0s autopkgtest [01:34:55]: starting date and time: 2025-12-06 01:34:55+0000 0s autopkgtest [01:34:55]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:34:55]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h77aa53v/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-s390x-10.secgroup --name adt-resolute-s390x-peptidebuilder-20251206-013454-juju-7f2275-prod-proposed-migration-environment-20-3b7f070d-b7ca-45bb-b87f-ca78a2deeb1b --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-peptidebuilder-20251206-013454-juju-7f2275-prod-proposed-migration-environment-20-3b7f070d-b7ca-45bb-b87f-ca78a2deeb1b from image adt/ubuntu-resolute-s390x-server-20251205.img (UUID e0f6ccba-b422-4dad-b382-fbc5a99524c4)... 94s autopkgtest [01:36:29]: testbed dpkg architecture: s390x 94s autopkgtest [01:36:29]: testbed apt version: 3.1.12 94s autopkgtest [01:36:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s autopkgtest [01:36:29]: testbed release detected to be: None 95s autopkgtest [01:36:30]: updating testbed package index (apt update) 96s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 96s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [140 kB] 96s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.4 kB] 96s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [842 kB] 96s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [222 kB] 96s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [691 kB] 96s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [6484 B] 97s Fetched 2050 kB in 1s (2163 kB/s) 102s Reading package lists... 103s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 107s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 108s The following packages will be upgraded: 108s libnftnl11 libpython3-stdlib lxd-installer python3 python3-attr python3-gdbm 108s python3-minimal 108s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 201 kB of archives. 108s After this operation, 20.5 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.9-2 [28.1 kB] 108s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.9-2 [23.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.9-2 [10.8 kB] 108s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libnftnl11 s390x 1.3.1-1 [68.7 kB] 108s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.13.9-2 [11.0 kB] 108s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x lxd-installer all 14ubuntu0 [5428 B] 108s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3-attr all 25.4.0-1 [53.6 kB] 109s dpkg-preconfigure: unable to re-open stdin: No such file or directory 109s Fetched 201 kB in 0s (5020 kB/s) 109s (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 ... 61321 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.13.9-2_s390x.deb ... 109s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 109s Setting up python3-minimal (3.13.9-2) ... 109s (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 ... 61321 files and directories currently installed.) 109s Preparing to unpack .../0-python3_3.13.9-2_s390x.deb ... 110s running python pre-rtupdate hooks for python3.13... 110s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 110s Preparing to unpack .../1-libpython3-stdlib_3.13.9-2_s390x.deb ... 110s Unpacking libpython3-stdlib:s390x (3.13.9-2) over (3.13.7-1) ... 110s Preparing to unpack .../2-libnftnl11_1.3.1-1_s390x.deb ... 110s Unpacking libnftnl11:s390x (1.3.1-1) over (1.3.0-1) ... 110s Preparing to unpack .../3-python3-gdbm_3.13.9-2_s390x.deb ... 110s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 110s Preparing to unpack .../4-lxd-installer_14ubuntu0_all.deb ... 110s Unpacking lxd-installer (14ubuntu0) over (13ubuntu0) ... 110s Preparing to unpack .../5-python3-attr_25.4.0-1_all.deb ... 