0s autopkgtest [15:32:37]: starting date and time: 2025-12-03 15:32:37+0000 0s autopkgtest [15:32:37]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:32:37]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.up8evalz/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 peptidebuilder --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@sto01-3.secgroup --name adt-resolute-i386-peptidebuilder-20251203-153237-juju-7f2275-prod-proposed-migration-environment-15-e9215816-2f07-45fc-abf2-62a986a40f6a --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-peptidebuilder-20251203-153237-juju-7f2275-prod-proposed-migration-environment-15-e9215816-2f07-45fc-abf2-62a986a40f6a from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 46s autopkgtest [15:33:23]: testbed dpkg architecture: amd64 46s autopkgtest [15:33:23]: testbed apt version: 3.1.12 47s autopkgtest [15:33:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [15:33:24]: testbed release detected to be: None 48s autopkgtest [15:33:25]: updating testbed package index (apt update) 48s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 48s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [984 kB] 49s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.5 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [148 kB] 49s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [202 kB] 49s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [156 kB] 49s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6168 B] 49s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 49s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [745 kB] 49s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [334 kB] 49s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.3 kB] 49s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [10.6 kB] 49s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4780 B] 49s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [828 B] 50s Fetched 2764 kB in 1s (1885 kB/s) 50s Reading package lists... 51s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Reading package lists... 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s The following packages will be upgraded: 52s libpython3-stdlib python3 python3-gdbm python3-minimal 52s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 72.9 kB of archives. 52s After this operation, 2048 B of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 52s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 52s dpkg-preconfigure: unable to re-open stdin: No such file or directory 52s Fetched 72.9 kB in 0s (3519 kB/s) 52s (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.) 52s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 52s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 52s Setting up python3-minimal (3.13.9-2) ... 52s (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.) 52s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 52s running python pre-rtupdate hooks for python3.13... 52s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 52s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 52s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 52s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 52s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 52s Setting up python3-gdbm (3.13.9-2) ... 52s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 52s Setting up python3 (3.13.9-2) ... 52s running python rtupdate hooks for python3.13... 52s running python post-rtupdate hooks for python3.13... 53s Processing triggers for man-db (2.13.1-1) ... 53s autopkgtest [15:33:30]: upgrading testbed (apt dist-upgrade and autopurge) 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Solving dependencies... