0s autopkgtest [21:35:21]: starting date and time: 2026-01-23 21:35:21+0000 0s autopkgtest [21:35:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [21:35:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gbpjmeb9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:graphviz,src:apbs,src:binutils,src:ccls,src:cp2k,src:createrepo-c,src:gcc-11,src:gcc-12,src:gcc-13,src:gcc-14,src:gcc-15,src:gcc-snapshot,src:gdm3,src:hkl,src:hmmer,src:ktimetracker,src:libixion,src:liborcus,src:libpeas,src:libpeas2,src:libreoffice,src:libsndfile,src:libzstd,src:link-grammar,src:mosquitto,src:orthanc-python,src:psychopy,src:pyside2,src:python3-defaults,src:rumur,src:systemd,src:tifffile,src:vim --apt-upgrade snakemake --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=graphviz/14.1.1-2ubuntu3 apbs/3.4.1-7build1 binutils/2.45.50.20260119-1ubuntu1 ccls/0.20250815-0ubuntu1 cp2k/2025.2-3 createrepo-c/1.2.1-2build1 gcc-11/11.5.0-8ubuntu1 gcc-12/12.5.0-7ubuntu1 gcc-13/13.4.0-5ubuntu1 gcc-14/14.3.0-11ubuntu1 gcc-15/15.2.0-12ubuntu1 gcc-snapshot/1:20260121-1ubuntu1 gdm3/50~alpha.1-0ubuntu1 hkl/5.1.4-1 hmmer/3.4+dfsg-3 ktimetracker/4:6.0.0-1build1 libixion/0.20.0-6build1 liborcus/0.21.0-2build1 libpeas/1.36.0-8build1 libpeas2/2.2.0-2build1 libreoffice/4:25.8.4~rc2-0ubuntu2 libsndfile/1.2.2-4 libzstd/1.5.7+dfsg-3 link-grammar/5.13.0+dfsg-1build1 mosquitto/2.0.22-5 orthanc-python/7.0+ds-1build1 psychopy/2023.2.4+dfsg-4 pyside2/5.15.18-1 python3-defaults/3.14.2-1 rumur/2025.08.31-1 systemd/259-1ubuntu3 tifffile/20260114-1 vim/2:9.1.1882-1ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-12.secgroup --name adt-resolute-arm64-snakemake-20260123-213521-juju-7f2275-prod-proposed-migration-environment-15-a1ac83dd-4d87-4977-9fc3-62ee2898c767 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-snakemake-20260123-213521-juju-7f2275-prod-proposed-migration-environment-15-a1ac83dd-4d87-4977-9fc3-62ee2898c767 from image adt/ubuntu-resolute-arm64-server-20260123.img (UUID af50d520-9a73-4a18-8f4a-1e9db3030ff5)... 61s autopkgtest [21:36:22]: testbed dpkg architecture: arm64 61s autopkgtest [21:36:22]: testbed apt version: 3.1.13 62s autopkgtest [21:36:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [21:36:23]: testbed release detected to be: None 63s autopkgtest [21:36:24]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [97.3 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1021 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3892 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [12.3 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 64s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [900 kB] 65s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [22.3 kB] 65s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [11.5 kB] 65s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [556 B] 68s Fetched 2336 kB in 2s (1256 kB/s) 69s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 72s The following packages were automatically installed and are no longer required: 72s python3.13 python3.13-minimal 72s Use 'sudo apt autoremove' to remove them. 72s The following NEW packages will be installed: 72s libpython3.14-minimal libpython3.14-stdlib libsframe3 python3.14 72s python3.14-minimal 72s The following packages will be upgraded: 72s binutils binutils-aarch64-linux-gnu binutils-common gcc-15-base libatomic1 72s libbinutils libctf-nobfd0 libctf0 libgcc-s1 libgprofng0 libnss-systemd 72s libpam-systemd libplymouth5 libpython3-stdlib libstdc++6 libsystemd-shared 72s libsystemd0 libtasn1-6 libudev1 libzstd1 plymouth plymouth-theme-ubuntu-text 72s python3 python3-gdbm python3-jaraco.context python3-minimal systemd 72s systemd-cryptsetup systemd-resolved systemd-sysv systemd-userdbd udev 72s vim-common vim-tiny xxd zstd 72s 36 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 22.1 MB of archives. 72s After this operation, 26.0 MB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 72s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 72s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 72s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libzstd1 arm64 1.5.7+dfsg-3 [277 kB] 72s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 72s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 72s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 72s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 systemd-userdbd arm64 259-1ubuntu3 [50.7 kB] 72s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libnss-systemd arm64 259-1ubuntu3 [284 kB] 72s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libsystemd0 arm64 259-1ubuntu3 [532 kB] 72s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 systemd-sysv arm64 259-1ubuntu3 [9248 B] 72s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 systemd-resolved arm64 259-1ubuntu3 [291 kB] 72s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpam-systemd arm64 259-1ubuntu3 [267 kB] 72s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libsystemd-shared arm64 259-1ubuntu3 [2435 kB] 73s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 systemd arm64 259-1ubuntu3 [3060 kB] 73s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 systemd-cryptsetup arm64 259-1ubuntu3 [122 kB] 73s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 udev arm64 259-1ubuntu3 [1468 kB] 73s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libudev1 arm64 259-1ubuntu3 [209 kB] 73s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libstdc++6 arm64 15.2.0-12ubuntu1 [760 kB] 73s Get:21 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libatomic1 arm64 15.2.0-12ubuntu1 [11.2 kB] 73s Get:22 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 gcc-15-base arm64 15.2.0-12ubuntu1 [59.6 kB] 73s Get:23 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libgcc-s1 arm64 15.2.0-12ubuntu1 [61.1 kB] 73s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libtasn1-6 arm64 4.21.0-2 [44.4 kB] 73s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 vim-tiny arm64 2:9.1.1882-1ubuntu2 [826 kB] 73s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 vim-common all 2:9.1.1882-1ubuntu2 [402 kB] 73s Get:27 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 xxd arm64 2:9.1.1882-1ubuntu2 [70.4 kB] 73s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libplymouth5 arm64 24.004.60+git20250831.4a3c171d-0ubuntu5 [141 kB] 73s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60+git20250831.4a3c171d-0ubuntu5 [9982 B] 73s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth arm64 24.004.60+git20250831.4a3c171d-0ubuntu5 [133 kB] 73s Get:31 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 73s Get:32 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libgprofng0 arm64 2.45.50.20260119-1ubuntu1 [789 kB] 73s Get:33 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libctf0 arm64 2.45.50.20260119-1ubuntu1 [101 kB] 73s Get:34 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libctf-nobfd0 arm64 2.45.50.20260119-1ubuntu1 [104 kB] 73s Get:35 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.45.50.20260119-1ubuntu1 [1007 kB] 73s Get:36 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libbinutils arm64 2.45.50.20260119-1ubuntu1 [800 kB] 73s Get:37 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 binutils arm64 2.45.50.20260119-1ubuntu1 [227 kB] 73s Get:38 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 binutils-common arm64 2.45.50.20260119-1ubuntu1 [222 kB] 73s Get:39 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libsframe3 arm64 2.45.50.20260119-1ubuntu1 [21.4 kB] 73s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-jaraco.context all 6.0.1-2 [8198 B] 73s Get:41 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 zstd arm64 1.5.7+dfsg-3 [596 kB] 73s dpkg-preconfigure: unable to re-open stdin: No such file or directory 73s Fetched 22.1 MB in 1s (21.8 MB/s) 73s Selecting previously unselected package libpython3.14-minimal:arm64. 74s (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 ... 135220 files and directories currently installed.) 74s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 74s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 74s Selecting previously unselected package python3.14-minimal. 74s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 74s Unpacking python3.14-minimal (3.14.2-1) ... 74s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 74s Setting up python3.14-minimal (3.14.2-1) ... 75s (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 ... 135562 files and directories currently installed.) 75s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 75s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 75s Setting up python3-minimal (3.14.2-1) ... 76s (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 ... 135562 files and directories currently installed.) 