0s autopkgtest [08:49:47]: starting date and time: 2026-01-23 08:49:47+0000 0s autopkgtest [08:49:47]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [08:49:47]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rusioytd/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 propka --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-2.secgroup --name adt-resolute-i386-propka-20260123-084947-juju-7f2275-prod-proposed-migration-environment-15-4dc5f3af-c073-4622-93f8-11569dc26e64 --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/ 4s Creating nova instance adt-resolute-i386-propka-20260123-084947-juju-7f2275-prod-proposed-migration-environment-15-4dc5f3af-c073-4622-93f8-11569dc26e64 from image adt/ubuntu-resolute-amd64-server-20260123.img (UUID 789dbc23-4f1b-4e7c-bcab-98e6eebf04f2)... 124s autopkgtest [08:51:51]: testbed dpkg architecture: amd64 124s autopkgtest [08:51:51]: testbed apt version: 3.1.13 125s autopkgtest [08:51:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 125s autopkgtest [08:51:52]: testbed release detected to be: None 126s autopkgtest [08:51:53]: updating testbed package index (apt update) 126s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 126s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 126s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 126s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1058 kB] 127s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 127s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [95.5 kB] 127s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [124 kB] 127s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [104 kB] 127s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3384 B] 127s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 127s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 127s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 127s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [402 kB] 127s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [926 kB] 127s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [22.3 kB] 127s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [11.6 kB] 127s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 127s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [564 B] 128s Fetched 2920 kB in 1s (2557 kB/s) 129s Reading package lists... 130s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 130s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 131s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Calculating upgrade... 132s The following packages were automatically installed and are no longer required: 132s python3.13 python3.13-minimal 132s Use 'sudo apt autoremove' to remove them. 132s The following NEW packages will be installed: 132s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 132s The following packages will be upgraded: 132s libpython3-stdlib python3 python3-gdbm python3-minimal 132s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 6769 kB of archives. 132s After this operation, 24.5 MB of additional disk space will be used. 132s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 132s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 132s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 132s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 132s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 132s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 133s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 133s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 133s dpkg-preconfigure: unable to re-open stdin: No such file or directory 133s Fetched 6769 kB in 1s (8325 kB/s) 133s Selecting previously unselected package libpython3.14-minimal:amd64. 133s (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 ... 124176 files and directories currently installed.) 133s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 133s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 133s Selecting previously unselected package python3.14-minimal. 133s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 133s Unpacking python3.14-minimal (3.14.2-1) ... 133s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 134s Setting up python3.14-minimal (3.14.2-1) ... 135s (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 ... 124518 files and directories currently installed.) 135s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 135s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 135s Setting up python3-minimal (3.14.2-1) ... 135s (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 ... 124518 files and directories currently installed.) 135s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 135s running python pre-rtupdate hooks for python3.14... 135s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 135s Selecting previously unselected package libpython3.14-stdlib:amd64. 135s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 135s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 136s Selecting previously unselected package python3.14. 136s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 136s Unpacking python3.14 (3.14.2-1) ... 136s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 136s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 136s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 136s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 136s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 136s Setting up python3.14 (3.14.2-1) ... 137s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 137s Setting up python3-gdbm (3.14.2-1) ... 137s Setting up python3 (3.14.2-1) ... 137s running python rtupdate hooks for python3.14... 137s running python post-rtupdate hooks for python3.14... 137s Processing triggers for man-db (2.13.1-1) ... 138s Processing triggers for systemd (259-1ubuntu2) ... 138s autopkgtest [08:52:05]: upgrading testbed (apt dist-upgrade and autopurge) 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 139s The following packages were automatically installed and are no longer required: 139s python3.13 python3.13-minimal 139s Use 'sudo apt autoremove' to remove them. 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s Solving dependencies... 140s The following packages will be REMOVED: 140s python3.13* python3.13-minimal* 140s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 140s After this operation, 7860 kB disk space will be freed. 140s (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 ... 124948 files and directories currently installed.) 140s Removing python3.13 (3.13.11-1) ... 140s Removing python3.13-minimal (3.13.11-1) ... 141s Processing triggers for man-db (2.13.1-1) ... 142s Processing triggers for systemd (259-1ubuntu2) ... 142s (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 ... 124921 files and directories currently installed.) 142s Purging configuration files for python3.13-minimal (3.13.11-1) ... 144s autopkgtest [08:52:11]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 144s autopkgtest [08:52:11]: @@@@@@@@@@@@@@@@@@@@ apt-source propka 146s Get:1 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (dsc) [2286 B] 146s Get:2 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (tar) [376 kB] 146s Get:3 http://ftpmaster.internal/ubuntu resolute/universe propka 3.5.1-2 (diff) [5096 B] 147s gpgv: Signature made Wed Oct 16 14:47:53 2024 UTC 147s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 147s gpgv: issuer "emollier@debian.org" 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./propka_3.5.1-2.dsc: no acceptable signature found 147s autopkgtest [08:52:14]: testing package propka version 3.5.1-2 147s autopkgtest [08:52:14]: build not needed 147s autopkgtest [08:52:14]: test pybuild-autopkgtest: preparing testbed 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Solving dependencies... 