110s Unpacking python3-attr (25.4.0-1) over (25.3.0-1) ... 110s Setting up python3-gdbm (3.13.9-2) ... 110s Setting up libnftnl11:s390x (1.3.1-1) ... 110s Setting up lxd-installer (14ubuntu0) ... 112s Setting up libpython3-stdlib:s390x (3.13.9-2) ... 112s Setting up python3 (3.13.9-2) ... 112s running python rtupdate hooks for python3.13... 112s running python post-rtupdate hooks for python3.13... 112s Setting up python3-attr (25.4.0-1) ... 113s Processing triggers for man-db (2.13.1-1) ... 114s Processing triggers for libc-bin (2.42-2ubuntu2) ... 114s autopkgtest [01:36:49]: upgrading testbed (apt dist-upgrade and autopurge) 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Solving dependencies... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [01:36:53]: rebooting testbed after setup commands that affected boot 157s autopkgtest [01:37:32]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP Tue Oct 7 12:36:22 UTC 2025 161s autopkgtest [01:37:36]: @@@@@@@@@@@@@@@@@@@@ apt-source peptidebuilder 163s Get:1 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (dsc) [2239 B] 163s Get:2 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (tar) [468 kB] 163s Get:3 http://ftpmaster.internal/ubuntu resolute/universe peptidebuilder 1.1.0-3 (diff) [4016 B] 163s gpgv: Signature made Fri Oct 8 20:54:03 2021 UTC 163s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 163s gpgv: issuer "tille@debian.org" 163s gpgv: Can't check signature: No public key 163s dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found 163s autopkgtest [01:37:38]: testing package peptidebuilder version 1.1.0-3 163s autopkgtest [01:37:38]: build not needed 163s autopkgtest [01:37:38]: test run-unit-test: preparing testbed 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Solving dependencies... 166s The following NEW packages will be installed: 166s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 166s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 166s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 166s liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 166s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 166s python3-biopython python3-cairo python3-charset-normalizer python3-freetype 166s python3-numpy python3-numpy-dev python3-peptidebuilder python3-pil 166s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 166s xfonts-encodings xfonts-utils xml-core 166s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 27.7 MB of archives. 166s After this operation, 86.2 MB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 166s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7 [254 kB] 166s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-9ubuntu1 [629 kB] 166s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7 [2983 kB] 167s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 167s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libfontenc1 s390x 1:1.1.8-1build2 [14.5 kB] 167s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.13.3+dfsg-1build1 [430 kB] 167s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x x11-common all 1:7.7+24ubuntu1 [22.4 kB] 167s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 168s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 168s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 168s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.15.0-2.3ubuntu1 [38.1 kB] 168s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.15.0-2.3ubuntu1 [149 kB] 168s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libpixman-1-0 s390x 0.46.4-1 [217 kB] 168s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-render0 s390x 1.17.0-2build1 [16.9 kB] 168s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-shm0 