76s Preparing to unpack .../python3_3.14.2-1_arm64.deb ... 76s running python pre-rtupdate hooks for python3.14... 76s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 76s Preparing to unpack .../libzstd1_1.5.7+dfsg-3_arm64.deb ... 76s Unpacking libzstd1:arm64 (1.5.7+dfsg-3) over (1.5.7+dfsg-2) ... 76s Setting up libzstd1:arm64 (1.5.7+dfsg-3) ... 76s Selecting previously unselected package libpython3.14-stdlib:arm64. 76s (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 ... 135563 files and directories currently installed.) 76s Preparing to unpack .../0-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 76s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 76s Selecting previously unselected package python3.14. 76s Preparing to unpack .../1-python3.14_3.14.2-1_arm64.deb ... 76s Unpacking python3.14 (3.14.2-1) ... 76s Preparing to unpack .../2-libpython3-stdlib_3.14.2-1_arm64.deb ... 76s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.9-3) ... 76s Preparing to unpack .../3-systemd-userdbd_259-1ubuntu3_arm64.deb ... 76s Unpacking systemd-userdbd (259-1ubuntu3) over (259-1ubuntu2) ... 76s Preparing to unpack .../4-libnss-systemd_259-1ubuntu3_arm64.deb ... 76s Unpacking libnss-systemd:arm64 (259-1ubuntu3) over (259-1ubuntu2) ... 77s Preparing to unpack .../5-libsystemd0_259-1ubuntu3_arm64.deb ... 77s Unpacking libsystemd0:arm64 (259-1ubuntu3) over (259-1ubuntu2) ... 77s Setting up libsystemd0:arm64 (259-1ubuntu3) ... 77s (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 ... 135994 files and directories currently installed.) 77s Preparing to unpack .../systemd-sysv_259-1ubuntu3_arm64.deb ... 77s Unpacking systemd-sysv (259-1ubuntu3) over (259-1ubuntu2) ... 77s Preparing to unpack .../systemd-resolved_259-1ubuntu3_arm64.deb ... 77s Unpacking systemd-resolved (259-1ubuntu3) over (259-1ubuntu2) ... 77s Preparing to unpack .../libpam-systemd_259-1ubuntu3_arm64.deb ... 77s Unpacking libpam-systemd:arm64 (259-1ubuntu3) over (259-1ubuntu2) ... 77s Preparing to unpack .../libsystemd-shared_259-1ubuntu3_arm64.deb ... 77s Unpacking libsystemd-shared:arm64 (259-1ubuntu3) over (259-1ubuntu2) ... 77s Setting up libsystemd-shared:arm64 (259-1ubuntu3) ... 77s (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 ... 135994 files and directories currently installed.) 77s Preparing to unpack .../systemd_259-1ubuntu3_arm64.deb ... 77s Unpacking systemd (259-1ubuntu3) over (259-1ubuntu2) ... 78s Preparing to unpack .../systemd-cryptsetup_259-1ubuntu3_arm64.deb ... 78s Unpacking systemd-cryptsetup (259-1ubuntu3) over (259-1ubuntu2) ... 78s Preparing to unpack .../udev_259-1ubuntu3_arm64.deb ... 78s Unpacking udev (259-1ubuntu3) over (259-1ubuntu2) ... 78s Preparing to unpack .../libudev1_259-1ubuntu3_arm64.deb ... 78s Unpacking libudev1:arm64 (259-1ubuntu3) over (259-1ubuntu2) ... 78s Setting up libudev1:arm64 (259-1ubuntu3) ... 78s (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 ... 135994 files and directories currently installed.) 78s Preparing to unpack .../libstdc++6_15.2.0-12ubuntu1_arm64.deb ... 78s Unpacking libstdc++6:arm64 (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 78s Preparing to unpack .../libatomic1_15.2.0-12ubuntu1_arm64.deb ... 78s Unpacking libatomic1:arm64 (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 78s Preparing to unpack .../gcc-15-base_15.2.0-12ubuntu1_arm64.deb ... 78s Unpacking gcc-15-base:arm64 (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 78s Setting up gcc-15-base:arm64 (15.2.0-12ubuntu1) ... 79s (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 ... 135994 files and directories currently installed.) 79s Preparing to unpack .../libgcc-s1_15.2.0-12ubuntu1_arm64.deb ... 79s Unpacking libgcc-s1:arm64 (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 79s Setting up libgcc-s1:arm64 (15.2.0-12ubuntu1) ... 79s (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 ... 135994 files and directories currently installed.) 79s Preparing to unpack .../00-libtasn1-6_4.21.0-2_arm64.deb ... 79s Unpacking libtasn1-6:arm64 (4.21.0-2) over (4.20.0-2ubuntu1) ... 79s Preparing to unpack .../01-vim-tiny_2%3a9.1.1882-1ubuntu2_arm64.deb ... 79s Unpacking vim-tiny (2:9.1.1882-1ubuntu2) over (2:9.1.1882-1ubuntu1) ... 79s Preparing to unpack .../02-vim-common_2%3a9.1.1882-1ubuntu2_all.deb ... 79s Unpacking vim-common (2:9.1.1882-1ubuntu2) over (2:9.1.1882-1ubuntu1) ... 79s Preparing to unpack .../03-xxd_2%3a9.1.1882-1ubuntu2_arm64.deb ... 79s Unpacking xxd (2:9.1.1882-1ubuntu2) over (2:9.1.1882-1ubuntu1) ... 79s Preparing to unpack .../04-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu5_arm64.deb ... 79s Unpacking libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 79s Preparing to unpack .../05-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu5_arm64.deb ... 79s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 79s Preparing to unpack .../06-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu5_arm64.deb ... 79s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 79s Preparing to unpack .../07-python3-gdbm_3.14.2-1_arm64.deb ... 80s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 80s Preparing to unpack .../08-libgprofng0_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking libgprofng0:arm64 (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../09-libctf0_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking libctf0:arm64 (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../10-libctf-nobfd0_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking libctf-nobfd0:arm64 (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../11-binutils-aarch64-linux-gnu_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking binutils-aarch64-linux-gnu (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../12-libbinutils_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking libbinutils:arm64 (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../13-binutils_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking binutils (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Preparing to unpack .../14-binutils-common_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking binutils-common:arm64 (2.45.50.20260119-1ubuntu1) over (2.45.50.20251209-1ubuntu1) ... 80s Selecting previously unselected package libsframe3:arm64. 80s Preparing to unpack .../15-libsframe3_2.45.50.20260119-1ubuntu1_arm64.deb ... 80s Unpacking libsframe3:arm64 (2.45.50.20260119-1ubuntu1) ... 81s Preparing to unpack .../16-python3-jaraco.context_6.0.1-2_all.deb ... 81s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 81s Preparing to unpack .../17-zstd_1.5.7+dfsg-3_arm64.deb ... 81s Unpacking zstd (1.5.7+dfsg-3) over (1.5.7+dfsg-2) ... 81s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 81s Setting up binutils-common:arm64 (2.45.50.20260119-1ubuntu1) ... 81s Setting up libsframe3:arm64 (2.45.50.20260119-1ubuntu1) ... 81s Setting up libctf-nobfd0:arm64 (2.45.50.20260119-1ubuntu1) ... 81s Setting up libnss-systemd:arm64 (259-1ubuntu3) ... 81s Setting up systemd (259-1ubuntu3) ... 81s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 81s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 82s Setting up xxd (2:9.1.1882-1ubuntu2) ... 82s Setting up vim-common (2:9.1.1882-1ubuntu2) ... 82s Setting up systemd-cryptsetup (259-1ubuntu3) ... 82s Setting up libatomic1:arm64 (15.2.0-12ubuntu1) ... 82s Setting up udev (259-1ubuntu3) ... 83s Setting up libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 83s Setting up libtasn1-6:arm64 (4.21.0-2) ... 83s Setting up python3.14 (3.14.2-1) ... 84s Setting up libbinutils:arm64 (2.45.50.20260119-1ubuntu1) ... 84s Setting up libstdc++6:arm64 (15.2.0-12ubuntu1) ... 84s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 84s Setting up systemd-resolved (259-1ubuntu3) ... 85s Could not execute systemctl: at /usr/bin/deb-systemd-invoke line 148. 85s Setting up libctf0:arm64 (2.45.50.20260119-1ubuntu1) ... 85s Setting up systemd-userdbd (259-1ubuntu3) ... 85s Setting up systemd-sysv (259-1ubuntu3) ... 85s Setting up python3-gdbm (3.14.2-1) ... 85s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 85s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 86s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 86s Setting up binutils-aarch64-linux-gnu (2.45.50.20260119-1ubuntu1) ... 86s Setting up python3 (3.14.2-1) ... 86s running python rtupdate hooks for python3.14... 86s running python post-rtupdate hooks for python3.14... 86s Setting up vim-tiny (2:9.1.1882-1ubuntu2) ... 86s Setting up libgprofng0:arm64 (2.45.50.20260119-1ubuntu1) ... 86s Setting up libpam-systemd:arm64 (259-1ubuntu3) ... 86s Setting up zstd (1.5.7+dfsg-3) ... 86s Setting up python3-jaraco.context (6.0.1-2) ... 87s Setting up binutils (2.45.50.20260119-1ubuntu1) ... 87s Installing new version of config file /etc/gprofng.rc ... 