148s The following NEW packages will be installed: 148s autoconf automake autopoint autotools-dev binutils-i686-linux-gnu 148s build-essential cpp cpp-15 cpp-15-i686-linux-gnu cpp-15-x86-64-linux-gnu 148s cpp-i686-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-i386 debhelper 148s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 148s dwz fonts-font-awesome fonts-lato fonts-mathjax g++ g++-15 148s g++-15-i686-linux-gnu g++-15-x86-64-linux-gnu g++-i686-linux-gnu 148s g++-x86-64-linux-gnu gcc gcc-11-base:i386 gcc-15 gcc-15-base:i386 148s gcc-15-cross-base gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base 148s gcc-15-x86-64-linux-gnu gcc-i686-linux-gnu gcc-x86-64-linux-gnu gettext 148s help2man intltool-debian libarchive-zip-perl libasan6:i386 libasan8 148s libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libblas3 148s libc-gconv-modules-extra:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross 148s libc6-i386-cross libcc1-0 libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl 148s libfile-stripnondeterminism-perl libgcc-11-dev:i386 libgcc-15-dev 148s libgcc-15-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5 148s libgomp1 libgomp1:i386 libgomp1-i386-cross libhwasan0 libisl23 libitm1 148s libitm1:i386 libitm1-i386-cross libjs-jquery libjs-mathjax libjson-perl 148s liblapack3 liblsan0 libmpc3 libquadmath0 libquadmath0:i386 148s libquadmath0-i386-cross libstdc++-11-dev:i386 libstdc++-15-dev 148s libstdc++-15-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libtool 148s libtsan2 libubsan1 libubsan1:i386 libubsan1-i386-cross linux-libc-dev:i386 148s linux-libc-dev-i386-cross m4 po-debconf pybuild-plugin-autopkgtest 148s python-propka-doc python3-alabaster python3-all python3-defusedxml 148s python3-docutils python3-imagesize python3-iniconfig python3-numpy 148s python3-numpy-dev python3-pluggy python3-propka python3-pytest 148s python3-roman-numerals python3-snowballstemmer python3-sphinx 148s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3.13 148s python3.13-minimal sgml-base sphinx-common sphinx-rtd-theme-common xml-core 148s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 197 MB of archives. 148s After this operation, 726 MB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 149s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1build1 [2779 kB] 149s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 149s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 149s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 149s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 149s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 149s Get:8 http://ftpmaster.internal/ubuntu resolute/main i386 gcc-15-base i386 15.2.0-11ubuntu1 [59.1 kB] 149s Get:9 http://ftpmaster.internal/ubuntu resolute/main i386 libc-gconv-modules-extra i386 2.42-2ubuntu4 [1359 kB] 149s Get:10 http://ftpmaster.internal/ubuntu resolute/main i386 libgcc-s1 i386 15.2.0-11ubuntu1 [94.1 kB] 149s Get:11 http://ftpmaster.internal/ubuntu resolute/main i386 libc6 i386 2.42-2ubuntu4 [1824 kB] 149s Get:12 http://ftpmaster.internal/ubuntu resolute/main i386 libcrypt1 i386 1:4.5.1-1 [100 kB] 149s Get:13 http://ftpmaster.internal/ubuntu resolute/main i386 libatomic1 i386 15.2.0-11ubuntu1 [8414 B] 149s Get:14 http://ftpmaster.internal/ubuntu resolute/main i386 libstdc++6 i386 15.2.0-11ubuntu1 [877 kB] 150s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 150s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 150s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 150s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 150s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 150s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 150s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 150s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 150s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [12.9 MB] 150s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-11ubuntu1 [1030 B] 150s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 150s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 150s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-11ubuntu1 [47.4 kB] 150s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 150s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-11ubuntu1 [29.5 kB] 150s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-11ubuntu1 [3070 kB] 150s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-11ubuntu1 [1360 kB] 150s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-11ubuntu1 [2757 kB] 151s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-11ubuntu1 [1210 kB] 151s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-11ubuntu1 [1685 kB] 151s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-11ubuntu1 [153 kB] 151s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-11ubuntu1 [2863 kB] 151s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [25.4 MB] 151s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-11ubuntu1 [528 kB] 151s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 151s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 151s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-11ubuntu1 [2574 kB] 152s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [14.4 MB] 152s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-11ubuntu1 [24.6 kB] 152s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 152s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 152s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 152s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-i686-linux-gnu-base amd64 15.2.0-7ubuntu1cross1 [58.6 kB] 152s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-i686-linux-gnu amd64 15.2.0-7ubuntu1cross1 [13.8 MB] 152s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [5730 B] 152s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 binutils-i686-linux-gnu amd64 2.45.50.20251209-1ubuntu1 [1763 kB] 152s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-cross-base all 15.2.0-7ubuntu1cross1 [53.8 kB] 152s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-i386-cross all 2.42-0ubuntu3cross1 [1582 kB] 152s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1-i386-cross all 15.2.0-7ubuntu1cross1 [94.2 kB] 152s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1-i386-cross all 15.2.0-7ubuntu1cross1 [152 kB] 152s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1-i386-cross all 15.2.0-7ubuntu1cross1 [31.1 kB] 152s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1-i386-cross all 15.2.0-7ubuntu1cross1 [8158 B] 152s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8-i386-cross all 15.2.0-7ubuntu1cross1 [2906 kB] 152s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6-i386-cross all 15.2.0-7ubuntu1cross1 [827 kB] 152s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1-i386-cross all 15.2.0-7ubuntu1cross1 [1171 kB] 152s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0-i386-cross all 15.2.0-7ubuntu1cross1 [245 kB] 152s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev-i386-cross all 15.2.0-7ubuntu1cross1 [2755 kB] 152s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-i686-linux-gnu amd64 15.2.0-7ubuntu1cross1 [27.0 MB] 153s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [1220 B] 153s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev-i386-cross all 6.17.0-4.4cross1 [1503 kB] 153s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev-i386-cross all 2.42-0ubuntu3cross1 [1992 kB] 153s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev-i386-cross all 15.2.0-7ubuntu1cross1 [2655 kB] 153s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-i686-linux-gnu amd64 15.2.0-7ubuntu1cross1 [15.3 MB] 153s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [954 B] 153s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 crossbuild-essential-i386 all 12.12ubuntu2 [4146 B] 153s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 153s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 153s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 153s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 153s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 153s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 153s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 153s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 153s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 153s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 