0s autopkgtest [21:16:35]: starting date and time: 2025-12-05 21:16:35+0000 0s autopkgtest [21:16:35]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [21:16:35]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u2_7yswv/out --timeout-copy=6000 --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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-17.secgroup --name adt-resolute-arm64-peptidebuilder-20251205-211635-juju-7f2275-prod-proposed-migration-environment-20-58757726-2a3a-47bb-8002-4e3eaa771c45 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-peptidebuilder-20251205-211635-juju-7f2275-prod-proposed-migration-environment-20-58757726-2a3a-47bb-8002-4e3eaa771c45 from image adt/ubuntu-resolute-arm64-server-20251205.img (UUID 37bdf92c-2d31-48d2-a8f3-3e7306fd9ba8)... 47s autopkgtest [21:17:22]: testbed dpkg architecture: arm64 48s autopkgtest [21:17:23]: testbed apt version: 3.1.12 48s autopkgtest [21:17:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s autopkgtest [21:17:23]: testbed release detected to be: None 49s autopkgtest [21:17:24]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 49s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [847 kB] 50s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [143 kB] 50s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.4 kB] 50s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [222 kB] 50s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7468 B] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 50s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [704 kB] 50s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [19.6 kB] 50s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8180 B] 50s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [588 B] 53s Fetched 2100 kB in 1s (2084 kB/s) 53s Reading package lists... 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 56s The following packages will be upgraded: 56s libnftnl11 libpython3-stdlib lxd-installer python3 python3-attr python3-gdbm 56s python3-minimal 56s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 203 kB of archives. 56s After this operation, 16.4 kB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.9-2 [28.1 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.9-2 [23.0 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.8 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libnftnl11 arm64 1.3.1-1 [70.7 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.13.9-2 [11.0 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 lxd-installer all 14ubuntu0 [5428 B] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-attr all 25.4.0-1 [53.6 kB] 56s dpkg-preconfigure: unable to re-open stdin: No such file or directory 56s Fetched 203 kB in 0s (14.1 MB/s) 56s (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 ... 88300 files and directories currently installed.) 56s Preparing to unpack .../python3-minimal_3.13.9-2_arm64.deb ... 56s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 56s Setting up python3-minimal (3.13.9-2) ... 57s (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 ... 88300 files and directories currently installed.) 57s Preparing to unpack .../0-python3_3.13.9-2_arm64.deb ... 57s running python pre-rtupdate hooks for python3.13... 57s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 57s Preparing to unpack .../1-libpython3-stdlib_3.13.9-2_arm64.deb ... 57s Unpacking libpython3-stdlib:arm64 (3.13.9-2) over (3.13.7-1) ... 57s Preparing to unpack .../2-libnftnl11_1.3.1-1_arm64.deb ... 57s Unpacking libnftnl11:arm64 (1.3.1-1) over (1.3.0-1) ... 57s Preparing to unpack .../3-python3-gdbm_3.13.9-2_arm64.deb ... 57s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 57s Preparing to unpack .../4-lxd-installer_14ubuntu0_all.deb ... 57s Unpacking lxd-installer (14ubuntu0) over (13ubuntu0) ... 57s Preparing to unpack .../5-python3-attr_25.4.0-1_all.deb ... 57s Unpacking python3-attr (25.4.0-1) over (25.3.0-1) ... 57s Setting up python3-gdbm (3.13.9-2) ... 57s Setting up libnftnl11:arm64 (1.3.1-1) ... 57s Setting up lxd-installer (14ubuntu0) ... 58s Setting up libpython3-stdlib:arm64 (3.13.9-2) ... 