0s autopkgtest [11:33:41]: starting date and time: 2025-12-03 11:33:41+0000 0s autopkgtest [11:33:41]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [11:33:41]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ci0t5pup/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 peptidebuilder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- lxd -r lxd-armhf-10.145.243.239 lxd-armhf-10.145.243.239:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [11:34:02]: testbed dpkg architecture: armhf 23s autopkgtest [11:34:04]: testbed apt version: 3.1.12 27s autopkgtest [11:34:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [11:34:10]: testbed release detected to be: None 38s autopkgtest [11:34:19]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 40s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 40s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 40s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 40s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [25.2 kB] 40s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [147 kB] 40s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [981 kB] 40s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [187 kB] 40s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [678 kB] 40s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [8468 B] 40s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1414 kB] 40s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 41s Get:13 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [305 kB] 41s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1366 kB] 41s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.5 MB] 42s Get:16 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 45s Fetched 42.6 MB in 5s (7964 kB/s) 46s Reading package lists... 51s autopkgtest [11:34:32]: upgrading testbed (apt dist-upgrade and autopurge) 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s libpython3-stdlib python3 python3-gdbm python3-minimal 54s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 72.9 kB of archives. 54s After this operation, 2048 B of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.9-2 [28.1 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.9-2 [23.0 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.9-2 [10.8 kB] 54s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.13.9-2 [11.0 kB] 55s Fetched 72.9 kB in 0s (189 kB/s) 55s (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.) 55s Preparing to unpack .../python3-minimal_3.13.9-2_armhf.deb ... 55s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 55s Setting up python3-minimal (3.13.9-2) ... 55s (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.) 55s Preparing to unpack .../python3_3.13.9-2_armhf.deb ... 55s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 55s Preparing to unpack .../libpython3-stdlib_3.13.9-2_armhf.deb ... 55s Unpacking libpython3-stdlib:armhf (3.13.9-2) over (3.13.7-1) ... 55s Preparing to unpack .../python3-gdbm_3.13.9-2_armhf.deb ... 55s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 55s Setting up python3-gdbm (3.13.9-2) ... 55s Setting up libpython3-stdlib:armhf (3.13.9-2) ... 55s Setting up python3 (3.13.9-2) ... 55s Processing triggers for man-db (2.13.1-1) ... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [11:34:42]: rebooting testbed after setup commands that affected boot 103s autopkgtest [11:35:24]: 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 130s autopkgtest [11:35:51]: @@@@@@@@@@@@@@@@@@@@ apt-source peptidebuilder 141s Get:1 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (dsc) [2239 B] 141s Get:2 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (tar) [468 kB] 141s Get:3 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (diff) [4016 B] 141s gpgv: Signature made Fri Oct 8 20:54:03 2021 UTC 141s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 141s gpgv: issuer "tille@debian.org" 141s gpgv: Can't check signature: No public key 141s dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found 142s autopkgtest [11:36:03]: testing package peptidebuilder version 1.1.0-3 144s autopkgtest [11:36:05]: build not needed 146s autopkgtest [11:36:07]: test run-unit-test: preparing testbed 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Solving dependencies... 