87s Processing triggers for dbus (1.16.2-2ubuntu2) ... 87s Processing triggers for shared-mime-info (2.4-5build2) ... 89s Processing triggers for procps (2:4.0.4-9ubuntu1) ... 89s Processing triggers for initramfs-tools (0.150ubuntu7) ... 89s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 107s System running in EFI mode, skipping. 107s Processing triggers for libc-bin (2.42-2ubuntu4) ... 107s Processing triggers for man-db (2.13.1-1) ... 108s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 108s Processing triggers for initramfs-tools (0.150ubuntu7) ... 108s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 124s System running in EFI mode, skipping. 124s autopkgtest [21:37:25]: upgrading testbed (apt dist-upgrade and autopurge) 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Calculating upgrade... 125s The following packages were automatically installed and are no longer required: 125s python3.13 python3.13-minimal 125s Use 'sudo apt autoremove' to remove them. 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Solving dependencies... 126s The following packages will be REMOVED: 126s python3.13* python3.13-minimal* 126s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 126s After this operation, 7766 kB disk space will be freed. 126s (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 ... 135994 files and directories currently installed.) 126s Removing python3.13 (3.13.11-1) ... 126s Removing python3.13-minimal (3.13.11-1) ... 127s Processing triggers for man-db (2.13.1-1) ... 128s Processing triggers for systemd (259-1ubuntu3) ... 128s (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 ... 135967 files and directories currently installed.) 128s Purging configuration files for python3.13-minimal (3.13.11-1) ... 128s autopkgtest [21:37:29]: rebooting testbed after setup commands that affected boot 166s autopkgtest [21:38:07]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 169s autopkgtest [21:38:10]: @@@@@@@@@@@@@@@@@@@@ apt-source snakemake 171s Get:1 http://ftpmaster.internal/ubuntu resolute/universe snakemake 7.32.4-8.1 (dsc) [3330 B] 171s Get:2 http://ftpmaster.internal/ubuntu resolute/universe snakemake 7.32.4-8.1 (tar) [8886 kB] 171s Get:3 http://ftpmaster.internal/ubuntu resolute/universe snakemake 7.32.4-8.1 (diff) [29.9 kB] 171s gpgv: Signature made Mon Dec 29 15:32:14 2025 UTC 171s gpgv: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314 171s gpgv: issuer "bage@debian.org" 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./snakemake_7.32.4-8.1.dsc: no acceptable signature found 171s autopkgtest [21:38:12]: testing package snakemake version 7.32.4-8.1 172s autopkgtest [21:38:13]: build not needed 173s autopkgtest [21:38:14]: test command1: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Solving dependencies... 174s The following NEW packages will be installed: 174s coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 174s coinor-libcoinutils3v5 coinor-libosi1v5 docutils-common 174s fonts-glyphicons-halflings git git-man libblas3 libdatrie1 liberror-perl 174s libgfortran5 libjs-bootstrap libjs-jquery liblapack3 python3-configargparse 174s python3-connection-pool python3-datrie python3-decorator python3-docutils 174s python3-dpath python3-fastjsonschema python3-git python3-gitdb 174s python3-humanfriendly python3-jupyter-core python3-nbformat python3-plac 174s python3-platformdirs python3-psutil python3-pulp python3-retry 174s python3-roman-numerals python3-smart-open python3-smmap python3-stopit 174s python3-tabulate python3-throttler python3-toposort python3-traitlets 174s python3-wrapt python3-yte sgml-base snakemake xml-core 174s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 14.0 MB of archives. 174s After this operation, 57.6 MB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 174s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 174s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 174s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcoinutils3v5 arm64 2.11.12+ds-1 [450 kB] 174s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libosi1v5 arm64 0.108.11+ds-1 [258 kB] 174s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libclp1 arm64 1.17.10+ds-1build1 [851 kB] 174s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcgl1 arm64 0.60.9+ds-1build1 [394 kB] 174s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-libcbc3.1 arm64 2.10.12+ds-1build1 [720 kB] 174s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 174s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 174s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.22.4+dfsg-1 [130 kB] 174s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 174s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liberror-perl all 0.17030-1 [23.5 kB] 174s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 git-man all 1:2.51.0-1ubuntu1 [1179 kB] 174s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 git arm64 1:2.51.0-1ubuntu1 [4431 kB] 174s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 174s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 174s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 174s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-configargparse all 1.7-2 [31.7 kB] 174s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-connection-pool all 0.0.3-2build1 [5792 B] 174s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datrie arm64 0.8.3-2 [184 kB] 174s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 174s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman-numerals all 4.1.0-1 [8660 B] 174s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 174s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dpath all 2.2.0-2 [20.3 kB] 174s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 174s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-smmap all 6.0.0-1build1 [20.7 kB] 174s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gitdb all 4.0.12-1 [46.4 kB] 175s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-git all 3.1.46-1 [149 kB] 175s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6build1 [70.9 kB] 175s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 175s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-traitlets all 5.14.3+really5.14.3-2 [71.7 kB] 175s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-jupyter-core all 5.9.1-1 [28.9 kB] 175s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-nbformat all 5.10.4-1 [39.2 kB] 175s Get:35 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-plac all 1.4.3-2 [63.2 kB] 175s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.1.0-1ubuntu1 [191 kB] 175s Get:37 http://ftpmaster.internal/ubuntu resolute/universe arm64 coinor-cbc arm64 2.10.12+ds-1build1 [14.3 kB] 175s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pulp all 2.7.0+dfsg-4 [71.4 kB] 175s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-retry all 0.9.2-5 [6160 B] 175s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-wrapt arm64 1.17.3-3 [40.1 kB] 175s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-smart-open all 7.5.0-1 [56.9 kB] 175s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-stopit all 1.1.2-3 [12.8 kB] 175s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tabulate all 0.9.0-1build1 [45.4 kB] 175s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-throttler all 1.2.2-4ubuntu1 [7758 B] 175s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-toposort all 1.10-2 [6348 B] 175s Get:46 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-yte all 1.5.4-1 [12.0 kB] 175s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 snakemake all 7.32.4-8.1 [275 kB] 175s Fetched 14.0 MB in 1s (17.7 MB/s) 175s Selecting previously unselected package libblas3:arm64. 175s (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 ... 135969 files and directories currently installed.) 175s Preparing to unpack .../00-libblas3_3.12.1-7ubuntu1_arm64.deb ... 175s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 175s Selecting previously unselected package libgfortran5:arm64. 175s Preparing to unpack .../01-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 175s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 175s Selecting previously unselected package liblapack3:arm64. 175s Preparing to unpack .../02-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 175s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 176s Selecting previously unselected package coinor-libcoinutils3v5:arm64. 176s Preparing to unpack .../03-coinor-libcoinutils3v5_2.11.12+ds-1_arm64.deb ... 176s Unpacking coinor-libcoinutils3v5:arm64 (2.11.12+ds-1) ... 176s Selecting previously unselected package coinor-libosi1v5:arm64. 176s Preparing to unpack .../04-coinor-libosi1v5_0.108.11+ds-1_arm64.deb ... 176s Unpacking coinor-libosi1v5:arm64 (0.108.11+ds-1) ... 