153s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 153s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 153s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20251231 [122 kB] 153s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 153s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 153s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.22.4+dfsg-1 [130 kB] 153s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 154s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 154s Get:88 http://ftpmaster.internal/ubuntu resolute/universe i386 gcc-11-base i386 11.5.0-7ubuntu2 [46.5 kB] 154s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 help2man amd64 1.49.3 [201 kB] 154s Get:90 http://ftpmaster.internal/ubuntu resolute/universe i386 libasan6 i386 11.5.0-7ubuntu2 [2122 kB] 154s Get:91 http://ftpmaster.internal/ubuntu resolute/main i386 linux-libc-dev i386 6.18.0-9.9 [1861 kB] 154s Get:92 http://ftpmaster.internal/ubuntu resolute/main i386 libcrypt-dev i386 1:4.5.1-1 [131 kB] 154s Get:93 http://ftpmaster.internal/ubuntu resolute/main i386 libc6-dev i386 2.42-2ubuntu4 [1945 kB] 154s Get:94 http://ftpmaster.internal/ubuntu resolute/main i386 libgomp1 i386 15.2.0-11ubuntu1 [155 kB] 154s Get:95 http://ftpmaster.internal/ubuntu resolute/main i386 libitm1 i386 15.2.0-11ubuntu1 [31.6 kB] 154s Get:96 http://ftpmaster.internal/ubuntu resolute/main i386 libubsan1 i386 15.2.0-11ubuntu1 [1172 kB] 154s Get:97 http://ftpmaster.internal/ubuntu resolute/main i386 libquadmath0 i386 15.2.0-11ubuntu1 [246 kB] 154s Get:98 http://ftpmaster.internal/ubuntu resolute/universe i386 libgcc-11-dev i386 11.5.0-7ubuntu2 [2450 kB] 154s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 154s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 154s Get:101 http://ftpmaster.internal/ubuntu resolute/universe i386 libstdc++-11-dev i386 11.5.0-7ubuntu2 [2459 kB] 154s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 154s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 154s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 155s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-propka-doc all 3.5.1-2 [157 kB] 155s Get:106 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 155s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 155s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman-numerals all 4.1.0-1 [8660 B] 155s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 155s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-imagesize all 1.4.1-1build1 [6900 B] 155s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 155s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 155s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-propka all 3.5.1-2 [70.1 kB] 155s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 155s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 155s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-common all 8.2.3-12 [657 kB] 155s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 155s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-sphinx all 8.2.3-12 [483 kB] 155s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 155s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 155s Preconfiguring packages ... 155s Fetched 197 MB in 6s (30.8 MB/s) 155s Selecting previously unselected package python3.13-minimal. 155s (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 ... 124923 files and directories currently installed.) 155s Preparing to unpack .../000-python3.13-minimal_3.13.11-1_amd64.deb ... 155s Unpacking python3.13-minimal (3.13.11-1) ... 155s Selecting previously unselected package fonts-lato. 155s Preparing to unpack .../001-fonts-lato_2.015-1build1_all.deb ... 155s Unpacking fonts-lato (2.015-1build1) ... 155s Selecting previously unselected package python3-numpy-dev:amd64. 155s Preparing to unpack .../002-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 155s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 155s Selecting previously unselected package libblas3:amd64. 155s Preparing to unpack .../003-libblas3_3.12.1-7ubuntu1_amd64.deb ... 155s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package libgfortran5:amd64. 155s Preparing to unpack .../004-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 155s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 156s Selecting previously unselected package liblapack3:amd64. 156s Preparing to unpack .../005-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 156s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 156s Selecting previously unselected package python3-numpy. 156s Preparing to unpack .../006-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 156s Unpacking python3-numpy (1:2.3.5+ds-3) ... 156s Selecting previously unselected package gcc-15-base:i386. 156s Preparing to unpack .../007-gcc-15-base_15.2.0-11ubuntu1_i386.deb ... 156s Unpacking gcc-15-base:i386 (15.2.0-11ubuntu1) ... 156s Selecting previously unselected package libc-gconv-modules-extra:i386. 156s Preparing to unpack .../008-libc-gconv-modules-extra_2.42-2ubuntu4_i386.deb ... 156s Unpacking libc-gconv-modules-extra:i386 (2.42-2ubuntu4) ... 156s Selecting previously unselected package libgcc-s1:i386. 156s Preparing to unpack .../009-libgcc-s1_15.2.0-11ubuntu1_i386.deb ... 156s Unpacking libgcc-s1:i386 (15.2.0-11ubuntu1) ... 156s Selecting previously unselected package libc6:i386. 156s Preparing to unpack .../010-libc6_2.42-2ubuntu4_i386.deb ... 156s Unpacking libc6:i386 (2.42-2ubuntu4) ... 156s Selecting previously unselected package libcrypt1:i386. 156s Preparing to unpack .../011-libcrypt1_1%3a4.5.1-1_i386.deb ... 156s Unpacking libcrypt1:i386 (1:4.5.1-1) ... 156s Selecting previously unselected package libatomic1:i386. 156s Preparing to unpack .../012-libatomic1_15.2.0-11ubuntu1_i386.deb ... 156s Unpacking libatomic1:i386 (15.2.0-11ubuntu1) ... 156s Selecting previously unselected package libstdc++6:i386. 156s Preparing to unpack .../013-libstdc++6_15.2.0-11ubuntu1_i386.deb ... 156s Unpacking libstdc++6:i386 (15.2.0-11ubuntu1) ... 156s Selecting previously unselected package python3.13. 156s Preparing to unpack .../014-python3.13_3.13.11-1_amd64.deb ... 156s Unpacking python3.13 (3.13.11-1) ... 156s Selecting previously unselected package m4. 156s Preparing to unpack .../015-m4_1.4.20-2_amd64.deb ... 156s Unpacking m4 (1.4.20-2) ... 156s Selecting previously unselected package autoconf. 156s Preparing to unpack .../016-autoconf_2.72-3.1ubuntu1_all.deb ... 156s Unpacking autoconf (2.72-3.1ubuntu1) ... 157s Selecting previously unselected package autotools-dev. 157s Preparing to unpack .../017-autotools-dev_20240727.1_all.deb ... 157s Unpacking autotools-dev (20240727.1) ... 157s Selecting previously unselected package automake. 157s Preparing to unpack .../018-automake_1%3a1.18.1-3build1_all.deb ... 157s Unpacking automake (1:1.18.1-3build1) ... 157s Selecting previously unselected package autopoint. 157s Preparing to unpack .../019-autopoint_0.23.2-1_all.deb ... 157s Unpacking autopoint (0.23.2-1) ... 157s Selecting previously unselected package libisl23:amd64. 157s Preparing to unpack .../020-libisl23_0.27-1build1_amd64.deb ... 157s Unpacking libisl23:amd64 (0.27-1build1) ... 157s Selecting previously unselected package libmpc3:amd64. 157s Preparing to unpack .../021-libmpc3_1.3.1-2_amd64.deb ... 157s Unpacking libmpc3:amd64 (1.3.1-2) ... 157s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 157s Preparing to unpack .../022-cpp-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package cpp-15. 157s Preparing to unpack .../023-cpp-15_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package cpp-x86-64-linux-gnu. 157s Preparing to unpack .../024-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 157s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 157s Selecting previously unselected package cpp. 157s Preparing to unpack .../025-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 157s Unpacking cpp (4:15.2.0-4ubuntu1) ... 157s Selecting previously unselected package libcc1-0:amd64. 