148s The following NEW packages will be installed: 148s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 148s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 148s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 148s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 148s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 148s libxrender1 python3-biopython python3-cairo python3-charset-normalizer 148s python3-freetype python3-numpy python3-numpy-dev python3-peptidebuilder 148s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 148s x11-common xfonts-encodings xfonts-utils xml-core 149s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 25.1 MB of archives. 149s After this operation, 74.6 MB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 149s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7 [133 kB] 149s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-9ubuntu1 [334 kB] 149s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7 [2091 kB] 149s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 150s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libfontenc1 armhf 1:1.1.8-1build2 [11.7 kB] 150s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.13.3+dfsg-1build1 [334 kB] 150s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 150s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 150s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 150s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 152s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.15.0-2.3ubuntu1 [38.1 kB] 152s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.15.0-2.3ubuntu1 [114 kB] 152s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 152s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2build1 [15.5 kB] 152s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2build1 [5962 B] 152s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 152s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-1build1 [489 kB] 152s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 152s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-9ubuntu1 [129 kB] 152s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 152s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.1.0-1 [512 kB] 152s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 152s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 152s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 152s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.17-1 [139 kB] 152s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 152s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libraqm0 armhf 0.10.3-1 [12.7 kB] 152s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 152s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 152s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 152s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 152s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 152s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 152s Get:35 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-charset-normalizer armhf 3.4.4-1 [167 kB] 152s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libopenjp2-7 armhf 2.5.3-2.1 [174 kB] 152s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pil armhf 12.0.0-1ubuntu1 [462 kB] 152s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cairo armhf 1.27.0-2build1 [135 kB] 152s Get:39 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-freetype all 2.5.1-2 [92.2 kB] 152s Get:40 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rlpycairo all 0.3.0-4 [9332 B] 152s Get:41 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-reportlab all 4.4.5-1 [1148 kB] 152s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 152s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19 [20.3 kB] 152s Get:44 http://ftpmaster.internal/ubuntu resolute/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 152s Get:45 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython armhf 1.86+dfsg-1 [1652 kB] 152s Get:46 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-peptidebuilder all 1.1.0-3 [13.3 kB] 153s Fetched 25.1 MB in 4s (6442 kB/s) 153s Selecting previously unselected package python3-numpy-dev:armhf. 