176s Selecting previously unselected package coinor-libclp1:arm64. 176s Preparing to unpack .../05-coinor-libclp1_1.17.10+ds-1build1_arm64.deb ... 176s Unpacking coinor-libclp1:arm64 (1.17.10+ds-1build1) ... 176s Selecting previously unselected package coinor-libcgl1:arm64. 176s Preparing to unpack .../06-coinor-libcgl1_0.60.9+ds-1build1_arm64.deb ... 176s Unpacking coinor-libcgl1:arm64 (0.60.9+ds-1build1) ... 176s Selecting previously unselected package coinor-libcbc3.1:arm64. 176s Preparing to unpack .../07-coinor-libcbc3.1_2.10.12+ds-1build1_arm64.deb ... 176s Unpacking coinor-libcbc3.1:arm64 (2.10.12+ds-1build1) ... 176s Selecting previously unselected package sgml-base. 176s Preparing to unpack .../08-sgml-base_1.31+nmu1_all.deb ... 176s Unpacking sgml-base (1.31+nmu1) ... 176s Selecting previously unselected package xml-core. 176s Preparing to unpack .../09-xml-core_0.19build1_all.deb ... 176s Unpacking xml-core (0.19build1) ... 176s Selecting previously unselected package docutils-common. 176s Preparing to unpack .../10-docutils-common_0.22.4+dfsg-1_all.deb ... 176s Unpacking docutils-common (0.22.4+dfsg-1) ... 176s Selecting previously unselected package fonts-glyphicons-halflings. 176s Preparing to unpack .../11-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 176s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 176s Selecting previously unselected package liberror-perl. 176s Preparing to unpack .../12-liberror-perl_0.17030-1_all.deb ... 176s Unpacking liberror-perl (0.17030-1) ... 176s Selecting previously unselected package git-man. 176s Preparing to unpack .../13-git-man_1%3a2.51.0-1ubuntu1_all.deb ... 176s Unpacking git-man (1:2.51.0-1ubuntu1) ... 176s Selecting previously unselected package git. 176s Preparing to unpack .../14-git_1%3a2.51.0-1ubuntu1_arm64.deb ... 176s Unpacking git (1:2.51.0-1ubuntu1) ... 176s Selecting previously unselected package libdatrie1:arm64. 176s Preparing to unpack .../15-libdatrie1_0.2.14-1_arm64.deb ... 176s Unpacking libdatrie1:arm64 (0.2.14-1) ... 176s Selecting previously unselected package libjs-bootstrap. 176s Preparing to unpack .../16-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 176s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 176s Selecting previously unselected package libjs-jquery. 176s Preparing to unpack .../17-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 176s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 176s Selecting previously unselected package python3-configargparse. 176s Preparing to unpack .../18-python3-configargparse_1.7-2_all.deb ... 176s Unpacking python3-configargparse (1.7-2) ... 177s Selecting previously unselected package python3-connection-pool. 177s Preparing to unpack .../19-python3-connection-pool_0.0.3-2build1_all.deb ... 177s Unpacking python3-connection-pool (0.0.3-2build1) ... 177s Selecting previously unselected package python3-datrie. 177s Preparing to unpack .../20-python3-datrie_0.8.3-2_arm64.deb ... 177s Unpacking python3-datrie (0.8.3-2) ... 177s Selecting previously unselected package python3-decorator. 177s Preparing to unpack .../21-python3-decorator_5.2.1-2_all.deb ... 177s Unpacking python3-decorator (5.2.1-2) ... 177s Selecting previously unselected package python3-roman-numerals. 177s Preparing to unpack .../22-python3-roman-numerals_4.1.0-1_all.deb ... 177s Unpacking python3-roman-numerals (4.1.0-1) ... 177s Selecting previously unselected package python3-docutils. 177s Preparing to unpack .../23-python3-docutils_0.22.4+dfsg-1_all.deb ... 177s Unpacking python3-docutils (0.22.4+dfsg-1) ... 177s Selecting previously unselected package python3-dpath. 177s Preparing to unpack .../24-python3-dpath_2.2.0-2_all.deb ... 177s Unpacking python3-dpath (2.2.0-2) ... 177s Selecting previously unselected package python3-fastjsonschema. 177s Preparing to unpack .../25-python3-fastjsonschema_2.21.1-1_all.deb ... 177s Unpacking python3-fastjsonschema (2.21.1-1) ... 177s Selecting previously unselected package python3-smmap. 177s Preparing to unpack .../26-python3-smmap_6.0.0-1build1_all.deb ... 177s Unpacking python3-smmap (6.0.0-1build1) ... 177s Selecting previously unselected package python3-gitdb. 177s Preparing to unpack .../27-python3-gitdb_4.0.12-1_all.deb ... 177s Unpacking python3-gitdb (4.0.12-1) ... 177s Selecting previously unselected package python3-git. 177s Preparing to unpack .../28-python3-git_3.1.46-1_all.deb ... 177s Unpacking python3-git (3.1.46-1) ... 177s Selecting previously unselected package python3-humanfriendly. 177s Preparing to unpack .../29-python3-humanfriendly_10.0-6build1_all.deb ... 177s Unpacking python3-humanfriendly (10.0-6build1) ... 177s Selecting previously unselected package python3-platformdirs. 177s Preparing to unpack .../30-python3-platformdirs_4.5.1-1_all.deb ... 177s Unpacking python3-platformdirs (4.5.1-1) ... 177s Selecting previously unselected package python3-traitlets. 177s Preparing to unpack .../31-python3-traitlets_5.14.3+really5.14.3-2_all.deb ... 177s Unpacking python3-traitlets (5.14.3+really5.14.3-2) ... 177s Selecting previously unselected package python3-jupyter-core. 177s Preparing to unpack .../32-python3-jupyter-core_5.9.1-1_all.deb ... 177s Unpacking python3-jupyter-core (5.9.1-1) ... 177s Selecting previously unselected package python3-nbformat. 177s Preparing to unpack .../33-python3-nbformat_5.10.4-1_all.deb ... 177s Unpacking python3-nbformat (5.10.4-1) ... 177s Selecting previously unselected package python3-plac. 177s Preparing to unpack .../34-python3-plac_1.4.3-2_all.deb ... 177s Unpacking python3-plac (1.4.3-2) ... 177s Selecting previously unselected package python3-psutil. 177s Preparing to unpack .../35-python3-psutil_7.1.0-1ubuntu1_arm64.deb ... 177s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 177s Selecting previously unselected package coinor-cbc. 177s Preparing to unpack .../36-coinor-cbc_2.10.12+ds-1build1_arm64.deb ... 177s Unpacking coinor-cbc (2.10.12+ds-1build1) ... 177s Selecting previously unselected package python3-pulp. 177s Preparing to unpack .../37-python3-pulp_2.7.0+dfsg-4_all.deb ... 177s Unpacking python3-pulp (2.7.0+dfsg-4) ... 177s Selecting previously unselected package python3-retry. 177s Preparing to unpack .../38-python3-retry_0.9.2-5_all.deb ... 177s Unpacking python3-retry (0.9.2-5) ... 177s Selecting previously unselected package python3-wrapt. 177s Preparing to unpack .../39-python3-wrapt_1.17.3-3_arm64.deb ... 177s Unpacking python3-wrapt (1.17.3-3) ... 177s Selecting previously unselected package python3-smart-open. 178s Preparing to unpack .../40-python3-smart-open_7.5.0-1_all.deb ... 178s Unpacking python3-smart-open (7.5.0-1) ... 178s Selecting previously unselected package python3-stopit. 178s Preparing to unpack .../41-python3-stopit_1.1.2-3_all.deb ... 178s Unpacking python3-stopit (1.1.2-3) ... 178s Selecting previously unselected package python3-tabulate. 178s Preparing to unpack .../42-python3-tabulate_0.9.0-1build1_all.deb ... 178s Unpacking python3-tabulate (0.9.0-1build1) ... 178s Selecting previously unselected package python3-throttler. 178s Preparing to unpack .../43-python3-throttler_1.2.2-4ubuntu1_all.deb ... 178s Unpacking python3-throttler (1.2.2-4ubuntu1) ... 178s Selecting previously unselected package python3-toposort. 178s Preparing to unpack .../44-python3-toposort_1.10-2_all.deb ... 178s Unpacking python3-toposort (1.10-2) ... 178s Selecting previously unselected package python3-yte. 178s Preparing to unpack .../45-python3-yte_1.5.4-1_all.deb ... 178s Unpacking python3-yte (1.5.4-1) ... 178s Selecting previously unselected package snakemake. 178s Preparing to unpack .../46-snakemake_7.32.4-8.1_all.deb ... 178s Unpacking snakemake (7.32.4-8.1) ... 178s Setting up python3-toposort (1.10-2) ... 178s Setting up python3-configargparse (1.7-2) ... 178s Setting up libdatrie1:arm64 (0.2.14-1) ... 178s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 178s Setting up python3-tabulate (0.9.0-1build1) ... 178s Setting up python3-plac (1.4.3-2) ... 178s Setting up python3-platformdirs (4.5.1-1) ... 179s Setting up python3-psutil (7.1.0-1ubuntu1) ... 179s Setting up liberror-perl (0.17030-1) ... 179s Setting up python3-decorator (5.2.1-2) ... 179s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 179s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 179s Setting up python3-humanfriendly (10.0-6build1) ... 179s /usr/lib/python3/dist-packages/humanfriendly/testing.py:546: SyntaxWarning: 'return' in a 'finally' block 179s return super(MockedProgram, self).__exit__(*args, **kw) 179s Setting up python3-dpath (2.2.0-2) ... 179s Setting up python3-connection-pool (0.0.3-2build1) ... 180s Setting up python3-wrapt (1.17.3-3) ... 180s Setting up python3-throttler (1.2.2-4ubuntu1) ... 