157s Preparing to unpack .../026-libcc1-0_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libcc1-0:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libgomp1:amd64. 157s Preparing to unpack .../027-libgomp1_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libgomp1:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libitm1:amd64. 157s Preparing to unpack .../028-libitm1_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libitm1:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libasan8:amd64. 157s Preparing to unpack .../029-libasan8_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libasan8:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package liblsan0:amd64. 157s Preparing to unpack .../030-liblsan0_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking liblsan0:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libtsan2:amd64. 157s Preparing to unpack .../031-libtsan2_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libtsan2:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libubsan1:amd64. 157s Preparing to unpack .../032-libubsan1_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libubsan1:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libhwasan0:amd64. 157s Preparing to unpack .../033-libhwasan0_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libhwasan0:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libquadmath0:amd64. 157s Preparing to unpack .../034-libquadmath0_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libquadmath0:amd64 (15.2.0-11ubuntu1) ... 157s Selecting previously unselected package libgcc-15-dev:amd64. 157s Preparing to unpack .../035-libgcc-15-dev_15.2.0-11ubuntu1_amd64.deb ... 157s Unpacking libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 158s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 158s Preparing to unpack .../036-gcc-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 158s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 158s Selecting previously unselected package gcc-15. 158s Preparing to unpack .../037-gcc-15_15.2.0-11ubuntu1_amd64.deb ... 158s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 158s Selecting previously unselected package gcc-x86-64-linux-gnu. 158s Preparing to unpack .../038-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 158s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 158s Selecting previously unselected package gcc. 158s Preparing to unpack .../039-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 158s Unpacking gcc (4:15.2.0-4ubuntu1) ... 158s Selecting previously unselected package libstdc++-15-dev:amd64. 158s Preparing to unpack .../040-libstdc++-15-dev_15.2.0-11ubuntu1_amd64.deb ... 158s Unpacking libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 158s Selecting previously unselected package g++-15-x86-64-linux-gnu. 158s Preparing to unpack .../041-g++-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 158s Unpacking g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 159s Selecting previously unselected package g++-15. 159s Preparing to unpack .../042-g++-15_15.2.0-11ubuntu1_amd64.deb ... 159s Unpacking g++-15 (15.2.0-11ubuntu1) ... 159s Selecting previously unselected package g++-x86-64-linux-gnu. 159s Preparing to unpack .../043-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 159s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 159s Selecting previously unselected package g++. 159s Preparing to unpack .../044-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 159s Unpacking g++ (4:15.2.0-4ubuntu1) ... 159s Selecting previously unselected package build-essential. 159s Preparing to unpack .../045-build-essential_12.12ubuntu2_amd64.deb ... 159s Unpacking build-essential (12.12ubuntu2) ... 159s Selecting previously unselected package gcc-15-i686-linux-gnu-base:amd64. 159s Preparing to unpack .../046-gcc-15-i686-linux-gnu-base_15.2.0-7ubuntu1cross1_amd64.deb ... 159s Unpacking gcc-15-i686-linux-gnu-base:amd64 (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package cpp-15-i686-linux-gnu. 159s Preparing to unpack .../047-cpp-15-i686-linux-gnu_15.2.0-7ubuntu1cross1_amd64.deb ... 159s Unpacking cpp-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package cpp-i686-linux-gnu. 159s Preparing to unpack .../048-cpp-i686-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 159s Unpacking cpp-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 159s Selecting previously unselected package binutils-i686-linux-gnu. 159s Preparing to unpack .../049-binutils-i686-linux-gnu_2.45.50.20251209-1ubuntu1_amd64.deb ... 159s Unpacking binutils-i686-linux-gnu (2.45.50.20251209-1ubuntu1) ... 159s Selecting previously unselected package gcc-15-cross-base. 159s Preparing to unpack .../050-gcc-15-cross-base_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking gcc-15-cross-base (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libc6-i386-cross. 159s Preparing to unpack .../051-libc6-i386-cross_2.42-0ubuntu3cross1_all.deb ... 159s Unpacking libc6-i386-cross (2.42-0ubuntu3cross1) ... 159s Selecting previously unselected package libgcc-s1-i386-cross. 159s Preparing to unpack .../052-libgcc-s1-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libgcc-s1-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libgomp1-i386-cross. 159s Preparing to unpack .../053-libgomp1-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libgomp1-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libitm1-i386-cross. 159s Preparing to unpack .../054-libitm1-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libitm1-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libatomic1-i386-cross. 159s Preparing to unpack .../055-libatomic1-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libatomic1-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libasan8-i386-cross. 159s Preparing to unpack .../056-libasan8-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libasan8-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libstdc++6-i386-cross. 159s Preparing to unpack .../057-libstdc++6-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libstdc++6-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libubsan1-i386-cross. 159s Preparing to unpack .../058-libubsan1-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libubsan1-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libquadmath0-i386-cross. 159s Preparing to unpack .../059-libquadmath0-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libquadmath0-i386-cross (15.2.0-7ubuntu1cross1) ... 159s Selecting previously unselected package libgcc-15-dev-i386-cross. 159s Preparing to unpack .../060-libgcc-15-dev-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 159s Unpacking libgcc-15-dev-i386-cross (15.2.0-7ubuntu1cross1) ... 160s Selecting previously unselected package gcc-15-i686-linux-gnu. 160s Preparing to unpack .../061-gcc-15-i686-linux-gnu_15.2.0-7ubuntu1cross1_amd64.deb ... 160s Unpacking gcc-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 160s Selecting previously unselected package gcc-i686-linux-gnu. 160s Preparing to unpack .../062-gcc-i686-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 160s Unpacking gcc-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 160s Selecting previously unselected package linux-libc-dev-i386-cross. 160s Preparing to unpack .../063-linux-libc-dev-i386-cross_6.17.0-4.4cross1_all.deb ... 160s Unpacking linux-libc-dev-i386-cross (6.17.0-4.4cross1) ... 160s Selecting previously unselected package libc6-dev-i386-cross. 160s Preparing to unpack .../064-libc6-dev-i386-cross_2.42-0ubuntu3cross1_all.deb ... 160s Unpacking libc6-dev-i386-cross (2.42-0ubuntu3cross1) ... 160s Selecting previously unselected package libstdc++-15-dev-i386-cross. 160s Preparing to unpack .../065-libstdc++-15-dev-i386-cross_15.2.0-7ubuntu1cross1_all.deb ... 160s Unpacking libstdc++-15-dev-i386-cross (15.2.0-7ubuntu1cross1) ... 160s Selecting previously unselected package g++-15-i686-linux-gnu. 160s Preparing to unpack .../066-g++-15-i686-linux-gnu_15.2.0-7ubuntu1cross1_amd64.deb ... 