153s (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.) 153s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 153s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 153s Selecting previously unselected package libblas3:armhf. 153s Preparing to unpack .../01-libblas3_3.12.1-7_armhf.deb ... 153s Unpacking libblas3:armhf (3.12.1-7) ... 153s Selecting previously unselected package libgfortran5:armhf. 153s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_armhf.deb ... 153s Unpacking libgfortran5:armhf (15.2.0-9ubuntu1) ... 153s Selecting previously unselected package liblapack3:armhf. 153s Preparing to unpack .../03-liblapack3_3.12.1-7_armhf.deb ... 153s Unpacking liblapack3:armhf (3.12.1-7) ... 153s Selecting previously unselected package python3-numpy. 153s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 153s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 153s Selecting previously unselected package libfontenc1:armhf. 153s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build2_armhf.deb ... 153s Unpacking libfontenc1:armhf (1:1.1.8-1build2) ... 153s Selecting previously unselected package libfreetype6:armhf. 153s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1build1_armhf.deb ... 153s Unpacking libfreetype6:armhf (2.13.3+dfsg-1build1) ... 153s Selecting previously unselected package x11-common. 153s Preparing to unpack .../07-x11-common_1%3a7.7+24ubuntu1_all.deb ... 153s Unpacking x11-common (1:7.7+24ubuntu1) ... 153s Selecting previously unselected package xfonts-encodings. 153s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 153s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 153s Selecting previously unselected package xfonts-utils. 153s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 153s Unpacking xfonts-utils (1:7.7+7) ... 153s Selecting previously unselected package fonts-urw-base35. 153s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 154s Unpacking fonts-urw-base35 (20200910-8) ... 154s Selecting previously unselected package fontconfig-config. 154s Preparing to unpack .../11-fontconfig-config_2.15.0-2.3ubuntu1_armhf.deb ... 154s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 154s Selecting previously unselected package libfontconfig1:armhf. 154s Preparing to unpack .../12-libfontconfig1_2.15.0-2.3ubuntu1_armhf.deb ... 154s Unpacking libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 154s Selecting previously unselected package libpixman-1-0:armhf. 154s Preparing to unpack .../13-libpixman-1-0_0.46.4-1_armhf.deb ... 154s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 154s Selecting previously unselected package libxcb-render0:armhf. 154s Preparing to unpack .../14-libxcb-render0_1.17.0-2build1_armhf.deb ... 154s Unpacking libxcb-render0:armhf (1.17.0-2build1) ... 154s Selecting previously unselected package libxcb-shm0:armhf. 154s Preparing to unpack .../15-libxcb-shm0_1.17.0-2build1_armhf.deb ... 154s Unpacking libxcb-shm0:armhf (1.17.0-2build1) ... 154s Selecting previously unselected package libxrender1:armhf. 154s Preparing to unpack .../16-libxrender1_1%3a0.9.12-1_armhf.deb ... 154s Unpacking libxrender1:armhf (1:0.9.12-1) ... 154s Selecting previously unselected package libcairo2:armhf. 154s Preparing to unpack .../17-libcairo2_1.18.4-1build1_armhf.deb ... 154s Unpacking libcairo2:armhf (1.18.4-1build1) ... 154s Selecting previously unselected package libdeflate0:armhf. 154s Preparing to unpack .../18-libdeflate0_1.23-2_armhf.deb ... 154s Unpacking libdeflate0:armhf (1.23-2) ... 154s Selecting previously unselected package libgomp1:armhf. 154s Preparing to unpack .../19-libgomp1_15.2.0-9ubuntu1_armhf.deb ... 154s Unpacking libgomp1:armhf (15.2.0-9ubuntu1) ... 154s Selecting previously unselected package libgraphite2-3:armhf. 