58s Setting up python3 (3.13.9-2) ... 58s running python rtupdate hooks for python3.13... 58s running python post-rtupdate hooks for python3.13... 58s Setting up python3-attr (25.4.0-1) ... 58s Processing triggers for man-db (2.13.1-1) ... 58s Processing triggers for libc-bin (2.42-2ubuntu2) ... 59s autopkgtest [21:17:34]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [21:17:36]: rebooting testbed after setup commands that affected boot 94s autopkgtest [21:18:09]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 14:22:06 UTC 2025 96s autopkgtest [21:18:11]: @@@@@@@@@@@@@@@@@@@@ apt-source peptidebuilder 98s Get:1 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (dsc) [2239 B] 98s Get:2 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (tar) [468 kB] 98s Get:3 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (diff) [4016 B] 98s gpgv: Signature made Fri Oct 8 20:54:03 2021 UTC 98s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 98s gpgv: issuer "tille@debian.org" 98s gpgv: Can't check signature: No public key 98s dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found 98s autopkgtest [21:18:13]: testing package peptidebuilder version 1.1.0-3 98s autopkgtest [21:18:13]: build not needed 99s autopkgtest [21:18:14]: test run-unit-test: preparing testbed 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Solving dependencies... 100s The following NEW packages will be installed: 100s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 100s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 100s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 100s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 100s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 100s libxrender1 python3-biopython python3-cairo python3-charset-normalizer 100s python3-freetype python3-numpy python3-numpy-dev python3-peptidebuilder 100s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 100s x11-common xfonts-encodings xfonts-utils xml-core 100s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 25.8 MB of archives. 100s After this operation, 83.5 MB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 100s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB] 100s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-9ubuntu1 [450 kB] 100s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB] 100s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 101s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build2 [13.9 kB] 101s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 101s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 101s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 101s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 102s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 102s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 102s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 102s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 102s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 102s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 102s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 102s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 102s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-9ubuntu1 [147 kB] 102s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 102s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 102s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 102s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 102s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 102s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 102s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 102s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 102s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 102s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 102s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 102s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 102s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 102s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 102s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.4-2 [169 kB] 102s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 