160s Unpacking g++-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 161s Selecting previously unselected package g++-i686-linux-gnu. 161s Preparing to unpack .../067-g++-i686-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 161s Unpacking g++-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 161s Selecting previously unselected package crossbuild-essential-i386. 161s Preparing to unpack .../068-crossbuild-essential-i386_12.12ubuntu2_all.deb ... 161s Unpacking crossbuild-essential-i386 (12.12ubuntu2) ... 161s Selecting previously unselected package libdebhelper-perl. 161s Preparing to unpack .../069-libdebhelper-perl_13.28ubuntu1_all.deb ... 161s Unpacking libdebhelper-perl (13.28ubuntu1) ... 161s Selecting previously unselected package libtool. 161s Preparing to unpack .../070-libtool_2.5.4-9_all.deb ... 161s Unpacking libtool (2.5.4-9) ... 161s Selecting previously unselected package dh-autoreconf. 161s Preparing to unpack .../071-dh-autoreconf_21_all.deb ... 161s Unpacking dh-autoreconf (21) ... 161s Selecting previously unselected package libarchive-zip-perl. 161s Preparing to unpack .../072-libarchive-zip-perl_1.68-1_all.deb ... 161s Unpacking libarchive-zip-perl (1.68-1) ... 161s Selecting previously unselected package libfile-stripnondeterminism-perl. 161s Preparing to unpack .../073-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 161s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 161s Selecting previously unselected package dh-strip-nondeterminism. 161s Preparing to unpack .../074-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 161s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 161s Selecting previously unselected package debugedit. 161s Preparing to unpack .../075-debugedit_1%3a5.2-3_amd64.deb ... 161s Unpacking debugedit (1:5.2-3) ... 161s Selecting previously unselected package dwz. 161s Preparing to unpack .../076-dwz_0.16-2_amd64.deb ... 161s Unpacking dwz (0.16-2) ... 161s Selecting previously unselected package gettext. 161s Preparing to unpack .../077-gettext_0.23.2-1_amd64.deb ... 161s Unpacking gettext (0.23.2-1) ... 161s Selecting previously unselected package intltool-debian. 161s Preparing to unpack .../078-intltool-debian_0.35.0+20060710.6build1_all.deb ... 161s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 161s Selecting previously unselected package po-debconf. 161s Preparing to unpack .../079-po-debconf_1.0.22_all.deb ... 161s Unpacking po-debconf (1.0.22) ... 161s Selecting previously unselected package debhelper. 161s Preparing to unpack .../080-debhelper_13.28ubuntu1_all.deb ... 161s Unpacking debhelper (13.28ubuntu1) ... 161s Selecting previously unselected package dh-python. 161s Preparing to unpack .../081-dh-python_7.20251231_all.deb ... 161s Unpacking dh-python (7.20251231) ... 161s Selecting previously unselected package sgml-base. 161s Preparing to unpack .../082-sgml-base_1.31+nmu1_all.deb ... 161s Unpacking sgml-base (1.31+nmu1) ... 161s Selecting previously unselected package xml-core. 161s Preparing to unpack .../083-xml-core_0.19build1_all.deb ... 161s Unpacking xml-core (0.19build1) ... 161s Selecting previously unselected package docutils-common. 161s Preparing to unpack .../084-docutils-common_0.22.4+dfsg-1_all.deb ... 161s Unpacking docutils-common (0.22.4+dfsg-1) ... 161s Selecting previously unselected package fonts-font-awesome. 161s Preparing to unpack .../085-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 161s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 161s Selecting previously unselected package fonts-mathjax. 161s Preparing to unpack .../086-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 161s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 161s Selecting previously unselected package gcc-11-base:i386. 161s Preparing to unpack .../087-gcc-11-base_11.5.0-7ubuntu2_i386.deb ... 161s Unpacking gcc-11-base:i386 (11.5.0-7ubuntu2) ... 161s Selecting previously unselected package help2man. 161s Preparing to unpack .../088-help2man_1.49.3_amd64.deb ... 161s Unpacking help2man (1.49.3) ... 162s Selecting previously unselected package libasan6:i386. 162s Preparing to unpack .../089-libasan6_11.5.0-7ubuntu2_i386.deb ... 162s Unpacking libasan6:i386 (11.5.0-7ubuntu2) ... 162s Selecting previously unselected package linux-libc-dev:i386. 162s Preparing to unpack .../090-linux-libc-dev_6.18.0-9.9_i386.deb ... 162s Unpacking linux-libc-dev:i386 (6.18.0-9.9) ... 162s Selecting previously unselected package libcrypt-dev:i386. 162s Preparing to unpack .../091-libcrypt-dev_1%3a4.5.1-1_i386.deb ... 162s Unpacking libcrypt-dev:i386 (1:4.5.1-1) ... 162s Selecting previously unselected package libc6-dev:i386. 162s Preparing to unpack .../092-libc6-dev_2.42-2ubuntu4_i386.deb ... 162s Unpacking libc6-dev:i386 (2.42-2ubuntu4) ... 162s Selecting previously unselected package libgomp1:i386. 162s Preparing to unpack .../093-libgomp1_15.2.0-11ubuntu1_i386.deb ... 162s Unpacking libgomp1:i386 (15.2.0-11ubuntu1) ... 162s Selecting previously unselected package libitm1:i386. 162s Preparing to unpack .../094-libitm1_15.2.0-11ubuntu1_i386.deb ... 162s Unpacking libitm1:i386 (15.2.0-11ubuntu1) ... 162s Selecting previously unselected package libubsan1:i386. 162s Preparing to unpack .../095-libubsan1_15.2.0-11ubuntu1_i386.deb ... 162s Unpacking libubsan1:i386 (15.2.0-11ubuntu1) ... 162s Selecting previously unselected package libquadmath0:i386. 162s Preparing to unpack .../096-libquadmath0_15.2.0-11ubuntu1_i386.deb ... 162s Unpacking libquadmath0:i386 (15.2.0-11ubuntu1) ... 162s Selecting previously unselected package libgcc-11-dev:i386. 162s Preparing to unpack .../097-libgcc-11-dev_11.5.0-7ubuntu2_i386.deb ... 162s Unpacking libgcc-11-dev:i386 (11.5.0-7ubuntu2) ... 162s Selecting previously unselected package libjs-jquery. 162s Preparing to unpack .../098-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 162s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 162s Selecting previously unselected package libjson-perl. 162s Preparing to unpack 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.../104-python-propka-doc_3.5.1-2_all.deb ... 163s Unpacking python-propka-doc (3.5.1-2) ... 163s Selecting previously unselected package python3-all. 163s Preparing to unpack .../105-python3-all_3.14.2-1_amd64.deb ... 163s Unpacking python3-all (3.14.2-1) ... 163s Selecting previously unselected package python3-defusedxml. 163s Preparing to unpack .../106-python3-defusedxml_0.7.1-3build1_all.deb ... 163s Unpacking python3-defusedxml (0.7.1-3build1) ... 163s Selecting previously unselected package python3-roman-numerals. 163s Preparing to unpack .../107-python3-roman-numerals_4.1.0-1_all.deb ... 163s Unpacking python3-roman-numerals (4.1.0-1) ... 163s Selecting previously unselected package python3-docutils. 163s Preparing to unpack .../108-python3-docutils_0.22.4+dfsg-1_all.deb ... 163s Unpacking python3-docutils (0.22.4+dfsg-1) ... 163s Selecting previously unselected package python3-imagesize. 163s Preparing to unpack .../109-python3-imagesize_1.4.1-1build1_all.deb ... 163s Unpacking python3-imagesize (1.4.1-1build1) ... 163s Selecting previously unselected package python3-iniconfig. 163s Preparing to unpack .../110-python3-iniconfig_2.1.0-2_all.deb ... 163s Unpacking python3-iniconfig (2.1.0-2) ... 163s Selecting previously unselected package python3-pluggy. 163s Preparing to unpack .../111-python3-pluggy_1.6.0-2_all.deb ... 163s Unpacking python3-pluggy (1.6.0-2) ... 163s Selecting previously unselected package python3-propka. 163s Preparing to unpack .../112-python3-propka_3.5.1-2_all.deb ... 163s Unpacking python3-propka (3.5.1-2) ... 163s Selecting previously unselected package python3-pytest. 163s Preparing to unpack .../113-python3-pytest_9.0.2-2_all.deb ... 163s Unpacking python3-pytest (9.0.2-2) ... 164s Selecting previously unselected package python3-snowballstemmer. 164s Preparing to unpack .../114-python3-snowballstemmer_3.0.1-1_all.deb ... 164s Unpacking python3-snowballstemmer (3.0.1-1) ... 164s Selecting previously unselected package 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Setting up dh-python (7.20251231) ... 164s Setting up python3-iniconfig (2.1.0-2) ... 