180s Setting up python3-retry (0.9.2-5) ... 180s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 180s Setting up python3-fastjsonschema (2.21.1-1) ... 180s Setting up python3-stopit (1.1.2-3) ... 180s Setting up python3-traitlets (5.14.3+really5.14.3-2) ... 181s Setting up python3-roman-numerals (4.1.0-1) ... 181s Setting up git-man (1:2.51.0-1ubuntu1) ... 181s Setting up sgml-base (1.31+nmu1) ... 181s Setting up python3-datrie (0.8.3-2) ... 181s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 181s Setting up python3-smmap (6.0.0-1build1) ... 181s Setting up python3-jupyter-core (5.9.1-1) ... 181s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 181s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 181s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 181s Setting up python3-smart-open (7.5.0-1) ... 181s Setting up python3-nbformat (5.10.4-1) ... 181s Setting up python3-gitdb (4.0.12-1) ... 182s Setting up python3-yte (1.5.4-1) ... 182s Setting up coinor-libcoinutils3v5:arm64 (2.11.12+ds-1) ... 182s Setting up git (1:2.51.0-1ubuntu1) ... 182s Setting up coinor-libosi1v5:arm64 (0.108.11+ds-1) ... 182s Setting up xml-core (0.19build1) ... 182s Setting up coinor-libclp1:arm64 (1.17.10+ds-1build1) ... 182s Setting up python3-git (3.1.46-1) ... 182s Setting up coinor-libcgl1:arm64 (0.60.9+ds-1build1) ... 182s Setting up coinor-libcbc3.1:arm64 (2.10.12+ds-1build1) ... 182s Setting up coinor-cbc (2.10.12+ds-1build1) ... 182s Setting up python3-pulp (2.7.0+dfsg-4) ... 182s /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:325: SyntaxWarning: "\ " is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\ "? A raw string is also an option. 182s otherwise be interpreted by the Tcl shell: \ $ " [ 183s Processing triggers for libc-bin (2.42-2ubuntu4) ... 183s Processing triggers for man-db (2.13.1-1) ... 184s Processing triggers for sgml-base (1.31+nmu1) ... 184s Setting up docutils-common (0.22.4+dfsg-1) ... 184s Processing triggers for sgml-base (1.31+nmu1) ... 184s Setting up python3-docutils (0.22.4+dfsg-1) ... 184s Setting up snakemake (7.32.4-8.1) ... 186s autopkgtest [21:38:27]: test command1: cp tests/test_bash/Snakefile $AUTOPKGTEST_TMP && cd $AUTOPKGTEST_TMP && snakemake --cores 1 && grep -e bash test.out 186s autopkgtest [21:38:27]: test command1: [----------------------- 187s Building DAG of jobs... 187s Using shell: /usr/bin/bash 187s Provided cores: 1 (use --cores to define parallelism) 187s Rules claiming more threads will be scaled down. 187s Job stats: 187s job count 187s ----- ------- 187s a 1 187s total 1 187s 187s Select jobs to execute... 187s 187s [Fri Jan 23 21:38:28 2026] 187s rule a: 187s output: test.out 187s jobid: 0 187s reason: Missing output files: test.out 187s resources: tmpdir=/tmp 187s 187s [Fri Jan 23 21:38:28 2026] 187s Finished job 0. 187s 1 of 1 steps (100%) done 187s Complete log: .snakemake/log/2026-01-23T213828.114643.snakemake.log 187s bash 188s autopkgtest [21:38:29]: test command1: -----------------------] 188s command1 PASS 188s autopkgtest [21:38:29]: test command1: - - - - - - - - - - results - - - - - - - - - - 188s autopkgtest [21:38:29]: test run-unit-test: preparing testbed 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Solving dependencies... 189s The following NEW packages will be installed: 189s environment-modules fontconfig fontconfig-config fonts-dejavu-core 189s fonts-dejavu-mono glpk-utils graphviz libamd3 libaom3 libcairo2 libcdt6 189s libcgraph8 libcolamd3 libde265-0 libdeflate0 libfontconfig1 libgd3 libglpk40 189s libgomp1 libgraphite2-3 libgvc7 libgvplugin-gd8 libgvplugin-pango8 libgvpr2 189s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 189s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libltdl7 189s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 189s libpaper2 libpathplan4 libpixman-1-0 libsharpyuv0 libsm6 189s libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 189s libwebp7 libxcb-render0 libxcb-shm0 libxdot4 libxft2 libxpm4 libxrender1 189s libxss1 libxt6t64 python3-ftputil python3-iniconfig python3-numpy 189s python3-numpy-dev python3-pandas python3-pandas-lib python3-pluggy 189s python3-pytest python3-pytest-mock python3-pytz python3-requests-mock 189s r-base-core stress tcl8.6 unzip x11-common xdg-utils zip 195s 0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded. 195s Need to get 54.8 MB of archives. 195s After this operation, 178 MB of additional disk space will be used. 195s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 195s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 195s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 195s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 tcl8.6 arm64 8.6.17+dfsg-1 [14.9 kB] 195s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 environment-modules arm64 5.6.1-1 [365 kB] 195s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 195s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 195s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.4ubuntu1 [38.2 kB] 195s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.4ubuntu1 [143 kB] 195s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.4ubuntu1 [191 kB] 195s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 195s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.12.1+dfsg-1 [22.0 kB] 195s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd3 arm64 1:7.12.1+dfsg-1 [34.6 kB] 195s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.12.1+dfsg-1 [27.1 kB] 195s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libltdl7 arm64 2.5.4-9 [43.3 kB] 195s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 libglpk40 arm64 5.0-2 [347 kB] 195s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 glpk-utils arm64 5.0-2 [226 kB] 195s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libcdt6 arm64 14.1.1-2ubuntu3 [19.0 kB] 195s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libcgraph8 arm64 14.1.1-2ubuntu3 [53.6 kB] 195s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libpathplan4 arm64 14.1.1-2ubuntu3 [24.7 kB] 195s Get:21 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libxdot4 arm64 14.1.1-2ubuntu3 [23.1 kB] 195s Get:22 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libgvc7 arm64 14.1.1-2ubuntu3 [371 kB] 195s Get:23 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libgvpr2 arm64 14.1.1-2ubuntu3 [122 kB] 195s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 195s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 195s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 195s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 195s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 195s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 195s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libaom3 arm64 3.13.1-2 [1773 kB] 195s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-aomdec arm64 1.21.2-1 [13.9 kB] 195s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libde265-0 arm64 1.0.16-1build1 [148 kB] 195s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-libde265 arm64 1.21.2-1 [9696 B] 195s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif1 arm64 1.21.2-1 [502 kB] 195s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 195s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 195s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 195s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 195s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 195s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 195s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 195s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 195s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxpm4 arm64 1:3.5.17-1build3 [35.5 kB] 195s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libgd3 arm64 2.3.3-13ubuntu1 [124 kB] 195s Get:45 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libgvplugin-gd8 arm64 14.1.1-2ubuntu3 [24.8 kB] 195s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 195s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.0-4 [518 kB] 195s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 195s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 195s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.4-1 [237 kB] 195s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.4-1 [51.4 kB] 195s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.4-1 [27.9 kB] 195s Get:53 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 libgvplugin-pango8 arm64 14.1.1-2ubuntu3 [23.0 kB] 195s Get:54 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 graphviz arm64 14.1.1-2ubuntu3 [58.6 kB] 195s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 195s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 195s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 195s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 195s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 195s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 195s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 196s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 196s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 196s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ftputil all 5.1.0-1build1 [41.3 kB] 196s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 196s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 196s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 196s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 196s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 196s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 196s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-mock all 3.15.1-1 [11.9 kB] 196s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-requests-mock all 1.12.1-4 [17.9 kB] 196s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu2 [175 kB] 196s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 196s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 196s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 197s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 stress arm64 1.0.7-2 [17.6 kB] 197s Preconfiguring packages ... 