102s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 12.0.0-1ubuntu1 [486 kB] 102s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 102s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 102s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 102s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.5-1 [1148 kB] 102s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 102s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB] 102s Get:43 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 102s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.86+dfsg-1 [1675 kB] 102s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-peptidebuilder all 1.1.0-3 [13.3 kB] 103s Fetched 25.8 MB in 3s (9480 kB/s) 103s Selecting previously unselected package python3-numpy-dev:arm64. 103s (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 ... 88300 files and directories currently installed.) 103s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 103s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 103s Selecting previously unselected package libblas3:arm64. 103s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ... 103s Unpacking libblas3:arm64 (3.12.1-7) ... 103s Selecting previously unselected package libgfortran5:arm64. 103s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_arm64.deb ... 103s Unpacking libgfortran5:arm64 (15.2.0-9ubuntu1) ... 103s Selecting previously unselected package liblapack3:arm64. 103s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ... 103s Unpacking liblapack3:arm64 (3.12.1-7) ... 103s Selecting previously unselected package python3-numpy. 103s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 103s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 103s Selecting previously unselected package libfontenc1:arm64. 103s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build2_arm64.deb ... 103s Unpacking libfontenc1:arm64 (1:1.1.8-1build2) ... 103s Selecting previously unselected package x11-common. 103s Preparing to unpack .../06-x11-common_1%3a7.7+24ubuntu1_all.deb ... 103s Unpacking x11-common (1:7.7+24ubuntu1) ... 103s Selecting previously unselected package xfonts-encodings. 103s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 103s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 103s Selecting previously unselected package xfonts-utils. 103s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ... 103s Unpacking xfonts-utils (1:7.7+7) ... 103s Selecting previously unselected package fonts-urw-base35. 103s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 103s Unpacking fonts-urw-base35 (20200910-8) ... 104s Selecting previously unselected package fontconfig-config. 104s Preparing to unpack .../10-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 104s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 104s Selecting previously unselected package libfontconfig1:arm64. 104s Preparing to unpack .../11-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 104s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 104s Selecting previously unselected package libpixman-1-0:arm64. 104s Preparing to unpack .../12-libpixman-1-0_0.46.4-1_arm64.deb ... 104s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 104s Selecting previously unselected package libxcb-render0:arm64. 104s Preparing to unpack .../13-libxcb-render0_1.17.0-2build1_arm64.deb ... 104s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 104s Selecting previously unselected package libxcb-shm0:arm64. 104s Preparing to unpack .../14-libxcb-shm0_1.17.0-2build1_arm64.deb ... 104s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 104s Selecting previously unselected package libxrender1:arm64. 104s Preparing to unpack .../15-libxrender1_1%3a0.9.12-1_arm64.deb ... 104s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 104s Selecting previously unselected package libcairo2:arm64. 104s Preparing to unpack .../16-libcairo2_1.18.4-1build1_arm64.deb ... 104s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 104s Selecting previously unselected package libdeflate0:arm64. 104s Preparing to unpack .../17-libdeflate0_1.23-2_arm64.deb ... 