s390x 1.17.0-2build1 [5916 B] 168s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 168s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libcairo2 s390x 1.18.4-1build1 [580 kB] 168s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 168s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-9ubuntu1 [154 kB] 168s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 168s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.1.0-1 [576 kB] 168s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 168s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 168s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 168s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.17-1 [176 kB] 168s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libraqm0 s390x 0.10.3-1 [15.6 kB] 168s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 168s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 168s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 168s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 168s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 168s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 168s Get:34 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-charset-normalizer s390x 3.4.4-2 [181 kB] 168s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libopenjp2-7 s390x 2.5.3-2.1 [207 kB] 168s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pil s390x 12.0.0-1ubuntu1 [540 kB] 168s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x python3-cairo s390x 1.27.0-2build1 [140 kB] 168s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-freetype all 2.5.1-2 [92.2 kB] 168s Get:39 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rlpycairo all 0.3.0-4 [9332 B] 168s Get:40 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-reportlab all 4.4.5-1 [1148 kB] 168s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 168s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19 [20.3 kB] 168s Get:43 http://ftpmaster.internal/ubuntu resolute/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 168s Get:44 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython s390x 1.86+dfsg-1 [1710 kB] 168s Get:45 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-peptidebuilder all 1.1.0-3 [13.3 kB] 170s Fetched 27.7 MB in 2s (11.1 MB/s) 171s Selecting previously unselected package python3-numpy-dev:s390x. 171s (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 ... 61321 files and directories currently installed.) 171s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 171s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 171s Selecting previously unselected package libblas3:s390x. 171s Preparing to unpack .../01-libblas3_3.12.1-7_s390x.deb ... 171s Unpacking libblas3:s390x (3.12.1-7) ... 171s Selecting previously unselected package libgfortran5:s390x. 171s Preparing to unpack .../02-libgfortran5_15.2.0-9ubuntu1_s390x.deb ... 171s Unpacking libgfortran5:s390x (15.2.0-9ubuntu1) ... 171s Selecting previously unselected package liblapack3:s390x. 171s Preparing to unpack .../03-liblapack3_3.12.1-7_s390x.deb ... 171s Unpacking liblapack3:s390x (3.12.1-7) ... 171s Selecting previously unselected package python3-numpy. 171s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 171s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 171s Selecting previously unselected package libfontenc1:s390x. 171s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build2_s390x.deb ... 171s Unpacking libfontenc1:s390x (1:1.1.8-1build2) ... 171s Selecting previously unselected package libfreetype6:s390x. 171s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1build1_s390x.deb ... 171s Unpacking libfreetype6:s390x (2.13.3+dfsg-1build1) ... 