (15.1.0-5ubuntu1) ... 194s Setting up python3-freetype (2.5.1-1) ... 194s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 194s Setting up python3-decorator (5.2.1-2) ... 194s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 194s Setting up libblas3:arm64 (3.12.1-2build1) ... 194s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 194s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 194s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 194s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1) ... 194s Setting up python3-wrapt (1.15.0-4build1) ... 195s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 195s Setting up libgfortran5:arm64 (15.1.0-5ubuntu1) ... 195s Setting up libwebp7:arm64 (1.5.0-0.1) ... 195s Setting up libhts3t64:arm64 (1.21+ds-1) ... 195s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 195s Setting up ncbi-acc-download (0.2.8-3) ... 195s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 195s Setting up sgml-base (1.31+nmu1) ... 195s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 195s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 195s Setting up liblapack3:arm64 (3.12.1-2build1) ... 195s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 195s Setting up python3-pysam (0.23.0+ds-1build1) ... 195s Setting up python3-smart-open (7.1.0-1) ... 195s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 195s Setting up xfonts-utils (1:7.7+7) ... 195s Setting up libraqm0:arm64 (0.10.2-1) ... 195s Setting up python3-numpy (1:2.2.4+ds-1) ... 198s Setting up libtiff6:arm64 (4.7.0-3ubuntu1) ... 198s Setting up xml-core (0.19) ... 199s Setting up python3-scipy (1.15.3-1) ... 204s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 204s Setting up fonts-urw-base35 (20200910-8) ... 204s Setting up python3-pil:arm64 (11.1.0-5build1) ... 205s Setting up python3-sklearn (1.4.2+dfsg-8) ... 208s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 208s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 208s Setting up libcairo2:arm64 (1.18.4-1) ... 208s Setting up python3-cairo (1.27.0-2) ... 208s Setting up python3-rlpycairo (0.3.0-3) ... 208s Setting up python3-reportlab (4.3.1-1) ... 209s Processing triggers for libc-bin (2.41-6ubuntu2) ... 209s Processing triggers for man-db (2.13.1-1) ... 210s Processing triggers for sgml-base (1.31+nmu1) ... 210s Setting up w3c-sgml-lib (1.3-3) ... 239s Setting up python3-biopython (1.85+dfsg-4) ... 240s Setting up insilicoseq (2.0.1-1) ... 240s Setting up idseq-bench (0.0~git20210602.27fb6dc-2) ... 241s autopkgtest [20:38:15]: test run-unit-test: [----------------------- 247s Failed to download file with id NC_016845.1 from NCBI 247s NCBI Entrez returned error code 500, are ID(s) NC_016845.1 valid? 247s Generating IDseq benchmark data... 247s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all' 249s Traceback (most recent call last): 249s File "/usr/bin/idseq-bench-generate", line 33, in 249s sys.exit(load_entry_point('idseq-bench==0.2.6', 'console_scripts', 'idseq-bench-generate')()) 249s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 249s File "/usr/lib/python3/dist-packages/idseq_bench/generate.py", line 287, in main 249s create_benchmark(benchmark_config) 249s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 249s File "/usr/lib/python3/dist-packages/idseq_bench/generate.py", line 222, in create_benchmark 249s Genome.fetch_all() 249s ~~~~~~~~~~~~~~~~^^ 249s File "/usr/lib/python3/dist-packages/idseq_bench/genome.py", line 59, in fetch_all 249s af = Genome.fetch_versioned_accession_id(f) 249s File "/usr/lib/python3/dist-packages/idseq_bench/genome.py", line 45, in fetch_versioned_accession_id 249s check_call(command) 249s ~~~~~~~~~~^^^^^^^^^ 249s File "/usr/lib/python3/dist-packages/idseq_bench/util.py", line 35, in check_call 249s p = subprocess.run(command, shell=shell, check=True, stdout=stdout) 249s File "/usr/lib/python3.13/subprocess.py", line 577, in run 249s raise CalledProcessError(retcode, process.args, 249s output=stdout, stderr=stderr) 249s subprocess.CalledProcessError: Command 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all' returned non-zero exit status 1. 250s autopkgtest [20:38:24]: test run-unit-test: -----------------------] 250s autopkgtest [20:38:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 250s run-unit-test FAIL non-zero exit status 1 251s autopkgtest [20:38:25]: @@@@@@@@@@@@@@@@@@@@ summary 251s run-unit-test FAIL non-zero exit status 1 274s nova [W] Using flock in prodstack6-arm64 274s Creating nova instance adt-questing-arm64-idseq-bench-20250605-203414-juju-7f2275-prod-proposed-migration-environment-21-16b0c22f-15b1-44eb-9bdb-c06306f69a56 from image adt/ubuntu-questing-arm64-server-20250605.img (UUID 6c8936a7-52d0-45c3-917a-9e7e5ce4a4c3)... 274s nova [W] Timed out waiting for 0f0711d8-5578-43bc-88ef-c87f78b112ea to get deleted.