104s Unpacking libdeflate0:arm64 (1.23-2) ... 104s Selecting previously unselected package libgomp1:arm64. 104s Preparing to unpack .../18-libgomp1_15.2.0-9ubuntu1_arm64.deb ... 104s Unpacking libgomp1:arm64 (15.2.0-9ubuntu1) ... 104s Selecting previously unselected package libgraphite2-3:arm64. 104s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 104s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 104s Selecting previously unselected package libharfbuzz0b:arm64. 104s Preparing to unpack .../20-libharfbuzz0b_12.1.0-1_arm64.deb ... 104s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 104s Selecting previously unselected package libimagequant0:arm64. 104s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 104s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 104s Selecting previously unselected package libjpeg-turbo8:arm64. 104s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 104s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 104s Selecting previously unselected package libjpeg8:arm64. 104s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 104s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 104s Selecting previously unselected package liblcms2-2:arm64. 104s Preparing to unpack .../24-liblcms2-2_2.17-1_arm64.deb ... 104s Unpacking liblcms2-2:arm64 (2.17-1) ... 104s Selecting previously unselected package liblerc4:arm64. 104s Preparing to unpack .../25-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 104s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 104s Selecting previously unselected package libraqm0:arm64. 104s Preparing to unpack .../26-libraqm0_0.10.3-1_arm64.deb ... 104s Unpacking libraqm0:arm64 (0.10.3-1) ... 104s Selecting previously unselected package libsharpyuv0:arm64. 104s Preparing to unpack .../27-libsharpyuv0_1.5.0-0.1_arm64.deb ... 104s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 104s Selecting previously unselected package libjbig0:arm64. 104s Preparing to unpack .../28-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 104s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 104s Selecting previously unselected package libwebp7:arm64. 104s Preparing to unpack .../29-libwebp7_1.5.0-0.1_arm64.deb ... 104s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 104s Selecting previously unselected package libtiff6:arm64. 104s Preparing to unpack .../30-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 104s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 104s Selecting previously unselected package libwebpdemux2:arm64. 104s Preparing to unpack .../31-libwebpdemux2_1.5.0-0.1_arm64.deb ... 104s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 104s Selecting previously unselected package libwebpmux3:arm64. 105s Preparing to unpack .../32-libwebpmux3_1.5.0-0.1_arm64.deb ... 105s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 105s Selecting previously unselected package python3-charset-normalizer. 105s Preparing to unpack .../33-python3-charset-normalizer_3.4.4-2_arm64.deb ... 105s Unpacking python3-charset-normalizer (3.4.4-2) ... 105s Selecting previously unselected package libopenjp2-7:arm64. 105s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_arm64.deb ... 105s Unpacking libopenjp2-7:arm64 (2.5.3-2.1) ... 105s Selecting previously unselected package python3-pil:arm64. 105s Preparing to unpack .../35-python3-pil_12.0.0-1ubuntu1_arm64.deb ... 105s Unpacking python3-pil:arm64 (12.0.0-1ubuntu1) ... 105s Selecting previously unselected package python3-cairo. 105s Preparing to unpack .../36-python3-cairo_1.27.0-2build1_arm64.deb ... 105s Unpacking python3-cairo (1.27.0-2build1) ... 105s Selecting previously unselected package python3-freetype. 105s Preparing to unpack .../37-python3-freetype_2.5.1-2_all.deb ... 105s Unpacking python3-freetype (2.5.1-2) ... 105s Selecting previously unselected package python3-rlpycairo. 105s Preparing to unpack .../38-python3-rlpycairo_0.3.0-4_all.deb ... 105s Unpacking python3-rlpycairo (0.3.0-4) ... 105s Selecting previously unselected package python3-reportlab. 105s Preparing to unpack .../39-python3-reportlab_4.4.5-1_all.deb ... 