171s Selecting previously unselected package x11-common. 171s Preparing to unpack .../07-x11-common_1%3a7.7+24ubuntu1_all.deb ... 171s Unpacking x11-common (1:7.7+24ubuntu1) ... 172s Selecting previously unselected package xfonts-encodings. 172s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 172s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 172s Selecting previously unselected package xfonts-utils. 172s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_s390x.deb ... 172s Unpacking xfonts-utils (1:7.7+7) ... 172s Selecting previously unselected package fonts-urw-base35. 172s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 172s Unpacking fonts-urw-base35 (20200910-8) ... 173s Selecting previously unselected package fontconfig-config. 173s Preparing to unpack .../11-fontconfig-config_2.15.0-2.3ubuntu1_s390x.deb ... 174s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 174s Selecting previously unselected package libfontconfig1:s390x. 174s Preparing to unpack .../12-libfontconfig1_2.15.0-2.3ubuntu1_s390x.deb ... 174s Unpacking libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 174s Selecting previously unselected package libpixman-1-0:s390x. 174s Preparing to unpack .../13-libpixman-1-0_0.46.4-1_s390x.deb ... 174s Unpacking libpixman-1-0:s390x (0.46.4-1) ... 174s Selecting previously unselected package libxcb-render0:s390x. 174s Preparing to unpack .../14-libxcb-render0_1.17.0-2build1_s390x.deb ... 174s Unpacking libxcb-render0:s390x (1.17.0-2build1) ... 174s Selecting previously unselected package libxcb-shm0:s390x. 174s Preparing to unpack .../15-libxcb-shm0_1.17.0-2build1_s390x.deb ... 174s Unpacking libxcb-shm0:s390x (1.17.0-2build1) ... 174s Selecting previously unselected package libxrender1:s390x. 174s Preparing to unpack .../16-libxrender1_1%3a0.9.12-1_s390x.deb ... 174s Unpacking libxrender1:s390x (1:0.9.12-1) ... 174s Selecting previously unselected package libcairo2:s390x. 174s Preparing to unpack .../17-libcairo2_1.18.4-1build1_s390x.deb ... 174s Unpacking libcairo2:s390x (1.18.4-1build1) ... 174s Selecting previously unselected package libdeflate0:s390x. 174s Preparing to unpack .../18-libdeflate0_1.23-2_s390x.deb ... 174s Unpacking libdeflate0:s390x (1.23-2) ... 175s Selecting previously unselected package libgomp1:s390x. 175s Preparing to unpack .../19-libgomp1_15.2.0-9ubuntu1_s390x.deb ... 175s Unpacking libgomp1:s390x (15.2.0-9ubuntu1) ... 175s Selecting previously unselected package libgraphite2-3:s390x. 175s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 175s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 175s Selecting previously unselected package libharfbuzz0b:s390x. 175s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_s390x.deb ... 175s Unpacking libharfbuzz0b:s390x (12.1.0-1) ... 175s Selecting previously unselected package libimagequant0:s390x. 175s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_s390x.deb ... 175s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 175s Selecting previously unselected package libjpeg-turbo8:s390x. 175s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 175s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 175s Selecting previously unselected package libjpeg8:s390x. 175s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_s390x.deb ... 175s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 175s Selecting previously unselected package liblcms2-2:s390x. 175s Preparing to unpack .../25-liblcms2-2_2.17-1_s390x.deb ... 175s Unpacking liblcms2-2:s390x (2.17-1) ... 175s Selecting previously unselected package libraqm0:s390x. 175s Preparing to unpack .../26-libraqm0_0.10.3-1_s390x.deb ... 175s Unpacking libraqm0:s390x (0.10.3-1) ... 