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [15:33:33]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 56s autopkgtest [15:33:33]: @@@@@@@@@@@@@@@@@@@@ apt-source peptidebuilder 57s Get:1 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (dsc) [2239 B] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (tar) [468 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (diff) [4016 B] 57s gpgv: Signature made Fri Oct 8 20:54:03 2021 UTC 57s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 57s gpgv: issuer "tille@debian.org" 57s gpgv: Can't check signature: No public key 57s dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found 57s autopkgtest [15:33:34]: testing package peptidebuilder version 1.1.0-3 57s autopkgtest [15:33:34]: build not needed 58s autopkgtest [15:33:35]: test run-unit-test: preparing testbed 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 58s The following NEW packages will be installed: 58s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 58s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 58s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 58s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 58s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 58s libxrender1 python3-biopython python3-cairo python3-charset-normalizer 58s python3-freetype python3-numpy python3-numpy-dev python3-peptidebuilder 58s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 58s x11-common xfonts-encodings xfonts-utils xml-core 58s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 28.7 MB of archives. 58s After this operation, 93.0 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 58s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 58s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 58s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 59s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 59s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 59s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 59s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 59s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 59s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 59s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 59s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 59s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 59s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 59s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 59s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 59s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 59s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 59s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 59s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 59s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 59s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 59s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 59s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 59s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 59s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 59s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 59s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 59s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 59s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 59s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 59s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 59s Get:34 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-1 [175 kB] 59s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 59s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 59s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 59s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 59s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 59s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.5-1 [1148 kB] 59s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 59s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 59s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 59s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 59s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-peptidebuilder all 1.1.0-3 [13.3 kB] 59s Fetched 28.7 MB in 1s (28.1 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) ... 60s Selecting previously unselected package libgfortran5:amd64. 60s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 60s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 60s Selecting previously unselected package liblapack3:amd64. 60s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 60s Unpacking liblapack3:amd64 (3.12.1-7) ... 60s Selecting previously unselected package python3-numpy. 60s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 60s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 60s Selecting previously unselected package libfontenc1:amd64. 60s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 60s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 60s Selecting previously unselected package x11-common. 