154s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 154s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 154s Selecting previously unselected package libharfbuzz0b:armhf. 154s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_armhf.deb ... 154s Unpacking libharfbuzz0b:armhf (12.1.0-1) ... 154s Selecting previously unselected package libimagequant0:armhf. 154s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_armhf.deb ... 154s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 154s Selecting previously unselected package libjpeg-turbo8:armhf. 154s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 154s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 154s Selecting previously unselected package libjpeg8:armhf. 154s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 154s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 154s Selecting previously unselected package liblcms2-2:armhf. 154s Preparing to unpack .../25-liblcms2-2_2.17-1_armhf.deb ... 154s Unpacking liblcms2-2:armhf (2.17-1) ... 154s Selecting previously unselected package liblerc4:armhf. 154s Preparing to unpack .../26-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 154s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 154s Selecting previously unselected package libraqm0:armhf. 154s Preparing to unpack .../27-libraqm0_0.10.3-1_armhf.deb ... 154s Unpacking libraqm0:armhf (0.10.3-1) ... 154s Selecting previously unselected package libsharpyuv0:armhf. 154s Preparing to unpack .../28-libsharpyuv0_1.5.0-0.1_armhf.deb ... 154s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 154s Selecting previously unselected package libjbig0:armhf. 154s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 154s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 155s Selecting previously unselected package libwebp7:armhf. 155s Preparing to unpack .../30-libwebp7_1.5.0-0.1_armhf.deb ... 155s Unpacking libwebp7:armhf (1.5.0-0.1) ... 155s Selecting previously unselected package libtiff6:armhf. 155s Preparing to unpack .../31-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 155s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 155s Selecting previously unselected package libwebpdemux2:armhf. 155s Preparing to unpack .../32-libwebpdemux2_1.5.0-0.1_armhf.deb ... 155s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 155s Selecting previously unselected package libwebpmux3:armhf. 155s Preparing to unpack .../33-libwebpmux3_1.5.0-0.1_armhf.deb ... 155s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 155s Selecting previously unselected package python3-charset-normalizer. 155s Preparing to unpack .../34-python3-charset-normalizer_3.4.4-1_armhf.deb ... 155s Unpacking python3-charset-normalizer (3.4.4-1) ... 155s Selecting previously unselected package libopenjp2-7:armhf. 155s Preparing to unpack .../35-libopenjp2-7_2.5.3-2.1_armhf.deb ... 155s Unpacking libopenjp2-7:armhf (2.5.3-2.1) ... 155s Selecting previously unselected package python3-pil:armhf. 155s Preparing to unpack .../36-python3-pil_12.0.0-1ubuntu1_armhf.deb ... 155s Unpacking python3-pil:armhf (12.0.0-1ubuntu1) ... 155s Selecting previously unselected package python3-cairo. 155s Preparing to unpack .../37-python3-cairo_1.27.0-2build1_armhf.deb ... 155s Unpacking python3-cairo (1.27.0-2build1) ... 155s Selecting previously unselected package python3-freetype. 155s Preparing to unpack .../38-python3-freetype_2.5.1-2_all.deb ... 155s Unpacking python3-freetype (2.5.1-2) ... 155s Selecting previously unselected package python3-rlpycairo. 155s Preparing to unpack .../39-python3-rlpycairo_0.3.0-4_all.deb ... 155s Unpacking python3-rlpycairo (0.3.0-4) ... 155s Selecting previously unselected package python3-reportlab. 155s Preparing to unpack .../40-python3-reportlab_4.4.5-1_all.deb ... 155s Unpacking python3-reportlab (4.4.5-1) ... 155s Selecting previously unselected package sgml-base. 155s Preparing to unpack .../41-sgml-base_1.31+nmu1_all.deb ... 155s Unpacking sgml-base (1.31+nmu1) ... 155s Selecting previously unselected package xml-core. 155s Preparing to unpack .../42-xml-core_0.19_all.deb ... 