175s Selecting previously unselected package libsharpyuv0:s390x. 175s Preparing to unpack .../27-libsharpyuv0_1.5.0-0.1_s390x.deb ... 175s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 175s Selecting previously unselected package libjbig0:s390x. 175s Preparing to unpack .../28-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 175s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 175s Selecting previously unselected package libwebp7:s390x. 175s Preparing to unpack .../29-libwebp7_1.5.0-0.1_s390x.deb ... 175s Unpacking libwebp7:s390x (1.5.0-0.1) ... 175s Selecting previously unselected package libtiff6:s390x. 175s Preparing to unpack .../30-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 175s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 176s Selecting previously unselected package libwebpdemux2:s390x. 176s Preparing to unpack .../31-libwebpdemux2_1.5.0-0.1_s390x.deb ... 176s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 176s Selecting previously unselected package libwebpmux3:s390x. 176s Preparing to unpack .../32-libwebpmux3_1.5.0-0.1_s390x.deb ... 176s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 176s Selecting previously unselected package python3-charset-normalizer. 176s Preparing to unpack .../33-python3-charset-normalizer_3.4.4-2_s390x.deb ... 176s Unpacking python3-charset-normalizer (3.4.4-2) ... 176s Selecting previously unselected package libopenjp2-7:s390x. 176s Preparing to unpack .../34-libopenjp2-7_2.5.3-2.1_s390x.deb ... 176s Unpacking libopenjp2-7:s390x (2.5.3-2.1) ... 176s Selecting previously unselected package python3-pil:s390x. 176s Preparing to unpack .../35-python3-pil_12.0.0-1ubuntu1_s390x.deb ... 176s Unpacking python3-pil:s390x (12.0.0-1ubuntu1) ... 176s Selecting previously unselected package python3-cairo. 176s Preparing to unpack .../36-python3-cairo_1.27.0-2build1_s390x.deb ... 176s Unpacking python3-cairo (1.27.0-2build1) ... 176s Selecting previously unselected package python3-freetype. 176s Preparing to unpack .../37-python3-freetype_2.5.1-2_all.deb ... 176s Unpacking python3-freetype (2.5.1-2) ... 176s Selecting previously unselected package python3-rlpycairo. 176s Preparing to unpack .../38-python3-rlpycairo_0.3.0-4_all.deb ... 176s Unpacking python3-rlpycairo (0.3.0-4) ... 176s Selecting previously unselected package python3-reportlab. 176s Preparing to unpack .../39-python3-reportlab_4.4.5-1_all.deb ... 176s Unpacking python3-reportlab (4.4.5-1) ... 177s Selecting previously unselected package sgml-base. 177s Preparing to unpack .../40-sgml-base_1.31+nmu1_all.deb ... 177s Unpacking sgml-base (1.31+nmu1) ... 177s Selecting previously unselected package xml-core. 177s Preparing to unpack .../41-xml-core_0.19_all.deb ... 177s Unpacking xml-core (0.19) ... 177s Selecting previously unselected package w3c-sgml-lib. 177s Preparing to unpack .../42-w3c-sgml-lib_1.3-3_all.deb ... 177s Unpacking w3c-sgml-lib (1.3-3) ... 177s Selecting previously unselected package python3-biopython. 177s Preparing to unpack .../43-python3-biopython_1.86+dfsg-1_s390x.deb ... 177s Unpacking python3-biopython (1.86+dfsg-1) ... 178s Selecting previously unselected package python3-peptidebuilder. 178s Preparing to unpack .../44-python3-peptidebuilder_1.1.0-3_all.deb ... 178s Unpacking python3-peptidebuilder (1.1.0-3) ... 178s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 178s Setting up liblcms2-2:s390x (2.17-1) ... 178s Setting up libpixman-1-0:s390x (0.46.4-1) ... 178s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 178s Setting up libxrender1:s390x (1:0.9.12-1) ... 178s Setting up libxcb-render0:s390x (1.17.0-2build1) ... 178s Setting up python3-charset-normalizer (3.4.4-2) ... 178s Setting up x11-common (1:7.7+24ubuntu1) ... 