60s Preparing to unpack .../06-x11-common_1%3a7.7+24ubuntu1_all.deb ... 60s Unpacking x11-common (1:7.7+24ubuntu1) ... 60s Selecting previously unselected package xfonts-encodings. 60s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 60s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 60s Selecting previously unselected package xfonts-utils. 60s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 60s Unpacking xfonts-utils (1:7.7+7) ... 60s Selecting previously unselected package fonts-urw-base35. 60s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 60s Unpacking fonts-urw-base35 (20200910-8) ... 60s Selecting previously unselected package fontconfig-config. 60s Preparing to unpack .../10-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 60s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 60s Selecting previously unselected package libfontconfig1:amd64. 60s Preparing to unpack .../11-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 60s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 60s Selecting previously unselected package libpixman-1-0:amd64. 60s Preparing to unpack .../12-libpixman-1-0_0.46.4-1_amd64.deb ... 60s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 60s Selecting previously unselected package libxcb-render0:amd64. 60s Preparing to unpack .../13-libxcb-render0_1.17.0-2build1_amd64.deb ... 60s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 60s Selecting previously unselected package libxcb-shm0:amd64. 60s Preparing to unpack .../14-libxcb-shm0_1.17.0-2build1_amd64.deb ... 60s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 60s Selecting previously unselected package libxrender1:amd64. 60s Preparing to unpack .../15-libxrender1_1%3a0.9.12-1_amd64.deb ... 60s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 60s Selecting previously unselected package libcairo2:amd64. 60s Preparing to unpack .../16-libcairo2_1.18.4-1build1_amd64.deb ... 60s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 60s Selecting previously unselected package libdeflate0:amd64. 60s Preparing to unpack .../17-libdeflate0_1.23-2_amd64.deb ... 60s Unpacking libdeflate0:amd64 (1.23-2) ... 60s Selecting previously unselected package libgomp1:amd64. 60s Preparing to unpack .../18-libgomp1_15.2.0-9ubuntu1_amd64.deb ... 60s Unpacking libgomp1:amd64 (15.2.0-9ubuntu1) ... 60s Selecting previously unselected package libgraphite2-3:amd64. 60s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 60s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 60s Selecting previously unselected package libharfbuzz0b:amd64. 60s Preparing to unpack .../20-libharfbuzz0b_12.1.0-1_amd64.deb ... 60s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 60s Selecting previously unselected package libimagequant0:amd64. 60s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 60s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 60s Selecting previously unselected package libjpeg-turbo8:amd64. 60s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 60s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 60s Selecting previously unselected package libjpeg8:amd64. 60s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 60s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 60s Selecting previously unselected package liblcms2-2:amd64. 60s Preparing to unpack .../24-liblcms2-2_2.17-1_amd64.deb ... 60s Unpacking liblcms2-2:amd64 (2.17-1) ... 60s Selecting previously unselected package liblerc4:amd64. 60s Preparing to unpack .../25-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 60s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 60s Selecting previously unselected package libraqm0:amd64. 60s Preparing to unpack .../26-libraqm0_0.10.3-1_amd64.deb ... 60s Unpacking libraqm0:amd64 (0.10.3-1) ... 60s Selecting previously unselected package libsharpyuv0:amd64. 60s Preparing to unpack .../27-libsharpyuv0_1.5.0-0.1_amd64.deb ... 60s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 60s Selecting previously unselected package libjbig0:amd64. 60s Preparing to unpack .../28-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 60s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 60s Selecting previously unselected package libwebp7:amd64. 60s Preparing to unpack .../29-libwebp7_1.5.0-0.1_amd64.deb ... 