164s Setting up gcc-11-base:i386 (11.5.0-7ubuntu2) ... 164s Setting up python3-propka (3.5.1-2) ... 165s Setting up fonts-lato (2.015-1build1) ... 165s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 165s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 165s Setting up python3-defusedxml (0.7.1-3build1) ... 165s Setting up libarchive-zip-perl (1.68-1) ... 165s Setting up python3-alabaster (0.7.16-0.1build1) ... 165s Setting up binutils-i686-linux-gnu (2.45.50.20251209-1ubuntu1) ... 165s Setting up libdebhelper-perl (13.28ubuntu1) ... 165s Setting up linux-libc-dev:i386 (6.18.0-9.9) ... 165s Setting up m4 (1.4.20-2) ... 165s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 165s Setting up help2man (1.49.3) ... 165s Setting up linux-libc-dev-i386-cross (6.17.0-4.4cross1) ... 165s Setting up autotools-dev (20240727.1) ... 165s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 165s 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 165s Setting up python3-snowballstemmer (3.0.1-1) ... 166s Setting up libquadmath0:amd64 (15.2.0-11ubuntu1) ... 166s Setting up libmpc3:amd64 (1.3.1-2) ... 166s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 166s Setting up gcc-15-i686-linux-gnu-base:amd64 (15.2.0-7ubuntu1cross1) ... 166s Setting up autopoint (0.23.2-1) ... 166s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 166s Setting up autoconf (2.72-3.1ubuntu1) ... 166s Setting up python3-pluggy (1.6.0-2) ... 166s Setting up libubsan1:amd64 (15.2.0-11ubuntu1) ... 166s Setting up dwz (0.16-2) ... 166s Setting up libhwasan0:amd64 (15.2.0-11ubuntu1) ... 166s Setting up libasan8:amd64 (15.2.0-11ubuntu1) ... 166s Setting up libjson-perl (4.10000-1) ... 166s Setting up debugedit (1:5.2-3) ... 166s Setting up libc6-i386-cross (2.42-0ubuntu3cross1) ... 166s Setting up python3-roman-numerals (4.1.0-1) ... 166s Setting up python3.13-minimal (3.13.11-1) ... 167s Setting up sgml-base (1.31+nmu1) ... 167s Setting up libtsan2:amd64 (15.2.0-11ubuntu1) ... 167s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 167s Setting up libisl23:amd64 (0.27-1build1) ... 167s Setting up gcc-15-cross-base (15.2.0-7ubuntu1cross1) ... 167s Setting up gcc-15-base:i386 (15.2.0-11ubuntu1) ... 167s Setting up libquadmath0-i386-cross (15.2.0-7ubuntu1cross1) ... 167s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 167s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 167s Setting up libcc1-0:amd64 (15.2.0-11ubuntu1) ... 167s Setting up liblsan0:amd64 (15.2.0-11ubuntu1) ... 167s Setting up libitm1:amd64 (15.2.0-11ubuntu1) ... 167s Setting up python3-imagesize (1.4.1-1build1) ... 167s Setting up automake (1:1.18.1-3build1) ... 167s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 167s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 167s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 167s 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 167s Setting up gettext (0.23.2-1) ... 167s Setting up libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 167s Setting up libatomic1-i386-cross (15.2.0-7ubuntu1cross1) ... 167s Setting up python3.13 (3.13.11-1) ... 169s Setting up python3-pytest (9.0.2-2) ... 170s Setting up python3-all (3.14.2-1) ... 170s Setting up cpp-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 170s Setting up libgomp1-i386-cross (15.2.0-7ubuntu1cross1) ... 170s Setting up libc6-dev-i386-cross (2.42-0ubuntu3cross1) ... 170s Setting up cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 170s Setting up intltool-debian (0.35.0+20060710.6build1) ... 170s Setting up gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 170s Setting up libgcc-s1-i386-cross (15.2.0-7ubuntu1cross1) ... 170s Setting up libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 170s Setting up sphinx-common (8.2.3-12) ... 170s Setting up libitm1-i386-cross (15.2.0-7ubuntu1cross1) ... 170s Setting up python3-numpy (1:2.3.5+ds-3) ... 174s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 174s Setting up python-propka-doc (3.5.1-2) ... 174s Setting up cpp-15 (15.2.0-11ubuntu1) ... 174s Setting up xml-core (0.19build1) ... 174s Setting up cpp-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 174s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up po-debconf (1.0.22) ... 174s Setting up libasan8-i386-cross (15.2.0-7ubuntu1cross1) ... 174s Setting up libstdc++6-i386-cross (15.2.0-7ubuntu1cross1) ... 174s Setting up gcc-15 (15.2.0-11ubuntu1) ... 174s Setting up cpp (4:15.2.0-4ubuntu1) ... 174s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up g++-15 (15.2.0-11ubuntu1) ... 174s Setting up libtool (2.5.4-9) ... 174s Setting up libubsan1-i386-cross (15.2.0-7ubuntu1cross1) ... 174s Setting up gcc (4:15.2.0-4ubuntu1) ... 174s Setting up dh-autoreconf (21) ... 174s Setting up libgcc-15-dev-i386-cross (15.2.0-7ubuntu1cross1) ... 174s Setting up libstdc++-15-dev-i386-cross (15.2.0-7ubuntu1cross1) ... 174s Setting up g++ (4:15.2.0-4ubuntu1) ... 174s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 174s Setting up build-essential (12.12ubuntu2) ... 174s Setting up gcc-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 174s Setting up debhelper (13.28ubuntu1) ... 174s Setting up g++-15-i686-linux-gnu (15.2.0-7ubuntu1cross1) ... 174s Setting up gcc-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up g++-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 174s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 174s Setting up crossbuild-essential-i386 (12.12ubuntu2) ... 174s Setting up libgcc-s1:i386 (15.2.0-11ubuntu1) ... 174s Setting up libc6:i386 (2.42-2ubuntu4) ... 174s Setting up libstdc++6:i386 (15.2.0-11ubuntu1) ... 174s Setting up libitm1:i386 (15.2.0-11ubuntu1) ... 174s Setting up libcrypt1:i386 (1:4.5.1-1) ... 174s Setting up libgomp1:i386 (15.2.0-11ubuntu1) ... 174s Setting up libasan6:i386 (11.5.0-7ubuntu2) ... 174s Setting up libquadmath0:i386 (15.2.0-11ubuntu1) ... 174s Setting up libatomic1:i386 (15.2.0-11ubuntu1) ... 174s Setting up libubsan1:i386 (15.2.0-11ubuntu1) ... 174s Setting up libgcc-11-dev:i386 (11.5.0-7ubuntu2) ... 174s Setting up libcrypt-dev:i386 (1:4.5.1-1) ... 174s Setting up libc6-dev:i386 (2.42-2ubuntu4) ... 174s Setting up libstdc++-11-dev:i386 (11.5.0-7ubuntu2) ... 174s Processing triggers for install-info (7.2-5) ... 174s Processing triggers for libc-bin (2.42-2ubuntu4) ... 174s Processing triggers for systemd (259-1ubuntu2) ... 175s Processing triggers for man-db (2.13.1-1) ... 177s Processing triggers for sgml-base (1.31+nmu1) ... 177s Setting up docutils-common (0.22.4+dfsg-1) ... 177s Processing triggers for sgml-base (1.31+nmu1) ... 177s Setting up python3-docutils (0.22.4+dfsg-1) ... 178s Setting up python3-sphinx (8.2.3-12) ... 180s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 180s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 181s autopkgtest [08:52:48]: test environment configured for cross building 181s autopkgtest [08:52:48]: test pybuild-autopkgtest: pybuild-autopkgtest 181s autopkgtest [08:52:48]: test pybuild-autopkgtest: [----------------------- 182s pybuild-autopkgtest 182s I: pybuild base:384: cd /tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build; python3.13 -m pytest -k 'not test_molecular_container' 183s ============================= test session starts ============================== 183s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 183s rootdir: /tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build 183s plugins: typeguard-4.4.4 183s collected 49 items / 2 deselected / 47 selected 183s 185s tests/test_basic_regression.py ....... [ 14%] 185s tests/test_hybrid36.py .. [ 19%] 185s tests/test_input.py .. [ 23%] 185s tests/test_lib.py .. [ 27%] 185s tests/test_protonate.py . [ 29%] 187s tests/test_run.py ........ [ 46%] 188s tests/test_streamio.py ........ [ 63%] 188s tests/test_vector_algebra.py ............... [ 95%] 189s tests/test_version.py .. [100%] 189s 189s ======================= 47 passed, 2 deselected in 5.95s ======================= 189s I: pybuild base:384: cd /tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 189s ============================= test session starts ============================== 189s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 189s rootdir: /tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build 189s plugins: typeguard-4.4.4 189s collected 49 items / 2 deselected / 47 selected 189s 189s tests/test_basic_regression.py FFFFFFF [ 14%] 189s tests/test_hybrid36.py .. [ 19%] 189s tests/test_input.py .. [ 23%] 189s tests/test_lib.py .. [ 27%] 189s tests/test_protonate.py . [ 29%] 189s tests/test_run.py FFFFFFFF [ 46%] 190s tests/test_streamio.py FFFFFFFF [ 63%] 190s tests/test_vector_algebra.py ............... [ 95%] 190s tests/test_version.py .. [100%] 190s 190s =================================== FAILURES =================================== 190s ________________ test_regression[sample-issue-140: no options] _________________ 190s 190s pdb = 'sample-issue-140' 190s options = ['/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/sample-issue-140.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_sample_issue_10 because of PROPKA file output; need to fix this. 190s __________________ test_regression[1FTJ-Chain-A: no options] ___________________ 190s 190s pdb = '1FTJ-Chain-A' 190s options = ['/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/1FTJ-Chain-A.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1FTJ_Chain_A__0 because of PROPKA file output; need to fix this. 190s ______________________ test_regression[1HPX: no options] _______________________ 190s 190s pdb = '1HPX' 190s options = ['/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/1HPX.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX__no_optio0 because of PROPKA file output; need to fix this. 190s ______________________ test_regression[4DFR: no options] _______________________ 190s 190s pdb = '4DFR' 190s options = ['/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/4DFR.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_4DFR__no_optio0 because of PROPKA file output; need to fix this. 190s ______________________ test_regression[3SGB: no options] _______________________ 190s 190s pdb = '3SGB' 190s options = ['/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/3SGB.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB__no_optio0 because of PROPKA file output; need to fix this. 190s ____________________ test_regression[3SGB: --titrate_only] _____________________ 190s 190s pdb = '3SGB-subset' 190s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/3SGB-subset.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_3SGB____titrat0 because of PROPKA file output; need to fix this. 190s _____________________ test_regression[1HPX-warn: --quiet] ______________________ 190s 190s pdb = '1HPX-warn' 190s options = ['--quiet', '/tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build/tests/pdb/1HPX-warn.pdb'] 190s tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param('sample-issue-140', [], id="sample-issue-140: no options"), 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('1HPX', [], id="1HPX: no options"), 190s pytest.param('4DFR', [], id="4DFR: no options"), 190s pytest.param('3SGB', [], id="3SGB: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")]) 190s def test_regression(pdb, options, tmp_path): 190s """Basic regression test of PROPKA functionality.""" 190s path_dict = get_test_dirs() 190s ref_path = None 190s 190s for ext in ["json", "dat"]: 190s ref_path = path_dict["results"] / f"{pdb}.{ext}" 190s if ref_path.is_file(): 190s ref_path = ref_path.resolve() 190s break 190s else: 190s _LOGGER.warning("Missing results file for comparison: {0:s}".format( 190s str(ref_path))) 190s ref_path = None 190s pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb)) 190s if pdb_path.is_file(): 190s pdb_path = pdb_path.resolve() 190s else: 190s errstr = "Missing PDB file: {0:s}".format(pdb_path) 190s raise FileNotFoundError(errstr) 190s tmp_path = Path(tmp_path).resolve() 190s 190s > run_propka(options, pdb_path, tmp_path) 190s 190s tests/test_basic_regression.py:170: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_basic_regression.py:77: in run_propka 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ------------------------------ Captured log call ------------------------------- 190s WARNING tests.test_basic_regression:test_basic_regression.py:73 Working in tmpdir /tmp/pytest-of-ubuntu/pytest-1/test_regression_1HPX_warn____q0 because of PROPKA file output; need to fix this. 190s __________________ test_single_file[1FTJ-Chain-A: no options] __________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1FTJ_Chain_A_0') 190s pdb = '1FTJ-Chain-A', options = () 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_file(tmpdir, pdb, options): 190s """Basic regression test using propka.run.single and local file for the 190s input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = str(pdb_path) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options) 190s 190s tests/test_run.py:31: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ____________________ test_single_file[3SGB: --titrate_only] ____________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_3SGB____titra0') 190s pdb = '3SGB-subset' 190s options = ('--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_file(tmpdir, pdb, options): 190s """Basic regression test using propka.run.single and local file for the 190s input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = str(pdb_path) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options) 190s 190s tests/test_run.py:31: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _____________________ test_single_file[1HPX-warn: --quiet] _____________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_file_1HPX_warn____0') 190s pdb = '1HPX-warn', options = ('--quiet',) 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_file(tmpdir, pdb, options): 190s """Basic regression test using propka.run.single and local file for the 190s input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = str(pdb_path) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options) 190s 190s tests/test_run.py:31: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _______________ test_single_filestream[1FTJ-Chain-A: no options] _______________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1FTJ_Ch0') 190s pdb = '1FTJ-Chain-A', options = () 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options, stream=filestream) 190s 190s tests/test_run.py:53: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _________________ test_single_filestream[3SGB: --titrate_only] _________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_3SGB___0') 190s pdb = '3SGB-subset' 190s options = ('--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139') 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options, stream=filestream) 190s 190s tests/test_run.py:53: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s __________________ test_single_filestream[1HPX-warn: --quiet] __________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_filestream_1HPX_wa0') 190s pdb = '1HPX-warn', options = ('--quiet',) 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', ( 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"), 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn',('--quiet',), id="1HPX-warn: --quiet"), 190s ]) 190s def test_single_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options, stream=filestream) 190s 190s tests/test_run.py:53: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ______________________________ test_single_nopka _______________________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_nopka0') 190s 190s def test_single_nopka(tmpdir): 190s """Basic test to check that the pKa file is not written when write_pka is 190s `False`""" 190s pdb = "1FTJ-Chain-A" 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s > pkrun.single(filename, stream=filestream, write_pka=False) 190s 190s tests/test_run.py:70: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _______________________ test_single_extra_files_logwarn ________________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_single_extra_files_logwar0') 190s caplog = <_pytest.logging.LogCaptureFixture object at 0x7eebe687c830> 190s 190s def test_single_extra_files_logwarn(tmpdir, caplog): 190s """Tests that a logging warning is thrown if passing files via optargs""" 190s pdb = "1FTJ-Chain-A" 190s options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb') 190s ref_path, pdb_path = get_paths(pdb) 190s filename = str(pdb_path) 190s 190s with tmpdir.as_cwd(): 190s > pkrun.single(filename, options) 190s 190s tests/test_run.py:82: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s /usr/lib/python3/dist-packages/propka/run.py:118: in single 190s parameters = read_parameter_file(options.