179s Setting up libdeflate0:s390x (1.23-2) ... 179s Setting up libxcb-shm0:s390x (1.17.0-2build1) ... 179s Setting up libgomp1:s390x (15.2.0-9ubuntu1) ... 179s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 179s Setting up libfontenc1:s390x (1:1.1.8-1build2) ... 179s Setting up libblas3:s390x (3.12.1-7) ... 180s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 180s Setting up libfreetype6:s390x (2.13.3+dfsg-1build1) ... 180s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 180s Setting up libimagequant0:s390x (2.18.0-1build1) ... 180s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 180s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 180s Setting up libgfortran5:s390x (15.2.0-9ubuntu1) ... 180s Setting up libwebp7:s390x (1.5.0-0.1) ... 180s Setting up libopenjp2-7:s390x (2.5.3-2.1) ... 180s Setting up libharfbuzz0b:s390x (12.1.0-1) ... 180s Setting up sgml-base (1.31+nmu1) ... 180s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 180s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 180s Setting up liblapack3:s390x (3.12.1-7) ... 180s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 180s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 180s Setting up python3-freetype (2.5.1-2) ... 180s Setting up xfonts-utils (1:7.7+7) ... 180s Setting up libraqm0:s390x (0.10.3-1) ... 180s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 189s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 189s Setting up xml-core (0.19) ... 190s Setting up fonts-urw-base35 (20200910-8) ... 191s Setting up python3-pil:s390x (12.0.0-1ubuntu1) ... 192s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 193s Setting up libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 193s Setting up libcairo2:s390x (1.18.4-1build1) ... 193s Setting up python3-cairo (1.27.0-2build1) ... 194s Setting up python3-rlpycairo (0.3.0-4) ... 194s Setting up python3-reportlab (4.4.5-1) ... 197s Processing triggers for libc-bin (2.42-2ubuntu2) ... 197s Processing triggers for man-db (2.13.1-1) ... 199s Processing triggers for sgml-base (1.31+nmu1) ... 199s Setting up w3c-sgml-lib (1.3-3) ... 307s Setting up python3-biopython (1.86+dfsg-1) ... 312s Setting up python3-peptidebuilder (1.1.0-3) ... 316s autopkgtest [01:40:11]: test run-unit-test: [----------------------- 316s Test 1 317s ATOM 1 N GLY A 1 -0.521 1.364 0.000 1.00 0.00 N 317s ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 317s ATOM 3 C GLY A 1 1.520 0.000 0.000 1.00 0.00 C 317s ATOM 4 O GLY A 1 2.144 -0.812 0.681 1.00 0.00 O 317s ATOM 5 N GLY A 2 2.116 0.911 -0.764 1.00 0.00 N 317s ATOM 6 CA GLY A 2 3.571 1.003 -0.842 1.00 0.00 C 317s ATOM 7 C GLY A 2 4.170 1.286 0.526 1.00 0.00 C 317s ATOM 8 O GLY A 2 5.209 0.730 0.881 1.00 0.00 O 317s ATOM 9 N GLY A 3 3.516 2.151 1.297 1.00 0.00 N 317s ATOM 10 CA GLY A 3 3.999 2.498 2.630 1.00 0.00 C 317s ATOM 11 C GLY A 3 4.074 1.266 3.517 1.00 0.00 C 317s ATOM 12 O GLY A 3 5.018 1.109 4.290 1.00 0.00 O 317s ATOM 13 N GLY A 4 3.079 0.390 3.407 1.00 0.00 N 317s ATOM 14 CA GLY A 4 3.046 -0.829 4.210 1.00 0.00 C 317s ATOM 15 C GLY A 4 4.268 -1.691 3.936 1.00 0.00 C 317s ATOM 16 O GLY A 4 4.839 -2.275 4.856 1.00 0.00 O 317s ATOM 17 N GLY A 5 4.671 -1.770 2.671 1.00 0.00 N 317s ATOM 18 CA GLY A 5 5.832 -2.569 2.291 1.00 0.00 C 317s ATOM 19 C GLY A 5 7.084 -2.076 2.999 1.00 0.00 C 317s ATOM 20 O GLY A 5 7.910 -2.875 3.437 1.00 0.00 O 317s ATOM 21 N GLY A 6 7.225 -0.758 3.112 1.00 0.00 N 317s ATOM 22 CA GLY A 6 8.387 -0.172 3.773 1.00 0.00 C 317s ATOM 23 C GLY A 6 8.479 -0.633 5.219 1.00 0.00 C 317s ATOM 24 O GLY A 6 9.395 -0.244 5.941 1.00 0.00 O 317s ATOM 25 OXT GLY A 6 7.638 -1.400 5.684 1.00 0.00 O 317s TER 26 GLY A 6 317s END 317s PASS 317s Test 