197s Fetched 54.8 MB in 7s (7619 kB/s) 197s Selecting previously unselected package python3-numpy-dev:arm64. 197s (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 ... 138532 files and directories currently installed.) 197s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 197s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 197s Selecting previously unselected package python3-numpy. 197s Preparing to unpack .../01-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 197s Unpacking python3-numpy (1:2.3.5+ds-3) ... 197s Selecting previously unselected package libtcl8.6:arm64. 197s Preparing to unpack .../02-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 197s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 197s Selecting previously unselected package tcl8.6. 197s Preparing to unpack .../03-tcl8.6_8.6.17+dfsg-1_arm64.deb ... 197s Unpacking tcl8.6 (8.6.17+dfsg-1) ... 197s Selecting previously unselected package environment-modules. 197s Preparing to unpack .../04-environment-modules_5.6.1-1_arm64.deb ... 197s Unpacking environment-modules (5.6.1-1) ... 197s Selecting previously unselected package fonts-dejavu-mono. 197s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8build1_all.deb ... 197s Unpacking fonts-dejavu-mono (2.37-8build1) ... 198s Selecting previously unselected package fonts-dejavu-core. 198s Preparing to unpack .../06-fonts-dejavu-core_2.37-8build1_all.deb ... 198s Unpacking fonts-dejavu-core (2.37-8build1) ... 198s Selecting previously unselected package fontconfig-config. 198s Preparing to unpack .../07-fontconfig-config_2.15.0-2.4ubuntu1_arm64.deb ... 198s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 198s Selecting previously unselected package libfontconfig1:arm64. 198s Preparing to unpack .../08-libfontconfig1_2.15.0-2.4ubuntu1_arm64.deb ... 198s Unpacking libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 198s Selecting previously unselected package fontconfig. 198s Preparing to unpack .../09-fontconfig_2.15.0-2.4ubuntu1_arm64.deb ... 198s Unpacking fontconfig (2.15.0-2.4ubuntu1) ... 198s Selecting previously unselected package libgomp1:arm64. 198s Preparing to unpack .../10-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 198s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 198s Selecting previously unselected package libsuitesparseconfig7:arm64. 198s Preparing to unpack .../11-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_arm64.deb ... 198s Unpacking libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 198s Selecting previously unselected package libamd3:arm64. 198s Preparing to unpack .../12-libamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 198s Unpacking libamd3:arm64 (1:7.12.1+dfsg-1) ... 198s Selecting previously unselected package libcolamd3:arm64. 198s Preparing to unpack .../13-libcolamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 198s Unpacking libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 198s Selecting previously unselected package libltdl7:arm64. 198s Preparing to unpack .../14-libltdl7_2.5.4-9_arm64.deb ... 198s Unpacking libltdl7:arm64 (2.5.4-9) ... 198s Selecting previously unselected package libglpk40:arm64. 198s Preparing to unpack .../15-libglpk40_5.0-2_arm64.deb ... 198s Unpacking libglpk40:arm64 (5.0-2) ... 198s Selecting previously unselected package glpk-utils. 198s Preparing to unpack .../16-glpk-utils_5.0-2_arm64.deb ... 198s Unpacking glpk-utils (5.0-2) ... 198s Selecting previously unselected package libcdt6:arm64. 198s Preparing to unpack .../17-libcdt6_14.1.1-2ubuntu3_arm64.deb ... 198s Unpacking libcdt6:arm64 (14.1.1-2ubuntu3) ... 198s Selecting previously unselected package libcgraph8:arm64. 198s Preparing to unpack .../18-libcgraph8_14.1.1-2ubuntu3_arm64.deb ... 198s Unpacking libcgraph8:arm64 (14.1.1-2ubuntu3) ... 198s Selecting previously unselected package libpathplan4:arm64. 198s Preparing to unpack .../19-libpathplan4_14.1.1-2ubuntu3_arm64.deb ... 198s Unpacking libpathplan4:arm64 (14.1.1-2ubuntu3) ... 198s Selecting previously unselected package libxdot4:arm64. 199s Preparing to unpack .../20-libxdot4_14.1.1-2ubuntu3_arm64.deb ... 199s Unpacking libxdot4:arm64 (14.1.1-2ubuntu3) ... 199s Selecting previously unselected package libgvc7:arm64. 199s Preparing to unpack .../21-libgvc7_14.1.1-2ubuntu3_arm64.deb ... 199s Unpacking libgvc7:arm64 (14.1.1-2ubuntu3) ... 199s Selecting previously unselected package libgvpr2:arm64. 199s Preparing to unpack .../22-libgvpr2_14.1.1-2ubuntu3_arm64.deb ... 199s Unpacking libgvpr2:arm64 (14.1.1-2ubuntu3) ... 199s Selecting previously unselected package libpixman-1-0:arm64. 199s Preparing to unpack .../23-libpixman-1-0_0.46.4-1_arm64.deb ... 199s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 199s Selecting previously unselected package libxcb-render0:arm64. 199s Preparing to unpack .../24-libxcb-render0_1.17.0-2build1_arm64.deb ... 199s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 199s Selecting previously unselected package libxcb-shm0:arm64. 199s Preparing to unpack .../25-libxcb-shm0_1.17.0-2build1_arm64.deb ... 199s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 199s Selecting previously unselected package libxrender1:arm64. 199s Preparing to unpack .../26-libxrender1_1%3a0.9.12-1_arm64.deb ... 199s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 199s Selecting previously unselected package libcairo2:arm64. 199s Preparing to unpack .../27-libcairo2_1.18.4-3_arm64.deb ... 199s Unpacking libcairo2:arm64 (1.18.4-3) ... 199s Selecting previously unselected package libsharpyuv0:arm64. 199s Preparing to unpack .../28-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 199s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 199s Selecting previously unselected package libaom3:arm64. 199s Preparing to unpack .../29-libaom3_3.13.1-2_arm64.deb ... 199s Unpacking libaom3:arm64 (3.13.1-2) ... 199s Selecting previously unselected package libheif-plugin-aomdec:arm64. 199s Preparing to unpack .../30-libheif-plugin-aomdec_1.21.2-1_arm64.deb ... 199s Unpacking libheif-plugin-aomdec:arm64 (1.21.2-1) ... 199s Selecting previously unselected package libde265-0:arm64. 199s Preparing to unpack .../31-libde265-0_1.0.16-1build1_arm64.deb ... 199s Unpacking libde265-0:arm64 (1.0.16-1build1) ... 199s Selecting previously unselected package libheif-plugin-libde265:arm64. 199s Preparing to unpack .../32-libheif-plugin-libde265_1.21.2-1_arm64.deb ... 199s Unpacking libheif-plugin-libde265:arm64 (1.21.2-1) ... 199s Selecting previously unselected package libheif1:arm64. 199s Preparing to unpack .../33-libheif1_1.21.2-1_arm64.deb ... 199s Unpacking libheif1:arm64 (1.21.2-1) ... 199s Selecting previously unselected package libimagequant0:arm64. 199s Preparing to unpack .../34-libimagequant0_2.18.0-1build1_arm64.deb ... 199s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 199s Selecting previously unselected package libjpeg-turbo8:arm64. 199s Preparing to unpack .../35-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 199s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 199s Selecting previously unselected package libjpeg8:arm64. 199s Preparing to unpack .../36-libjpeg8_8c-2ubuntu11_arm64.deb ... 199s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 199s Selecting previously unselected package libdeflate0:arm64. 199s Preparing to unpack .../37-libdeflate0_1.23-2_arm64.deb ... 199s Unpacking libdeflate0:arm64 (1.23-2) ... 199s Selecting previously unselected package libjbig0:arm64. 