155s Unpacking xml-core (0.19) ... 155s Selecting previously unselected package w3c-sgml-lib. 155s Preparing to unpack .../43-w3c-sgml-lib_1.3-3_all.deb ... 155s Unpacking w3c-sgml-lib (1.3-3) ... 155s Selecting previously unselected package python3-biopython. 155s Preparing to unpack .../44-python3-biopython_1.86+dfsg-1_armhf.deb ... 155s Unpacking python3-biopython (1.86+dfsg-1) ... 155s Selecting previously unselected package python3-peptidebuilder. 155s Preparing to unpack .../45-python3-peptidebuilder_1.1.0-3_all.deb ... 155s Unpacking python3-peptidebuilder (1.1.0-3) ... 155s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 155s Setting up liblcms2-2:armhf (2.17-1) ... 155s Setting up libpixman-1-0:armhf (0.46.4-1) ... 155s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 155s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 155s Setting up libxrender1:armhf (1:0.9.12-1) ... 155s Setting up libxcb-render0:armhf (1.17.0-2build1) ... 155s Setting up python3-charset-normalizer (3.4.4-1) ... 155s Setting up x11-common (1:7.7+24ubuntu1) ... 156s Setting up libdeflate0:armhf (1.23-2) ... 156s Setting up libxcb-shm0:armhf (1.17.0-2build1) ... 156s Setting up libgomp1:armhf (15.2.0-9ubuntu1) ... 156s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 156s Setting up libfontenc1:armhf (1:1.1.8-1build2) ... 156s Setting up libblas3:armhf (3.12.1-7) ... 156s 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 156s Setting up libfreetype6:armhf (2.13.3+dfsg-1build1) ... 156s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 156s Setting up libimagequant0:armhf (2.18.0-1build1) ... 156s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 156s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 156s Setting up libgfortran5:armhf (15.2.0-9ubuntu1) ... 156s Setting up libwebp7:armhf (1.5.0-0.1) ... 156s Setting up libopenjp2-7:armhf (2.5.3-2.1) ... 156s Setting up libharfbuzz0b:armhf (12.1.0-1) ... 156s Setting up sgml-base (1.31+nmu1) ... 156s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 156s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 156s Setting up liblapack3:armhf (3.12.1-7) ... 156s 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 156s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 156s Setting up python3-freetype (2.5.1-2) ... 156s Setting up xfonts-utils (1:7.7+7) ... 156s Setting up libraqm0:armhf (0.10.3-1) ... 156s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 158s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 158s Setting up xml-core (0.19) ... 158s Setting up fonts-urw-base35 (20200910-8) ... 158s Setting up python3-pil:armhf (12.0.0-1ubuntu1) ... 158s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 159s Setting up libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 159s Setting up libcairo2:armhf (1.18.4-1build1) ... 159s Setting up python3-cairo (1.27.0-2build1) ... 159s Setting up python3-rlpycairo (0.3.0-4) ... 159s Setting up python3-reportlab (4.4.5-1) ... 160s Processing triggers for libc-bin (2.42-2ubuntu2) ... 160s Processing triggers for man-db (2.13.1-1) ... 161s Processing triggers for sgml-base (1.31+nmu1) ... 161s Setting up w3c-sgml-lib (1.3-3) ... 188s Setting up python3-biopython (1.86+dfsg-1) ... 189s Setting up python3-peptidebuilder (1.1.0-3) ... 198s autopkgtest [11:36:59]: test run-unit-test: [----------------------- 199s Test 1 200s ATOM 1 N GLY A 1 -0.521 1.364 0.000 1.00 0.00 N 200s ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 200s ATOM 3 C GLY A 1 1.520 0.000 0.000 1.00 0.00 C 200s ATOM 4 O GLY A 1 2.144 -0.812 0.681 1.00 0.00 O 200s ATOM 5 N GLY A 2 2.116 0.911 -0.764 1.00 0.00 N 200s ATOM 6 CA GLY A 2 3.571 1.003 -0.842 1.00 0.00 C 200s ATOM 7 C GLY A 2 4.170 1.286 0.526 1.00 0.00 C 200s ATOM 8 O GLY A 2 5.209 0.730 0.881 1.00 0.00 O 200s ATOM 9 N GLY A 3 3.516 2.151 1.297 1.00 0.00 N 200s ATOM 10 CA GLY A 3 3.999 2.498 2.630 1.00 0.00 C 200s ATOM 11 C GLY A 3 4.074 1.266 3.517 1.00 0.00 C 200s ATOM 12 O GLY A 3 5.018 1.109 4.290 1.00 0.00 O 200s ATOM 13 N GLY A 