2 457s 1aq7 457s 1gfl 457s 1nbw 457s 1vca 457s 2o6r 457s 2r83 457s 3cap 457s 3cuq 457s 3vni 457s 7tim 458s PDBs/Aligned_150_AllAngles_1aq7_clean.pdb 458s PDBs/Aligned_150_AllAngles_1gfl_clean.pdb 458s PDBs/Aligned_150_AllAngles_1nbw_clean.pdb 458s PDBs/Aligned_150_AllAngles_1vca_clean.pdb 458s PDBs/Aligned_150_AllAngles_2o6r_clean.pdb 458s PDBs/Aligned_150_AllAngles_2r83_clean.pdb 458s PDBs/Aligned_150_AllAngles_3cap_clean.pdb 458s PDBs/Aligned_150_AllAngles_3cuq_clean.pdb 458s PDBs/Aligned_150_AllAngles_3vni_clean.pdb 458s PDBs/Aligned_150_AllAngles_7tim_clean.pdb 458s PDBs/Aligned_150_Backbone_1aq7_clean.pdb 458s PDBs/Aligned_150_Backbone_1gfl_clean.pdb 458s PDBs/Aligned_150_Backbone_1nbw_clean.pdb 458s PDBs/Aligned_150_Backbone_1vca_clean.pdb 458s PDBs/Aligned_150_Backbone_2o6r_clean.pdb 458s PDBs/Aligned_150_Backbone_2r83_clean.pdb 458s PDBs/Aligned_150_Backbone_3cap_clean.pdb 458s PDBs/Aligned_150_Backbone_3cuq_clean.pdb 458s PDBs/Aligned_150_Backbone_3vni_clean.pdb 458s PDBs/Aligned_150_Backbone_7tim_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_1aq7_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_1gfl_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_1nbw_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_1vca_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_2o6r_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_2r83_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_3cap_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_3cuq_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_3vni_clean.pdb 458s PDBs/Aligned_150_PhiPsiOmega_7tim_clean.pdb 458s PDBs/Aligned_150_PhiPsi_1aq7_clean.pdb 458s PDBs/Aligned_150_PhiPsi_1gfl_clean.pdb 458s PDBs/Aligned_150_PhiPsi_1nbw_clean.pdb 458s PDBs/Aligned_150_PhiPsi_1vca_clean.pdb 458s PDBs/Aligned_150_PhiPsi_2o6r_clean.pdb 458s PDBs/Aligned_150_PhiPsi_2r83_clean.pdb 458s PDBs/Aligned_150_PhiPsi_3cap_clean.pdb 458s PDBs/Aligned_150_PhiPsi_3cuq_clean.pdb 458s PDBs/Aligned_150_PhiPsi_3vni_clean.pdb 458s PDBs/Aligned_150_PhiPsi_7tim_clean.pdb 458s PDBs/Aligned_50_AllAngles_1aq7_clean.pdb 458s PDBs/Aligned_50_AllAngles_1gfl_clean.pdb 458s PDBs/Aligned_50_AllAngles_1nbw_clean.pdb 458s PDBs/Aligned_50_AllAngles_1vca_clean.pdb 458s PDBs/Aligned_50_AllAngles_2o6r_clean.pdb 458s PDBs/Aligned_50_AllAngles_2r83_clean.pdb 458s PDBs/Aligned_50_AllAngles_3cap_clean.pdb 458s PDBs/Aligned_50_AllAngles_3cuq_clean.pdb 458s PDBs/Aligned_50_AllAngles_3vni_clean.pdb 458s PDBs/Aligned_50_AllAngles_7tim_clean.pdb 458s PDBs/Aligned_50_Backbone_1aq7_clean.pdb 458s PDBs/Aligned_50_Backbone_1gfl_clean.pdb 458s PDBs/Aligned_50_Backbone_1nbw_clean.pdb 458s PDBs/Aligned_50_Backbone_1vca_clean.pdb 458s PDBs/Aligned_50_Backbone_2o6r_clean.pdb 458s PDBs/Aligned_50_Backbone_2r83_clean.pdb 458s PDBs/Aligned_50_Backbone_3cap_clean.pdb 458s PDBs/Aligned_50_Backbone_3cuq_clean.pdb 458s PDBs/Aligned_50_Backbone_3vni_clean.pdb 458s PDBs/Aligned_50_Backbone_7tim_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_1aq7_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_1gfl_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_1nbw_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_1vca_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_2o6r_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_2r83_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_3cap_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_3cuq_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_3vni_clean.pdb 458s PDBs/Aligned_50_PhiPsiOmega_7tim_clean.pdb 458s PDBs/Aligned_50_PhiPsi_1aq7_clean.pdb 458s PDBs/Aligned_50_PhiPsi_1gfl_clean.pdb 458s PDBs/Aligned_50_PhiPsi_1nbw_clean.pdb 458s PDBs/Aligned_50_PhiPsi_1vca_clean.pdb 458s