199s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 199s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 199s Selecting previously unselected package liblerc4:arm64. 199s Preparing to unpack .../39-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb 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Selecting previously unselected package libgraphite2-3:arm64. 200s Preparing to unpack .../45-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 200s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 200s Selecting previously unselected package libharfbuzz0b:arm64. 200s Preparing to unpack .../46-libharfbuzz0b_12.3.0-4_arm64.deb ... 200s Unpacking libharfbuzz0b:arm64 (12.3.0-4) ... 200s Selecting previously unselected package libthai-data. 200s Preparing to unpack .../47-libthai-data_0.1.30-1_all.deb ... 200s Unpacking libthai-data (0.1.30-1) ... 200s Selecting previously unselected package libthai0:arm64. 200s Preparing to unpack .../48-libthai0_0.1.30-1_arm64.deb ... 200s Unpacking libthai0:arm64 (0.1.30-1) ... 200s Selecting previously unselected package libpango-1.0-0:arm64. 200s Preparing to unpack .../49-libpango-1.0-0_1.56.4-1_arm64.deb ... 200s Unpacking libpango-1.0-0:arm64 (1.56.4-1) ... 200s Selecting previously unselected package libpangoft2-1.0-0:arm64. 200s Preparing to unpack .../50-libpangoft2-1.0-0_1.56.4-1_arm64.deb ... 200s Unpacking libpangoft2-1.0-0:arm64 (1.56.4-1) ... 200s Selecting previously unselected package libpangocairo-1.0-0:arm64. 200s Preparing to unpack .../51-libpangocairo-1.0-0_1.56.4-1_arm64.deb ... 200s Unpacking libpangocairo-1.0-0:arm64 (1.56.4-1) ... 200s Selecting previously unselected package libgvplugin-pango8:arm64. 200s Preparing to unpack .../52-libgvplugin-pango8_14.1.1-2ubuntu3_arm64.deb ... 200s Unpacking libgvplugin-pango8:arm64 (14.1.1-2ubuntu3) ... 200s Selecting previously unselected package graphviz. 200s Preparing to unpack .../53-graphviz_14.1.1-2ubuntu3_arm64.deb ... 200s Unpacking graphviz (14.1.1-2ubuntu3) ... 200s Selecting previously unselected package x11-common. 200s Preparing to unpack .../54-x11-common_1%3a7.7+24ubuntu1_all.deb ... 200s Unpacking x11-common (1:7.7+24ubuntu1) ... 200s Selecting previously unselected package libice6:arm64. 200s Preparing to unpack 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python3-requests-mock (1.12.1-4) ... 201s Selecting previously unselected package zip. 201s Preparing to unpack .../72-zip_3.0-15ubuntu2_arm64.deb ... 201s Unpacking zip (3.0-15ubuntu2) ... 201s Selecting previously unselected package unzip. 201s Preparing to unpack .../73-unzip_6.0-29ubuntu1_arm64.deb ... 201s Unpacking unzip (6.0-29ubuntu1) ... 201s Selecting previously unselected package xdg-utils. 201s Preparing to unpack .../74-xdg-utils_1.2.1-2ubuntu2_all.deb ... 201s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 201s Selecting previously unselected package r-base-core. 201s Preparing to unpack .../75-r-base-core_4.5.2-1ubuntu2_arm64.deb ... 201s Unpacking r-base-core (4.5.2-1ubuntu2) ... 202s Selecting previously unselected package stress. 202s Preparing to unpack .../76-stress_1.0.7-2_arm64.deb ... 202s Unpacking stress (1.0.7-2) ... 202s Setting up libxdot4:arm64 (14.1.1-2ubuntu3) ... 202s Setting up libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 202s Setting up python3-iniconfig (2.1.0-2) ... 202s Setting up libcdt6:arm64 (14.1.1-2ubuntu3) ... 202s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 202s Setting up libsharpyuv0:arm64 (1.5.0-0.1build1) ... 202s Setting up libaom3:arm64 (3.13.1-2) ... 202s Setting up python3-ftputil (5.1.0-1build1) ... 202s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 202s Setting up libxpm4:arm64 (1:3.5.17-1build3) ... 202s Setting up libxrender1:arm64 (1:0.9.12-1) ... 202s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 202s Setting up stress (1.0.7-2) ... 202s Setting up unzip (6.0-29ubuntu1) ... 202s Setting up x11-common (1:7.7+24ubuntu1) ... 203s Setting up libdeflate0:arm64 (1.23-2) ... 203s Setting up python3-pytz (2025.2-5) ... 203s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 203s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 203s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 203s Setting up zip (3.0-15ubuntu2) ... 203s Setting up libpathplan4:arm64 (14.1.1-2ubuntu3) ... 203s Setting up python3-requests-mock (1.12.1-4) ... 203s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 203s Setting up fonts-dejavu-mono (2.37-8build1) ... 203s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 203s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 203s Setting up fonts-dejavu-core (2.37-8build1) ... 203s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 203s Setting up python3-numpy (1:2.3.5+ds-3) ... 205s Setting up libltdl7:arm64 (2.5.4-9) ... 205s Setting up python3-pluggy (1.6.0-2) ... 205s Setting up libcgraph8:arm64 (14.1.1-2ubuntu3) ... 205s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 205s Setting up libgvpr2:arm64 (14.1.1-2ubuntu3) ... 205s Setting up libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 205s Setting up libharfbuzz0b:arm64 (12.3.0-4) ... 205s Setting up libthai-data (0.1.30-1) ... 205s Setting up libxss1:arm64 (1:1.2.3-1build4) ... 205s Setting up libpaper2:arm64 (2.2.5-0.3build1) ... 205s Setting up libde265-0:arm64 (1.0.16-1build1) ... 205s Setting up xdg-utils (1.2.1-2ubuntu2) ... 205s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 205s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 205s Setting up libice6:arm64 (2:1.1.1-1build1) ... 205s Setting up tcl8.6 (8.6.17+dfsg-1) ... 205s Setting up libamd3:arm64 (1:7.12.1+dfsg-1) ... 205s Setting up libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 205s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 206s Setting up python3-pytest (9.0.2-2) ... 206s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 206s Setting up libpaper-utils (2.2.5-0.3build1) ... 206s Setting up libthai0:arm64 (0.1.30-1) ... 206s Setting up python3-pandas (2.3.3+dfsg-3) ... 211s Setting up libglpk40:arm64 (5.0-2) ... 211s Setting up glpk-utils (5.0-2) ... 211s Setting up libgvc7:arm64 (14.1.1-2ubuntu3) ... 211s Setting up python3-pytest-mock (3.15.1-1) ... 211s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 211s Setting up environment-modules (5.6.1-1) ... 211s Setting up libsm6:arm64 (2:1.2.6-1) ... 211s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 211s Setting up libheif-plugin-libde265:arm64 (1.21.2-1) ... 211s Setting up libheif1:arm64 (1.21.2-1) ... 211s Setting up libheif-plugin-aomdec:arm64 (1.21.2-1) ... 211s Processing triggers for libc-bin (2.42-2ubuntu4) ... 211s Processing triggers for man-db (2.13.1-1) ... 212s Processing triggers for sgml-base (1.31+nmu1) ... 212s Setting up libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 212s Processing triggers for install-info (7.2-5) ... 212s Setting up fontconfig (2.15.0-2.4ubuntu1) ... 214s Regenerating fonts cache... done. 214s Setting up libxft2:arm64 (2.3.6-1build2) ... 214s Setting up libtk8.6:arm64 (8.6.17-1) ... 214s Setting up libpango-1.0-0:arm64 (1.56.4-1) ... 214s Setting up libcairo2:arm64 (1.18.4-3) ... 214s Setting up libgd3:arm64 (2.3.3-13ubuntu1) ... 214s Setting up libpangoft2-1.0-0:arm64 (1.56.4-1) ... 214s Setting up libpangocairo-1.0-0:arm64 (1.56.4-1) ... 214s Setting up libgvplugin-pango8:arm64 (14.1.1-2ubuntu3) ... 214s Setting up libgvplugin-gd8:arm64 (14.1.1-2ubuntu3) ... 214s Setting up r-base-core (4.5.2-1ubuntu2) ... 214s Creating config file /etc/R/Renviron with new version 214s Setting up graphviz (14.1.1-2ubuntu3) ... 215s Processing triggers for libc-bin (2.42-2ubuntu4) ... 215s autopkgtest [21:38:56]: test run-unit-test: [----------------------- 216s ============================= test session starts ============================== 216s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3 216s cachedir: .pytest_cache 216s rootdir: /tmp/autopkgtest.T4sAFD/autopkgtest_tmp 216s plugins: requests_mock-1.12.1, typeguard-4.4.4, mock-3.15.1 224s collecting ... collected 395 items / 97 deselected / 298 selected 224s 224s tests/test_expand.py::test_simple_expand PASSED [ 0%] 224s tests/test_expand.py::test_allow_missing PASSED [ 0%] 224s tests/test_google_lifesciences.py::test_google_lifesciences SKIPPED [ 1%] 224s tests/test_google_lifesciences.py::test_touch_remote_prefix SKIPPED [ 1%] 224s tests/test_google_lifesciences.py::test_cloud_checkpoints_issue574 SKIPPED [ 1%] 224s tests/test_io.py::test_wildcard_regex PASSED [ 2%] 224s tests/test_io.py::test_expand PASSED [ 2%] 224s tests/test_kubernetes.py::test_kubernetes_plain SKIPPED (Skipping GC...) 