105s Unpacking python3-reportlab (4.4.5-1) ... 105s Selecting previously unselected package sgml-base. 105s Preparing to unpack .../40-sgml-base_1.31+nmu1_all.deb ... 105s Unpacking sgml-base (1.31+nmu1) ... 105s Selecting previously unselected package xml-core. 105s Preparing to unpack .../41-xml-core_0.19_all.deb ... 105s Unpacking xml-core (0.19) ... 105s Selecting previously unselected package w3c-sgml-lib. 105s Preparing to unpack .../42-w3c-sgml-lib_1.3-3_all.deb ... 105s Unpacking w3c-sgml-lib (1.3-3) ... 105s Selecting previously unselected package python3-biopython. 105s Preparing to unpack .../43-python3-biopython_1.86+dfsg-1_arm64.deb ... 105s Unpacking python3-biopython (1.86+dfsg-1) ... 105s Selecting previously unselected package python3-peptidebuilder. 105s Preparing to unpack .../44-python3-peptidebuilder_1.1.0-3_all.deb ... 105s Unpacking python3-peptidebuilder (1.1.0-3) ... 105s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 105s Setting up liblcms2-2:arm64 (2.17-1) ... 105s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 105s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 105s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 105s Setting up libxrender1:arm64 (1:0.9.12-1) ... 105s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 105s Setting up python3-charset-normalizer (3.4.4-2) ... 105s Setting up x11-common (1:7.7+24ubuntu1) ... 106s Setting up libdeflate0:arm64 (1.23-2) ... 106s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 106s Setting up libgomp1:arm64 (15.2.0-9ubuntu1) ... 106s Setting up python3-freetype (2.5.1-2) ... 106s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 106s Setting up libfontenc1:arm64 (1:1.1.8-1build2) ... 106s Setting up libblas3:arm64 (3.12.1-7) ... 106s 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 106s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 106s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 106s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 106s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 106s Setting up libgfortran5:arm64 (15.2.0-9ubuntu1) ... 106s Setting up libwebp7:arm64 (1.5.0-0.1) ... 106s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 106s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 106s Setting up sgml-base (1.31+nmu1) ... 106s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 106s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 106s Setting up liblapack3:arm64 (3.12.1-7) ... 106s 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 106s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 106s Setting up xfonts-utils (1:7.7+7) ... 106s Setting up libraqm0:arm64 (0.10.3-1) ... 106s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 108s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 108s Setting up xml-core (0.19) ... 108s Setting up fonts-urw-base35 (20200910-8) ... 108s Setting up python3-pil:arm64 (12.0.0-1ubuntu1) ... 108s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 108s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 108s Setting up libcairo2:arm64 (1.18.4-1build1) ... 108s Setting up python3-cairo (1.27.0-2build1) ... 109s Setting up python3-rlpycairo (0.3.0-4) ... 109s Setting up python3-reportlab (4.4.5-1) ... 109s Processing triggers for libc-bin (2.42-2ubuntu2) ... 109s Processing triggers for man-db (2.13.1-1) ... 110s Processing triggers for sgml-base (1.31+nmu1) ... 110s Setting up w3c-sgml-lib (1.3-3) ... 135s Setting up python3-biopython (1.86+dfsg-1) ... 136s Setting up python3-peptidebuilder (1.1.0-3) ... 