PDBs/Aligned_50_PhiPsi_2o6r_clean.pdb 458s PDBs/Aligned_50_PhiPsi_2r83_clean.pdb 458s PDBs/Aligned_50_PhiPsi_3cap_clean.pdb 458s PDBs/Aligned_50_PhiPsi_3cuq_clean.pdb 458s PDBs/Aligned_50_PhiPsi_3vni_clean.pdb 458s PDBs/Aligned_50_PhiPsi_7tim_clean.pdb 458s PDBs/Aligned_AllAngles_1aq7_clean.pdb 458s PDBs/Aligned_AllAngles_1gfl_clean.pdb 458s PDBs/Aligned_AllAngles_1nbw_clean.pdb 458s PDBs/Aligned_AllAngles_1vca_clean.pdb 458s PDBs/Aligned_AllAngles_2o6r_clean.pdb 458s PDBs/Aligned_AllAngles_2r83_clean.pdb 458s PDBs/Aligned_AllAngles_3cap_clean.pdb 458s PDBs/Aligned_AllAngles_3cuq_clean.pdb 458s PDBs/Aligned_AllAngles_3vni_clean.pdb 458s PDBs/Aligned_AllAngles_7tim_clean.pdb 458s PDBs/Aligned_Backbone_1aq7_clean.pdb 458s PDBs/Aligned_Backbone_1gfl_clean.pdb 458s PDBs/Aligned_Backbone_1nbw_clean.pdb 458s PDBs/Aligned_Backbone_1vca_clean.pdb 458s PDBs/Aligned_Backbone_2o6r_clean.pdb 458s PDBs/Aligned_Backbone_2r83_clean.pdb 458s PDBs/Aligned_Backbone_3cap_clean.pdb 458s PDBs/Aligned_Backbone_3cuq_clean.pdb 458s PDBs/Aligned_Backbone_3vni_clean.pdb 458s PDBs/Aligned_Backbone_7tim_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_1aq7_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_1gfl_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_1nbw_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_1vca_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_2o6r_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_2r83_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_3cap_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_3cuq_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_3vni_clean.pdb 458s PDBs/Aligned_PhiPsiOmega_7tim_clean.pdb 458s PDBs/Aligned_PhiPsi_1aq7_clean.pdb 458s PDBs/Aligned_PhiPsi_1gfl_clean.pdb 458s PDBs/Aligned_PhiPsi_1nbw_clean.pdb 458s PDBs/Aligned_PhiPsi_1vca_clean.pdb 458s PDBs/Aligned_PhiPsi_2o6r_clean.pdb 458s PDBs/Aligned_PhiPsi_2r83_clean.pdb 458s PDBs/Aligned_PhiPsi_3cap_clean.pdb 458s PDBs/Aligned_PhiPsi_3cuq_clean.pdb 458s PDBs/Aligned_PhiPsi_3vni_clean.pdb 458s PDBs/Aligned_PhiPsi_7tim_clean.pdb 458s PDBs/AllAngles_1aq7_clean.pdb 458s PDBs/AllAngles_1gfl_clean.pdb 458s PDBs/AllAngles_1nbw_clean.pdb 458s PDBs/AllAngles_1vca_clean.pdb 458s PDBs/AllAngles_2o6r_clean.pdb 458s PDBs/AllAngles_2r83_clean.pdb 458s PDBs/AllAngles_3cap_clean.pdb 458s PDBs/AllAngles_3cuq_clean.pdb 458s PDBs/AllAngles_3vni_clean.pdb 458s PDBs/AllAngles_7tim_clean.pdb 458s PDBs/Backbone_1aq7_clean.pdb 458s PDBs/Backbone_1gfl_clean.pdb 458s PDBs/Backbone_1nbw_clean.pdb 458s PDBs/Backbone_1vca_clean.pdb 458s PDBs/Backbone_2o6r_clean.pdb 458s PDBs/Backbone_2r83_clean.pdb 458s PDBs/Backbone_3cap_clean.pdb 458s PDBs/Backbone_3cuq_clean.pdb 458s PDBs/Backbone_3vni_clean.pdb 458s PDBs/Backbone_7tim_clean.pdb 458s PDBs/PhiPsiOmega_1aq7_clean.pdb 458s PDBs/PhiPsiOmega_1gfl_clean.pdb 458s PDBs/PhiPsiOmega_1nbw_clean.pdb 458s PDBs/PhiPsiOmega_1vca_clean.pdb 458s PDBs/PhiPsiOmega_2o6r_clean.pdb 458s PDBs/PhiPsiOmega_2r83_clean.pdb 458s PDBs/PhiPsiOmega_3cap_clean.pdb 458s PDBs/PhiPsiOmega_3cuq_clean.pdb 458s PDBs/PhiPsiOmega_3vni_clean.pdb 458s PDBs/PhiPsiOmega_7tim_clean.pdb 458s PDBs/PhiPsi_1aq7_clean.pdb 458s PDBs/PhiPsi_1gfl_clean.pdb 458s PDBs/PhiPsi_1nbw_clean.pdb 458s PDBs/PhiPsi_1vca_clean.pdb 458s PDBs/PhiPsi_2o6r_clean.pdb 458s PDBs/PhiPsi_2r83_clean.pdb 458s PDBs/PhiPsi_3cap_clean.pdb 458s PDBs/PhiPsi_3cuq_clean.pdb 458s PDBs/PhiPsi_3vni_clean.pdb 458s PDBs/PhiPsi_7tim_clean.pdb 458s PASS 459s autopkgtest [01:42:34]: test run-unit-test: -----------------------] 459s autopkgtest [01:42:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 459s run-unit-test PASS 460s autopkgtest [01:42:35]: @@@@@@@@@@@@@@@@@@@@ summary 460s run-unit-test PASS