60s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 60s Selecting previously unselected package libtiff6:amd64. 60s Preparing to unpack .../30-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 60s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 60s Selecting previously unselected package libwebpdemux2:amd64. 60s Preparing to unpack .../31-libwebpdemux2_1.5.0-0.1_amd64.deb ... 60s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 60s Selecting previously unselected package libwebpmux3:amd64. 60s Preparing to unpack .../32-libwebpmux3_1.5.0-0.1_amd64.deb ... 60s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 60s Selecting previously unselected package python3-charset-normalizer. 60s Preparing to unpack .../33-python3-charset-normalizer_3.4.4-1_amd64.deb ... 60s Unpacking python3-charset-normalizer (3.4.4-1) ... 60s Selecting previously unselected package libopenjp2-7:amd64. 60s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_amd64.deb ... 60s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 60s Selecting previously unselected package python3-pil:amd64. 60s Preparing to unpack .../35-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 60s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 60s Selecting previously unselected package python3-cairo. 60s Preparing to unpack .../36-python3-cairo_1.27.0-2build1_amd64.deb ... 60s Unpacking python3-cairo (1.27.0-2build1) ... 60s Selecting previously unselected package python3-freetype. 60s Preparing to unpack .../37-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 .../38-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 .../39-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 .../40-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 .../41-xml-core_0.19_all.deb ... 60s Unpacking xml-core (0.19) ... 60s Selecting previously unselected package w3c-sgml-lib. 60s Preparing to unpack .../42-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 .../43-python3-biopython_1.86+dfsg-1_amd64.deb ... 60s Unpacking python3-biopython (1.86+dfsg-1) ... 60s Selecting previously unselected package python3-peptidebuilder. 60s Preparing to unpack .../44-python3-peptidebuilder_1.1.0-3_all.deb ... 60s Unpacking python3-peptidebuilder (1.1.0-3) ... 60s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 60s Setting up liblcms2-2:amd64 (2.17-1) ... 60s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 60s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 60s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 60s Setting up libxrender1:amd64 (1:0.9.12-1) ... 60s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 60s Setting up python3-charset-normalizer (3.4.4-1) ... 60s Setting up x11-common (1:7.7+24ubuntu1) ... 61s Setting up libdeflate0:amd64 (1.23-2) ... 61s Setting up 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 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 libwebp7:amd64 (1.5.0-0.1) ... 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 libjpeg8:amd64 (8c-2ubuntu11) ... 61s Setting up liblapack3:amd64 (3.12.1-7) ... 61s 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 61s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 61s Setting up xfonts-utils (1:7.7+7) ... 61s Setting up libraqm0:amd64 (0.10.3-1) ... 61s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 62s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 62s Setting up xml-core (0.19) ... 62s Setting up fonts-urw-base35 (20200910-8) ... 62s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 62s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 62s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 62s Setting up libcairo2:amd64 (1.18.4-1build1) ... 62s Setting up python3-cairo (1.27.0-2build1) ... 62s Setting up python3-rlpycairo (0.3.0-4) ... 62s Setting up python3-reportlab (4.4.5-1) ... 63s Processing triggers for libc-bin (2.42-2ubuntu2) ... 63s Processing triggers for man-db (2.13.1-1) ... 63s Processing triggers for sgml-base (1.31+nmu1) ... 63s Setting up w3c-sgml-lib (1.3-3) ... 79s Setting up python3-biopython (1.86+dfsg-1) ... 80s Setting up python3-peptidebuilder (1.1.0-3) ... 