4 3.079 0.390 3.407 1.00 0.00 N 200s ATOM 14 CA GLY A 4 3.046 -0.829 4.210 1.00 0.00 C 200s ATOM 15 C GLY A 4 4.268 -1.691 3.936 1.00 0.00 C 200s ATOM 16 O GLY A 4 4.839 -2.275 4.856 1.00 0.00 O 200s ATOM 17 N GLY A 5 4.671 -1.770 2.671 1.00 0.00 N 200s ATOM 18 CA GLY A 5 5.832 -2.569 2.291 1.00 0.00 C 200s ATOM 19 C GLY A 5 7.084 -2.076 2.999 1.00 0.00 C 200s ATOM 20 O GLY A 5 7.910 -2.875 3.437 1.00 0.00 O 200s ATOM 21 N GLY A 6 7.225 -0.758 3.112 1.00 0.00 N 200s ATOM 22 CA GLY A 6 8.387 -0.172 3.773 1.00 0.00 C 200s ATOM 23 C GLY A 6 8.479 -0.633 5.219 1.00 0.00 C 200s ATOM 24 O GLY A 6 9.395 -0.244 5.941 1.00 0.00 O 200s ATOM 25 OXT GLY A 6 7.638 -1.400 5.684 1.00 0.00 O 200s TER 26 GLY A 6 200s END 200s PASS 200s Test 2 227s 1aq7 227s 1gfl 227s 1nbw 227s 1vca 227s 2o6r 227s 2r83 227s 3cap 227s 3cuq 227s 3vni 227s 7tim 227s PDBs/Aligned_150_AllAngles_1aq7_clean.pdb 227s PDBs/Aligned_150_AllAngles_1gfl_clean.pdb 227s PDBs/Aligned_150_AllAngles_1nbw_clean.pdb 227s PDBs/Aligned_150_AllAngles_1vca_clean.pdb 227s PDBs/Aligned_150_AllAngles_2o6r_clean.pdb 227s PDBs/Aligned_150_AllAngles_2r83_clean.pdb 227s PDBs/Aligned_150_AllAngles_3cap_clean.pdb 227s PDBs/Aligned_150_AllAngles_3cuq_clean.pdb 227s PDBs/Aligned_150_AllAngles_3vni_clean.pdb 227s PDBs/Aligned_150_AllAngles_7tim_clean.pdb 227s PDBs/Aligned_150_Backbone_1aq7_clean.pdb 227s PDBs/Aligned_150_Backbone_1gfl_clean.pdb 227s PDBs/Aligned_150_Backbone_1nbw_clean.pdb 227s PDBs/Aligned_150_Backbone_1vca_clean.pdb 227s PDBs/Aligned_150_Backbone_2o6r_clean.pdb 227s PDBs/Aligned_150_Backbone_2r83_clean.pdb 227s PDBs/Aligned_150_Backbone_3cap_clean.pdb 227s PDBs/Aligned_150_Backbone_3cuq_clean.pdb 227s PDBs/Aligned_150_Backbone_3vni_clean.pdb 227s PDBs/Aligned_150_Backbone_7tim_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_1aq7_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_1gfl_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_1nbw_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_1vca_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_2o6r_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_2r83_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_3cap_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_3cuq_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_3vni_clean.pdb 227s PDBs/Aligned_150_PhiPsiOmega_7tim_clean.pdb 227s PDBs/Aligned_150_PhiPsi_1aq7_clean.pdb 227s PDBs/Aligned_150_PhiPsi_1gfl_clean.pdb 227s PDBs/Aligned_150_PhiPsi_1nbw_clean.pdb 227s PDBs/Aligned_150_PhiPsi_1vca_clean.pdb 227s PDBs/Aligned_150_PhiPsi_2o6r_clean.pdb 227s PDBs/Aligned_150_PhiPsi_2r83_clean.pdb 227s PDBs/Aligned_150_PhiPsi_3cap_clean.pdb 227s PDBs/Aligned_150_PhiPsi_3cuq_clean.pdb 227s PDBs/Aligned_150_PhiPsi_3vni_clean.pdb 227s PDBs/Aligned_150_PhiPsi_7tim_clean.pdb 227s PDBs/Aligned_50_AllAngles_1aq7_clean.pdb 227s PDBs/Aligned_50_AllAngles_1gfl_clean.pdb 227s PDBs/Aligned_50_AllAngles_1nbw_clean.pdb 227s PDBs/Aligned_50_AllAngles_1vca_clean.pdb 227s PDBs/Aligned_50_AllAngles_2o6r_clean.pdb 227s PDBs/Aligned_50_AllAngles_2r83_clean.pdb 227s PDBs/Aligned_50_AllAngles_3cap_clean.pdb 227s PDBs/Aligned_50_AllAngles_3cuq_clean.pdb 227s PDBs/Aligned_50_AllAngles_3vni_clean.pdb 227s PDBs/Aligned_50_AllAngles_7tim_clean.pdb 227s PDBs/Aligned_50_Backbone_1aq7_clean.pdb 227s PDBs/Aligned_50_Backbone_1gfl_clean.pdb 227s PDBs/Aligned_50_Backbone_1nbw_clean.pdb 227s PDBs/Aligned_50_Backbone_1vca_clean.pdb 227s PDBs/Aligned_50_Backbone_2o6r_clean.pdb 227s PDBs/Aligned_50_Backbone_2r83_clean.pdb 227s PDBs/Aligned_50_Backbone_3cap_clean.pdb 227s PDBs/Aligned_50_Backbone_3cuq_clean.pdb 227s PDBs/Aligned_50_Backbone_3vni_clean.pdb 227s PDBs/Aligned_50_Backbone_7tim_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_1aq7_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_1gfl_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_1nbw_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_1vca_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_2o6r_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_2r83_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_3cap_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_3cuq_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_3vni_clean.pdb 