137s autopkgtest [21:18:52]: test run-unit-test: [----------------------- 137s Test 1 137s ATOM 1 N GLY A 1 -0.521 1.364 0.000 1.00 0.00 N 137s ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 137s ATOM 3 C GLY A 1 1.520 0.000 0.000 1.00 0.00 C 137s ATOM 4 O GLY A 1 2.144 -0.812 0.681 1.00 0.00 O 137s ATOM 5 N GLY A 2 2.116 0.911 -0.764 1.00 0.00 N 137s ATOM 6 CA GLY A 2 3.571 1.003 -0.842 1.00 0.00 C 137s ATOM 7 C GLY A 2 4.170 1.286 0.526 1.00 0.00 C 137s ATOM 8 O GLY A 2 5.209 0.730 0.881 1.00 0.00 O 137s ATOM 9 N GLY A 3 3.516 2.151 1.297 1.00 0.00 N 137s ATOM 10 CA GLY A 3 3.999 2.498 2.630 1.00 0.00 C 137s ATOM 11 C GLY A 3 4.074 1.266 3.517 1.00 0.00 C 137s ATOM 12 O GLY A 3 5.018 1.109 4.290 1.00 0.00 O 137s ATOM 13 N GLY A 4 3.079 0.390 3.407 1.00 0.00 N 137s ATOM 14 CA GLY A 4 3.046 -0.829 4.210 1.00 0.00 C 137s ATOM 15 C GLY A 4 4.268 -1.691 3.936 1.00 0.00 C 137s ATOM 16 O GLY A 4 4.839 -2.275 4.856 1.00 0.00 O 137s ATOM 17 N GLY A 5 4.671 -1.770 2.671 1.00 0.00 N 137s ATOM 18 CA GLY A 5 5.832 -2.569 2.291 1.00 0.00 C 137s ATOM 19 C GLY A 5 7.084 -2.076 2.999 1.00 0.00 C 137s ATOM 20 O GLY A 5 7.910 -2.875 3.437 1.00 0.00 O 137s ATOM 21 N GLY A 6 7.225 -0.758 3.112 1.00 0.00 N 137s ATOM 22 CA GLY A 6 8.387 -0.172 3.773 1.00 0.00 C 137s ATOM 23 C GLY A 6 8.479 -0.633 5.219 1.00 0.00 C 137s ATOM 24 O GLY A 6 9.395 -0.244 5.941 1.00 0.00 O 137s ATOM 25 OXT GLY A 6 7.638 -1.400 5.684 1.00 0.00 O 137s TER 26 GLY A 6 137s END 137s PASS 137s Test 2 162s 1aq7 162s 1gfl 162s 1nbw 162s 1vca 162s 2o6r 162s 2r83 162s 3cap 162s 3cuq 162s 3vni 162s 7tim 163s PDBs/Aligned_150_AllAngles_1aq7_clean.pdb 163s PDBs/Aligned_150_AllAngles_1gfl_clean.pdb 163s PDBs/Aligned_150_AllAngles_1nbw_clean.pdb 163s PDBs/Aligned_150_AllAngles_1vca_clean.pdb 163s PDBs/Aligned_150_AllAngles_2o6r_clean.pdb 163s PDBs/Aligned_150_AllAngles_2r83_clean.pdb 163s PDBs/Aligned_150_AllAngles_3cap_clean.pdb 163s PDBs/Aligned_150_AllAngles_3cuq_clean.pdb 163s PDBs/Aligned_150_AllAngles_3vni_clean.pdb 163s PDBs/Aligned_150_AllAngles_7tim_clean.pdb 163s PDBs/Aligned_150_Backbone_1aq7_clean.pdb 163s PDBs/Aligned_150_Backbone_1gfl_clean.pdb 163s PDBs/Aligned_150_Backbone_1nbw_clean.pdb 163s PDBs/Aligned_150_Backbone_1vca_clean.pdb 163s PDBs/Aligned_150_Backbone_2o6r_clean.pdb 163s PDBs/Aligned_150_Backbone_2r83_clean.pdb 163s PDBs/Aligned_150_Backbone_3cap_clean.pdb 163s PDBs/Aligned_150_Backbone_3cuq_clean.pdb 163s PDBs/Aligned_150_Backbone_3vni_clean.pdb 163s PDBs/Aligned_150_Backbone_7tim_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_1aq7_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_1gfl_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_1nbw_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_1vca_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_2o6r_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_2r83_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_3cap_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_3cuq_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_3vni_clean.pdb 163s PDBs/Aligned_150_PhiPsiOmega_7tim_clean.pdb 163s PDBs/Aligned_150_PhiPsi_1aq7_clean.pdb 163s PDBs/Aligned_150_PhiPsi_1gfl_clean.pdb 163s PDBs/Aligned_150_PhiPsi_1nbw_clean.pdb 163s PDBs/Aligned_150_PhiPsi_1vca_clean.pdb 163s PDBs/Aligned_150_PhiPsi_2o6r_clean.pdb 163s PDBs/Aligned_150_PhiPsi_2r83_clean.pdb 163s PDBs/Aligned_150_PhiPsi_3cap_clean.pdb 163s PDBs/Aligned_150_PhiPsi_3cuq_clean.pdb 163s PDBs/Aligned_150_PhiPsi_3vni_clean.pdb 163s PDBs/Aligned_150_PhiPsi_7tim_clean.pdb 163s PDBs/Aligned_50_AllAngles_1aq7_clean.pdb 163s PDBs/Aligned_50_AllAngles_1gfl_clean.pdb 163s PDBs/Aligned_50_AllAngles_1nbw_clean.pdb 163s PDBs/Aligned_50_AllAngles_1vca_clean.pdb 163s PDBs/Aligned_50_AllAngles_2o6r_clean.pdb 163s PDBs/Aligned_50_AllAngles_2r83_clean.pdb 163s PDBs/Aligned_50_AllAngles_3cap_clean.pdb 163s PDBs/Aligned_50_AllAngles_3cuq_clean.pdb 163s PDBs/Aligned_50_AllAngles_3vni_clean.pdb 163s PDBs/Aligned_50_AllAngles_7tim_clean.pdb 163s PDBs/Aligned_50_Backbone_1aq7_clean.pdb 163s PDBs/Aligned_50_Backbone_1gfl_clean.pdb 163s PDBs/Aligned_50_Backbone_1nbw_clean.pdb 163s PDBs/Aligned_50_Backbone_1vca_clean.pdb 163s PDBs/Aligned_50_Backbone_2o6r_clean.pdb 163s PDBs/Aligned_50_Backbone_2r83_clean.pdb 163s PDBs/Aligned_50_Backbone_3cap_clean.pdb 163s PDBs/Aligned_50_Backbone_3cuq_clean.pdb 163s PDBs/Aligned_50_Backbone_3vni_clean.pdb 163s PDBs/Aligned_50_Backbone_7tim_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_1aq7_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_1gfl_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_1nbw_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_1vca_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_2o6r_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_2r83_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_3cap_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_3cuq_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_3vni_clean.pdb 