81s autopkgtest [15:33:58]: test environment configured for cross building 81s autopkgtest [15:33:58]: test run-unit-test: [----------------------- 81s Test 1 81s ATOM 1 N GLY A 1 -0.521 1.364 0.000 1.00 0.00 N 81s ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 81s ATOM 3 C GLY A 1 1.520 0.000 0.000 1.00 0.00 C 81s ATOM 4 O GLY A 1 2.144 -0.812 0.681 1.00 0.00 O 81s ATOM 5 N GLY A 2 2.116 0.911 -0.764 1.00 0.00 N 81s ATOM 6 CA GLY A 2 3.571 1.003 -0.842 1.00 0.00 C 81s ATOM 7 C GLY A 2 4.170 1.286 0.526 1.00 0.00 C 81s ATOM 8 O GLY A 2 5.209 0.730 0.881 1.00 0.00 O 81s ATOM 9 N GLY A 3 3.516 2.151 1.297 1.00 0.00 N 81s ATOM 10 CA GLY A 3 3.999 2.498 2.630 1.00 0.00 C 81s ATOM 11 C GLY A 3 4.074 1.266 3.517 1.00 0.00 C 81s ATOM 12 O GLY A 3 5.018 1.109 4.290 1.00 0.00 O 81s ATOM 13 N GLY A 4 3.079 0.390 3.407 1.00 0.00 N 81s ATOM 14 CA GLY A 4 3.046 -0.829 4.210 1.00 0.00 C 81s ATOM 15 C GLY A 4 4.268 -1.691 3.936 1.00 0.00 C 81s ATOM 16 O GLY A 4 4.839 -2.275 4.856 1.00 0.00 O 81s ATOM 17 N GLY A 5 4.671 -1.770 2.671 1.00 0.00 N 81s ATOM 18 CA GLY A 5 5.832 -2.569 2.291 1.00 0.00 C 81s ATOM 19 C GLY A 5 7.084 -2.076 2.999 1.00 0.00 C 81s ATOM 20 O GLY A 5 7.910 -2.875 3.437 1.00 0.00 O 81s ATOM 21 N GLY A 6 7.225 -0.758 3.112 1.00 0.00 N 81s ATOM 22 CA GLY A 6 8.387 -0.172 3.773 1.00 0.00 C 81s ATOM 23 C GLY A 6 8.479 -0.633 5.219 1.00 0.00 C 81s ATOM 24 O GLY A 6 9.395 -0.244 5.941 1.00 0.00 O 81s ATOM 25 OXT GLY A 6 7.638 -1.400 5.684 1.00 0.00 O 81s TER 26 GLY A 6 81s END 81s PASS 81s Test 2 94s 1aq7 94s 1gfl 94s 1nbw 94s 1vca 94s 2o6r 94s 2r83 94s 3cap 94s 3cuq 94s 3vni 94s 7tim 94s PDBs/Aligned_150_AllAngles_1aq7_clean.pdb 94s PDBs/Aligned_150_AllAngles_1gfl_clean.pdb 94s PDBs/Aligned_150_AllAngles_1nbw_clean.pdb 94s PDBs/Aligned_150_AllAngles_1vca_clean.pdb 94s PDBs/Aligned_150_AllAngles_2o6r_clean.pdb 94s PDBs/Aligned_150_AllAngles_2r83_clean.pdb 94s PDBs/Aligned_150_AllAngles_3cap_clean.pdb 94s PDBs/Aligned_150_AllAngles_3cuq_clean.pdb 94s PDBs/Aligned_150_AllAngles_3vni_clean.pdb 94s PDBs/Aligned_150_AllAngles_7tim_clean.pdb 94s PDBs/Aligned_150_Backbone_1aq7_clean.pdb 94s PDBs/Aligned_150_Backbone_1gfl_clean.pdb 94s PDBs/Aligned_150_Backbone_1nbw_clean.pdb 94s PDBs/Aligned_150_Backbone_1vca_clean.pdb 94s PDBs/Aligned_150_Backbone_2o6r_clean.pdb 94s PDBs/Aligned_150_Backbone_2r83_clean.pdb 94s PDBs/Aligned_150_Backbone_3cap_clean.pdb 94s PDBs/Aligned_150_Backbone_3cuq_clean.pdb 94s PDBs/Aligned_150_Backbone_3vni_clean.pdb 94s PDBs/Aligned_150_Backbone_7tim_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_1aq7_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_1gfl_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_1nbw_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_1vca_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_2o6r_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_2r83_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_3cap_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_3cuq_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_3vni_clean.pdb 94s PDBs/Aligned_150_PhiPsiOmega_7tim_clean.pdb 94s PDBs/Aligned_150_PhiPsi_1aq7_clean.pdb 94s PDBs/Aligned_150_PhiPsi_1gfl_clean.pdb 94s PDBs/Aligned_150_PhiPsi_1nbw_clean.pdb 94s PDBs/Aligned_150_PhiPsi_1vca_clean.pdb 94s PDBs/Aligned_150_PhiPsi_2o6r_clean.pdb 94s PDBs/Aligned_150_PhiPsi_2r83_clean.pdb 94s PDBs/Aligned_150_PhiPsi_3cap_clean.pdb 94s PDBs/Aligned_150_PhiPsi_3cuq_clean.pdb 94s PDBs/Aligned_150_PhiPsi_3vni_clean.pdb 94s PDBs/Aligned_150_PhiPsi_7tim_clean.pdb 94s PDBs/Aligned_50_AllAngles_1aq7_clean.pdb 94s PDBs/Aligned_50_AllAngles_1gfl_clean.pdb 94s PDBs/Aligned_50_AllAngles_1nbw_clean.pdb 94s PDBs/Aligned_50_AllAngles_1vca_clean.pdb 94s PDBs/Aligned_50_AllAngles_2o6r_clean.pdb 94s PDBs/Aligned_50_AllAngles_2r83_clean.pdb 94s PDBs/Aligned_50_AllAngles_3cap_clean.pdb 94s PDBs/Aligned_50_AllAngles_3cuq_clean.pdb 94s PDBs/Aligned_50_AllAngles_3vni_clean.pdb 94s PDBs/Aligned_50_AllAngles_7tim_clean.pdb 94s PDBs/Aligned_50_Backbone_1aq7_clean.pdb 94s PDBs/Aligned_50_Backbone_1gfl_clean.pdb 94s PDBs/Aligned_50_Backbone_1nbw_clean.pdb 94s PDBs/Aligned_50_Backbone_1vca_clean.pdb 94s PDBs/Aligned_50_Backbone_2o6r_clean.pdb 94s PDBs/Aligned_50_Backbone_2r83_clean.pdb 94s PDBs/Aligned_50_Backbone_3cap_clean.pdb 94s PDBs/Aligned_50_Backbone_3cuq_clean.pdb 94s PDBs/Aligned_50_Backbone_3vni_clean.pdb 94s