227s PDBs/Aligned_50_PhiPsiOmega_7tim_clean.pdb 227s PDBs/Aligned_50_PhiPsi_1aq7_clean.pdb 227s PDBs/Aligned_50_PhiPsi_1gfl_clean.pdb 227s PDBs/Aligned_50_PhiPsi_1nbw_clean.pdb 227s PDBs/Aligned_50_PhiPsi_1vca_clean.pdb 227s PDBs/Aligned_50_PhiPsi_2o6r_clean.pdb 227s PDBs/Aligned_50_PhiPsi_2r83_clean.pdb 227s PDBs/Aligned_50_PhiPsi_3cap_clean.pdb 227s PDBs/Aligned_50_PhiPsi_3cuq_clean.pdb 227s PDBs/Aligned_50_PhiPsi_3vni_clean.pdb 227s PDBs/Aligned_50_PhiPsi_7tim_clean.pdb 227s PDBs/Aligned_AllAngles_1aq7_clean.pdb 227s PDBs/Aligned_AllAngles_1gfl_clean.pdb 227s PDBs/Aligned_AllAngles_1nbw_clean.pdb 227s PDBs/Aligned_AllAngles_1vca_clean.pdb 227s PDBs/Aligned_AllAngles_2o6r_clean.pdb 227s PDBs/Aligned_AllAngles_2r83_clean.pdb 227s PDBs/Aligned_AllAngles_3cap_clean.pdb 227s PDBs/Aligned_AllAngles_3cuq_clean.pdb 227s PDBs/Aligned_AllAngles_3vni_clean.pdb 227s PDBs/Aligned_AllAngles_7tim_clean.pdb 227s PDBs/Aligned_Backbone_1aq7_clean.pdb 227s PDBs/Aligned_Backbone_1gfl_clean.pdb 227s PDBs/Aligned_Backbone_1nbw_clean.pdb 227s PDBs/Aligned_Backbone_1vca_clean.pdb 227s PDBs/Aligned_Backbone_2o6r_clean.pdb 227s PDBs/Aligned_Backbone_2r83_clean.pdb 227s PDBs/Aligned_Backbone_3cap_clean.pdb 227s PDBs/Aligned_Backbone_3cuq_clean.pdb 227s PDBs/Aligned_Backbone_3vni_clean.pdb 227s PDBs/Aligned_Backbone_7tim_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_1aq7_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_1gfl_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_1nbw_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_1vca_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_2o6r_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_2r83_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_3cap_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_3cuq_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_3vni_clean.pdb 227s PDBs/Aligned_PhiPsiOmega_7tim_clean.pdb 227s PDBs/Aligned_PhiPsi_1aq7_clean.pdb 227s PDBs/Aligned_PhiPsi_1gfl_clean.pdb 227s PDBs/Aligned_PhiPsi_1nbw_clean.pdb 227s PDBs/Aligned_PhiPsi_1vca_clean.pdb 227s PDBs/Aligned_PhiPsi_2o6r_clean.pdb 227s PDBs/Aligned_PhiPsi_2r83_clean.pdb 227s PDBs/Aligned_PhiPsi_3cap_clean.pdb 227s PDBs/Aligned_PhiPsi_3cuq_clean.pdb 227s PDBs/Aligned_PhiPsi_3vni_clean.pdb 227s PDBs/Aligned_PhiPsi_7tim_clean.pdb 227s PDBs/AllAngles_1aq7_clean.pdb 227s PDBs/AllAngles_1gfl_clean.pdb 227s PDBs/AllAngles_1nbw_clean.pdb 227s PDBs/AllAngles_1vca_clean.pdb 227s PDBs/AllAngles_2o6r_clean.pdb 227s PDBs/AllAngles_2r83_clean.pdb 227s PDBs/AllAngles_3cap_clean.pdb 227s PDBs/AllAngles_3cuq_clean.pdb 227s PDBs/AllAngles_3vni_clean.pdb 227s PDBs/AllAngles_7tim_clean.pdb 227s PDBs/Backbone_1aq7_clean.pdb 227s PDBs/Backbone_1gfl_clean.pdb 227s PDBs/Backbone_1nbw_clean.pdb 227s PDBs/Backbone_1vca_clean.pdb 227s PDBs/Backbone_2o6r_clean.pdb 227s PDBs/Backbone_2r83_clean.pdb 227s PDBs/Backbone_3cap_clean.pdb 227s PDBs/Backbone_3cuq_clean.pdb 227s PDBs/Backbone_3vni_clean.pdb 227s PDBs/Backbone_7tim_clean.pdb 227s PDBs/PhiPsiOmega_1aq7_clean.pdb 227s PDBs/PhiPsiOmega_1gfl_clean.pdb 227s PDBs/PhiPsiOmega_1nbw_clean.pdb 227s PDBs/PhiPsiOmega_1vca_clean.pdb 227s PDBs/PhiPsiOmega_2o6r_clean.pdb 227s PDBs/PhiPsiOmega_2r83_clean.pdb 227s PDBs/PhiPsiOmega_3cap_clean.pdb 227s PDBs/PhiPsiOmega_3cuq_clean.pdb 227s PDBs/PhiPsiOmega_3vni_clean.pdb 227s PDBs/PhiPsiOmega_7tim_clean.pdb 227s PDBs/PhiPsi_1aq7_clean.pdb 227s PDBs/PhiPsi_1gfl_clean.pdb 227s PDBs/PhiPsi_1nbw_clean.pdb 227s PDBs/PhiPsi_1vca_clean.pdb 227s PDBs/PhiPsi_2o6r_clean.pdb 227s PDBs/PhiPsi_2r83_clean.pdb 227s PDBs/PhiPsi_3cap_clean.pdb 227s PDBs/PhiPsi_3cuq_clean.pdb 227s PDBs/PhiPsi_3vni_clean.pdb 227s PDBs/PhiPsi_7tim_clean.pdb 227s PASS 227s autopkgtest [11:37:28]: test run-unit-test: -----------------------] 231s run-unit-test PASS 231s autopkgtest [11:37:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 235s autopkgtest [11:37:36]: @@@@@@@@@@@@@@@@@@@@ summary 235s run-unit-test PASS