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _______________ test_textio_filestream[1FTJ-Chain-A: no options] _______________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1FTJ_Ch0') 190s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_textio_filestream(tmpdir, pdb, options): 190s """Basic regression test using TextIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s filestream = open(pdb_path, 'r') 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:60: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _________________ test_textio_filestream[3SGB: --titrate_only] _________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_3SGB___0') 190s pdb = '3SGB-subset' 190s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '3SGB-subset.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_textio_filestream(tmpdir, pdb, options): 190s """Basic regression test using TextIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s filestream = open(pdb_path, 'r') 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:60: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s __________________ test_textio_filestream[1HPX-warn: --quiet] __________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_textio_filestream_1HPX_wa0') 190s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_textio_filestream(tmpdir, pdb, options): 190s """Basic regression test using TextIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s filestream = open(pdb_path, 'r') 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:60: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ______________ test_stringio_filestream[1FTJ-Chain-A: no options] ______________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1FTJ_0') 190s pdb = '1FTJ-Chain-A', options = ['1FTJ-Chain-A.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_stringio_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:84: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_3SGB_0') 190s pdb = '3SGB-subset' 190s options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '3SGB-subset.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_stringio_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:84: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ 190s 190s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_stringio_filestream_1HPX_0') 190s pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] 190s 190s @pytest.mark.parametrize("pdb, options", [ 190s pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), 190s pytest.param('3SGB-subset', [ 190s "--titrate_only", 190s "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], 190s id="3SGB: --titrate_only"), 190s pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), 190s ]) 190s def test_stringio_filestream(tmpdir, pdb, options): 190s """Basic regression test using StringIO streams for the input PDB file""" 190s # Get the relevant paths 190s ref_path, pdb_path = get_paths(pdb) 190s filename = f"{pdb}.pdb" 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s with tmpdir.as_cwd(): 190s > run_propka_stream(options, filestream, filename) 190s 190s tests/test_streamio.py:84: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s __________________________ test_valuerror_nofiletype ___________________________ 190s 190s def test_valuerror_nofiletype(): 190s """Tests for raised ValueError when an unknown filename is passed to 190s read_molecule_file""" 190s pdb = "1FTJ-Chain-A" 190s options = [] 190s 190s ref_path, pdb_path = get_paths(pdb) 190s 190s with open(pdb_path, 'r') as writer: 190s filestream = StringIO(writer.read()) 190s 190s errmsg = "Unknown input file type" 190s with pytest.raises(ValueError, match=errmsg): 190s > run_propka_stream(options, filestream, filename="test.dat") 190s 190s tests/test_streamio.py:103: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s ____________________________ test_valuerror_notpdb _____________________________ 190s 190s def test_valuerror_notpdb(): 190s """Tests for raised ValueError when a stream object that isn't a PDB 190s is passed to read_molecule_file""" 190s pdb = "1FTJ-Chain-A" 190s options = [] 190s 190s ref_path, pdb_path = get_paths(pdb) 190s 190s filestream = StringIO() 190s 190s errmsg = "The pdb file does not seem to contain any " 190s with pytest.raises(ValueError, match=errmsg): 190s > run_propka_stream(options, filestream, filename="test.pdb") 190s 190s tests/test_streamio.py:118: 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s tests/test_streamio.py:36: in run_propka_stream 190s parameters = read_parameter_file(args.parameters, Parameters()) 190s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 190s /usr/lib/python3/dist-packages/propka/input.py:153: in read_parameter_file 190s parameters.parse_line(line) 190s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 190s 190s self = Parameters(interaction_matrix=, sidechain_cutoffs= typeannotation = self.__annotations__.get(words[0]) 190s ^^^^^^^^^^^^^^^^^^^^ 190s E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? 190s 190s /usr/lib/python3/dist-packages/propka/parameters.py:148: AttributeError 190s =========================== short test summary info ============================ 190s FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] 190s FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] 190s FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... 190s FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... 190s FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... 190s FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] 190s FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... 190s FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... 190s FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... 190s FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... 190s FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... 190s FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... 190s FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... 190s FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... 190s FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... 190s FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] 190s FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] 190s FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... 190s FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] 190s FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] 190s FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] 190s FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... 190s FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... 190s ================= 23 failed, 24 passed, 2 deselected in 0.67s ================== 190s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=1: cd /tmp/autopkgtest.D9w3L2/autopkgtest_tmp/build; python3.14 -m pytest -k 'not test_molecular_container' 190s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 190s make: *** [/tmp/uuQ2vFl3ii/run:4: pybuild-autopkgtest] Error 25 190s pybuild-autopkgtest: error: /tmp/uuQ2vFl3ii/run pybuild-autopkgtest returned exit code 2 190s autopkgtest [08:52:57]: test pybuild-autopkgtest: -----------------------] 191s pybuild-autopkgtest FAIL non-zero exit status 25 191s autopkgtest [08:52:58]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 191s autopkgtest [08:52:58]: @@@@@@@@@@@@@@@@@@@@ summary 191s pybuild-autopkgtest FAIL non-zero exit status 25