PDBs/Aligned_50_Backbone_7tim_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_1aq7_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_1gfl_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_1nbw_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_1vca_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_2o6r_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_2r83_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_3cap_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_3cuq_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_3vni_clean.pdb 94s PDBs/Aligned_50_PhiPsiOmega_7tim_clean.pdb 94s PDBs/Aligned_50_PhiPsi_1aq7_clean.pdb 94s PDBs/Aligned_50_PhiPsi_1gfl_clean.pdb 94s PDBs/Aligned_50_PhiPsi_1nbw_clean.pdb 94s PDBs/Aligned_50_PhiPsi_1vca_clean.pdb 94s PDBs/Aligned_50_PhiPsi_2o6r_clean.pdb 94s PDBs/Aligned_50_PhiPsi_2r83_clean.pdb 94s PDBs/Aligned_50_PhiPsi_3cap_clean.pdb 94s PDBs/Aligned_50_PhiPsi_3cuq_clean.pdb 94s PDBs/Aligned_50_PhiPsi_3vni_clean.pdb 94s PDBs/Aligned_50_PhiPsi_7tim_clean.pdb 94s PDBs/Aligned_AllAngles_1aq7_clean.pdb 94s PDBs/Aligned_AllAngles_1gfl_clean.pdb 94s PDBs/Aligned_AllAngles_1nbw_clean.pdb 94s PDBs/Aligned_AllAngles_1vca_clean.pdb 94s PDBs/Aligned_AllAngles_2o6r_clean.pdb 94s PDBs/Aligned_AllAngles_2r83_clean.pdb 94s PDBs/Aligned_AllAngles_3cap_clean.pdb 94s PDBs/Aligned_AllAngles_3cuq_clean.pdb 94s PDBs/Aligned_AllAngles_3vni_clean.pdb 94s PDBs/Aligned_AllAngles_7tim_clean.pdb 94s PDBs/Aligned_Backbone_1aq7_clean.pdb 94s PDBs/Aligned_Backbone_1gfl_clean.pdb 94s PDBs/Aligned_Backbone_1nbw_clean.pdb 94s PDBs/Aligned_Backbone_1vca_clean.pdb 94s PDBs/Aligned_Backbone_2o6r_clean.pdb 94s PDBs/Aligned_Backbone_2r83_clean.pdb 94s PDBs/Aligned_Backbone_3cap_clean.pdb 94s PDBs/Aligned_Backbone_3cuq_clean.pdb 94s PDBs/Aligned_Backbone_3vni_clean.pdb 94s PDBs/Aligned_Backbone_7tim_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_1aq7_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_1gfl_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_1nbw_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_1vca_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_2o6r_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_2r83_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_3cap_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_3cuq_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_3vni_clean.pdb 94s PDBs/Aligned_PhiPsiOmega_7tim_clean.pdb 94s PDBs/Aligned_PhiPsi_1aq7_clean.pdb 94s PDBs/Aligned_PhiPsi_1gfl_clean.pdb 94s PDBs/Aligned_PhiPsi_1nbw_clean.pdb 94s PDBs/Aligned_PhiPsi_1vca_clean.pdb 94s PDBs/Aligned_PhiPsi_2o6r_clean.pdb 94s PDBs/Aligned_PhiPsi_2r83_clean.pdb 94s PDBs/Aligned_PhiPsi_3cap_clean.pdb 94s PDBs/Aligned_PhiPsi_3cuq_clean.pdb 94s PDBs/Aligned_PhiPsi_3vni_clean.pdb 94s PDBs/Aligned_PhiPsi_7tim_clean.pdb 94s PDBs/AllAngles_1aq7_clean.pdb 94s PDBs/AllAngles_1gfl_clean.pdb 94s PDBs/AllAngles_1nbw_clean.pdb 94s PDBs/AllAngles_1vca_clean.pdb 94s PDBs/AllAngles_2o6r_clean.pdb 94s PDBs/AllAngles_2r83_clean.pdb 94s PDBs/AllAngles_3cap_clean.pdb 94s PDBs/AllAngles_3cuq_clean.pdb 94s PDBs/AllAngles_3vni_clean.pdb 94s PDBs/AllAngles_7tim_clean.pdb 94s PDBs/Backbone_1aq7_clean.pdb 94s PDBs/Backbone_1gfl_clean.pdb 94s PDBs/Backbone_1nbw_clean.pdb 94s PDBs/Backbone_1vca_clean.pdb 94s PDBs/Backbone_2o6r_clean.pdb 94s PDBs/Backbone_2r83_clean.pdb 94s PDBs/Backbone_3cap_clean.pdb 94s PDBs/Backbone_3cuq_clean.pdb 94s PDBs/Backbone_3vni_clean.pdb 94s PDBs/Backbone_7tim_clean.pdb 94s PDBs/PhiPsiOmega_1aq7_clean.pdb 94s PDBs/PhiPsiOmega_1gfl_clean.pdb 94s PDBs/PhiPsiOmega_1nbw_clean.pdb 94s PDBs/PhiPsiOmega_1vca_clean.pdb 94s PDBs/PhiPsiOmega_2o6r_clean.pdb 94s PDBs/PhiPsiOmega_2r83_clean.pdb 94s PDBs/PhiPsiOmega_3cap_clean.pdb 94s PDBs/PhiPsiOmega_3cuq_clean.pdb 95s PDBs/PhiPsiOmega_3vni_clean.pdb 95s PDBs/PhiPsiOmega_7tim_clean.pdb 95s PDBs/PhiPsi_1aq7_clean.pdb 95s PDBs/PhiPsi_1gfl_clean.pdb 95s PDBs/PhiPsi_1nbw_clean.pdb 95s PDBs/PhiPsi_1vca_clean.pdb 95s PDBs/PhiPsi_2o6r_clean.pdb 95s PDBs/PhiPsi_2r83_clean.pdb 95s PDBs/PhiPsi_3cap_clean.pdb 95s PDBs/PhiPsi_3cuq_clean.pdb 95s PDBs/PhiPsi_3vni_clean.pdb 95s PDBs/PhiPsi_7tim_clean.pdb 95s diff expected and generated 95s PASS 95s autopkgtest [15:34:12]: test run-unit-test: -----------------------] 95s autopkgtest [15:34:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 95s run-unit-test PASS 95s autopkgtest [15:34:12]: @@@@@@@@@@@@@@@@@@@@ summary 95s run-unit-test PASS