163s PDBs/Aligned_50_PhiPsiOmega_7tim_clean.pdb 163s PDBs/Aligned_50_PhiPsi_1aq7_clean.pdb 163s PDBs/Aligned_50_PhiPsi_1gfl_clean.pdb 163s PDBs/Aligned_50_PhiPsi_1nbw_clean.pdb 163s PDBs/Aligned_50_PhiPsi_1vca_clean.pdb 163s PDBs/Aligned_50_PhiPsi_2o6r_clean.pdb 163s PDBs/Aligned_50_PhiPsi_2r83_clean.pdb 163s PDBs/Aligned_50_PhiPsi_3cap_clean.pdb 163s PDBs/Aligned_50_PhiPsi_3cuq_clean.pdb 163s PDBs/Aligned_50_PhiPsi_3vni_clean.pdb 163s PDBs/Aligned_50_PhiPsi_7tim_clean.pdb 163s PDBs/Aligned_AllAngles_1aq7_clean.pdb 163s PDBs/Aligned_AllAngles_1gfl_clean.pdb 163s PDBs/Aligned_AllAngles_1nbw_clean.pdb 163s PDBs/Aligned_AllAngles_1vca_clean.pdb 163s PDBs/Aligned_AllAngles_2o6r_clean.pdb 163s PDBs/Aligned_AllAngles_2r83_clean.pdb 163s PDBs/Aligned_AllAngles_3cap_clean.pdb 163s PDBs/Aligned_AllAngles_3cuq_clean.pdb 163s PDBs/Aligned_AllAngles_3vni_clean.pdb 163s PDBs/Aligned_AllAngles_7tim_clean.pdb 163s PDBs/Aligned_Backbone_1aq7_clean.pdb 163s PDBs/Aligned_Backbone_1gfl_clean.pdb 163s PDBs/Aligned_Backbone_1nbw_clean.pdb 163s PDBs/Aligned_Backbone_1vca_clean.pdb 163s PDBs/Aligned_Backbone_2o6r_clean.pdb 163s PDBs/Aligned_Backbone_2r83_clean.pdb 163s PDBs/Aligned_Backbone_3cap_clean.pdb 163s PDBs/Aligned_Backbone_3cuq_clean.pdb 163s PDBs/Aligned_Backbone_3vni_clean.pdb 163s PDBs/Aligned_Backbone_7tim_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_1aq7_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_1gfl_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_1nbw_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_1vca_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_2o6r_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_2r83_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_3cap_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_3cuq_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_3vni_clean.pdb 163s PDBs/Aligned_PhiPsiOmega_7tim_clean.pdb 163s PDBs/Aligned_PhiPsi_1aq7_clean.pdb 163s PDBs/Aligned_PhiPsi_1gfl_clean.pdb 163s PDBs/Aligned_PhiPsi_1nbw_clean.pdb 163s PDBs/Aligned_PhiPsi_1vca_clean.pdb 163s PDBs/Aligned_PhiPsi_2o6r_clean.pdb 163s PDBs/Aligned_PhiPsi_2r83_clean.pdb 163s PDBs/Aligned_PhiPsi_3cap_clean.pdb 163s PDBs/Aligned_PhiPsi_3cuq_clean.pdb 163s PDBs/Aligned_PhiPsi_3vni_clean.pdb 163s PDBs/Aligned_PhiPsi_7tim_clean.pdb 163s PDBs/AllAngles_1aq7_clean.pdb 163s PDBs/AllAngles_1gfl_clean.pdb 163s PDBs/AllAngles_1nbw_clean.pdb 163s PDBs/AllAngles_1vca_clean.pdb 163s PDBs/AllAngles_2o6r_clean.pdb 163s PDBs/AllAngles_2r83_clean.pdb 163s PDBs/AllAngles_3cap_clean.pdb 163s PDBs/AllAngles_3cuq_clean.pdb 163s PDBs/AllAngles_3vni_clean.pdb 163s PDBs/AllAngles_7tim_clean.pdb 163s PDBs/Backbone_1aq7_clean.pdb 163s PDBs/Backbone_1gfl_clean.pdb 163s PDBs/Backbone_1nbw_clean.pdb 163s PDBs/Backbone_1vca_clean.pdb 163s PDBs/Backbone_2o6r_clean.pdb 163s PDBs/Backbone_2r83_clean.pdb 163s PDBs/Backbone_3cap_clean.pdb 163s PDBs/Backbone_3cuq_clean.pdb 163s PDBs/Backbone_3vni_clean.pdb 163s PDBs/Backbone_7tim_clean.pdb 163s PDBs/PhiPsiOmega_1aq7_clean.pdb 163s PDBs/PhiPsiOmega_1gfl_clean.pdb 163s PDBs/PhiPsiOmega_1nbw_clean.pdb 163s PDBs/PhiPsiOmega_1vca_clean.pdb 163s PDBs/PhiPsiOmega_2o6r_clean.pdb 163s PDBs/PhiPsiOmega_2r83_clean.pdb 163s PDBs/PhiPsiOmega_3cap_clean.pdb 163s PDBs/PhiPsiOmega_3cuq_clean.pdb 163s PDBs/PhiPsiOmega_3vni_clean.pdb 163s PDBs/PhiPsiOmega_7tim_clean.pdb 163s PDBs/PhiPsi_1aq7_clean.pdb 163s PDBs/PhiPsi_1gfl_clean.pdb 163s PDBs/PhiPsi_1nbw_clean.pdb 163s PDBs/PhiPsi_1vca_clean.pdb 163s PDBs/PhiPsi_2o6r_clean.pdb 163s PDBs/PhiPsi_2r83_clean.pdb 163s PDBs/PhiPsi_3cap_clean.pdb 163s PDBs/PhiPsi_3cuq_clean.pdb 163s PDBs/PhiPsi_3vni_clean.pdb 163s PDBs/PhiPsi_7tim_clean.pdb 163s PASS 163s autopkgtest [21:19:18]: test run-unit-test: -----------------------] 164s run-unit-test PASS 164s autopkgtest [21:19:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 164s autopkgtest [21:19:19]: @@@@@@@@@@@@@@@@@@@@ summary 164s run-unit-test PASS