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tests/tests.py::test_modules_all_exclude_2 PASSED [ 81%] 1162s tests/tests.py::test_modules_specific PASSED [ 81%] 1162s tests/tests.py::test_use_rule_same_module PASSED [ 81%] 1162s tests/tests.py::test_module_no_prefixing_modified_paths PASSED [ 82%] 1162s tests/tests.py::test_module_worfklow_namespacing PASSED [ 82%] 1162s tests/tests.py::test_handover PASSED [ 82%] 1162s tests/tests.py::test_source_path PASSED [ 83%] 1162s tests/tests.py::test_filesep_windows_targets SKIPPED (Windows stuff) [ 83%] 1162s tests/tests.py::test_filesep_on_windows SKIPPED (Windows stuff) [ 83%] 1162s tests/tests.py::test_set_resources PASSED [ 84%] 1163s tests/tests.py::test_github_issue1069 PASSED [ 84%] 1164s tests/tests.py::test_touch_pipeline_with_temp_dir PASSED [ 84%] 1165s tests/tests.py::test_all_temp PASSED [ 85%] 1165s tests/tests.py::test_strict_mode PASSED [ 85%] 1185s tests/tests.py::test_github_issue1158 PASSED [ 85%] 1185s tests/tests.py::test_converting_path_for_r_script PASSED [ 86%] 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tests/tests.py::test_github_issue1882 PASSED [ 97%] 1336s tests/tests.py::test_inferred_resources PASSED [ 98%] 1337s tests/tests.py::test_workflow_profile PASSED [ 98%] 1338s tests/tests.py::test_no_workflow_profile PASSED [ 98%] 1338s tests/tests.py::test_localrule PASSED [ 99%] 1338s tests/tests.py::test_module_wildcard_constraints PASSED [ 99%] 1339s tests/tests.py::test_config_yte PASSED [100%] 1339s 1339s =================================== FAILURES =================================== 1339s _______________________________ test_config_ref ________________________________ 1339s 1339s self = 1339s url = 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s def resolve_from_url(self, url): 1339s """ 1339s Resolve the given URL. 1339s """ 1339s url, fragment = urldefrag(url) 1339s if not url: 1339s url = self.base_uri 1339s 1339s try: 1339s > document = self.store[url] 1339s ^^^^^^^^^^^^^^^ 1339s 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:1096: 1339s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1339s 1339s self = {'https://json-schema.org/draft/2019-09/meta/content': {'$schema': 'https://json-schema.org/draft/2019-09/schema', '$i...t': 'json', '$ref': '/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.json#/definitions/jsonbar'}}}}}} 1339s uri = 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s def __getitem__(self, uri): 1339s > return self.store[self.normalize(uri)] 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s E KeyError: 'file:///tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s /usr/lib/python3/dist-packages/jsonschema/_utils.py:20: KeyError 1339s 1339s During handling of the above exception, another exception occurred: 1339s 1339s self = 1339s url = 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s def resolve_from_url(self, url): 1339s """ 1339s Resolve the given URL. 1339s """ 1339s url, fragment = urldefrag(url) 1339s if not url: 1339s url = self.base_uri 1339s 1339s try: 1339s document = self.store[url] 1339s except KeyError: 1339s try: 1339s > document = self.resolve_remote(url) 1339s ^^^^^^^^^^^^^^^^^^^^^^^^ 1339s 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:1099: 1339s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:1196: in resolve_remote 1339s result = self.handlers[scheme](uri) 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/snakemake/utils.py:74: in 1339s "file": lambda uri: _load_configfile(re.sub("^file://", "", uri)) 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1339s 1339s configpath_or_obj = 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s filetype = 'Config' 1339s 1339s def _load_configfile(configpath_or_obj, filetype="Config"): 1339s "Tries to load a configfile first as JSON, then as YAML, into a dict." 1339s import yaml 1339s 1339s if isinstance(configpath_or_obj, str) or isinstance(configpath_or_obj, Path): 1339s > obj = open(configpath_or_obj, encoding="utf-8") 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s E FileNotFoundError: [Errno 2] No such file or directory: 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s /usr/lib/python3/dist-packages/snakemake/io.py:1694: FileNotFoundError 1339s 1339s During handling of the above exception, another exception occurred: 1339s 1339s config_schema_ref = local('/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/config.ref.schema.yaml') 1339s 1339s def test_config_ref(config_schema_ref): 1339s config = {} 1339s > validate(config, str(config_schema_ref)) 1339s 1339s tests/test_schema.py:127: 1339s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1339s /usr/lib/python3/dist-packages/snakemake/utils.py:141: in validate 1339s DefaultValidator(schema, resolver=resolver).validate(data) 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:434: in validate 1339s for error in self.iter_errors(*args, **kwargs): 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:368: in iter_errors 1339s for error in errors: 1339s ^^^^^^ 1339s /usr/lib/python3/dist-packages/snakemake/utils.py:89: in set_defaults 1339s for error in validate_properties(validator, properties, instance, schema): 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/_keywords.py:295: in properties 1339s yield from validator.descend( 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:416: in descend 1339s for error in errors: 1339s ^^^^^^ 1339s /usr/lib/python3/dist-packages/snakemake/utils.py:89: in set_defaults 1339s for error in validate_properties(validator, properties, instance, schema): 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/_keywords.py:295: in properties 1339s yield from validator.descend( 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:416: in descend 1339s for error in errors: 1339s ^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/_keywords.py:274: in ref 1339s yield from validator._validate_reference(ref=ref, instance=instance) 1339s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:461: in _validate_reference 1339s scope, resolved = resolve(ref) 1339s ^^^^^^^^^^^^ 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:1085: in resolve 1339s return url, self._remote_cache(url) 1339s ^^^^^^^^^^^^^^^^^^^^^^^ 1339s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1339s 1339s self = 1339s url = 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s def resolve_from_url(self, url): 1339s """ 1339s Resolve the given URL. 1339s """ 1339s url, fragment = urldefrag(url) 1339s if not url: 1339s url = self.base_uri 1339s 1339s try: 1339s document = self.store[url] 1339s except KeyError: 1339s try: 1339s document = self.resolve_remote(url) 1339s except Exception as exc: 1339s > raise exceptions._RefResolutionError(exc) 1339s E jsonschema.exceptions._RefResolutionError: [Errno 2] No such file or directory: 'file:/tmp/pytest-of-ubuntu/pytest-0/test_config_ref0/schema/bar.schema.yaml' 1339s 1339s /usr/lib/python3/dist-packages/jsonschema/validators.py:1101: _RefResolutionError 1339s ------------------------------ Captured log call ------------------------------- 1339s CRITICAL snakemake.logging:logging.py:582 No validator found for JSON Schema version identifier 'https://json-schema.org/draft/2020-12/schema#' 1339s CRITICAL snakemake.logging:logging.py:582 Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema' 1339s CRITICAL snakemake.logging:logging.py:582 Note that schema file may not be validated correctly. 1339s =============================== warnings summary =============================== 1339s tests/test_schema.py: 10 warnings 1339s tests/tests.py: 6 warnings 1339s /usr/lib/python3/dist-packages/snakemake/utils.py:50: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need. 1339s from jsonschema import validators, RefResolver 1339s 1339s tests/testapi.py::test_keep_logger 1339s /usr/lib/python3/dist-packages/stopit/__init__.py:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 1339s import pkg_resources 1339s 1339s tests/testapi.py::test_lockexception 1339s /usr/lib/python3/dist-packages/_pytest/python.py:170: PytestReturnNotNoneWarning: Test functions should return None, but tests/testapi.py::test_lockexception returned . 1339s Did you mean to use `assert` instead of `return`? 1339s See https://docs.pytest.org/en/stable/how-to/assert.html#return-not-none for more information. 1339s warnings.warn( 1339s 1339s tests/tests.py::test_glpk_solver 1339s :898: DeprecationWarning: This process (pid=3752) is multi-threaded, use of fork() may lead to deadlocks in the child. 1339s 1339s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1339s =========================== short test summary info ============================ 1339s FAILED tests/test_schema.py::test_config_ref - jsonschema.exceptions._RefReso... 1339s = 1 failed, 251 passed, 46 skipped, 97 deselected, 19 warnings in 1121.69s (0:18:41) = 1340s autopkgtest [21:57:41]: test run-unit-test: -----------------------] 1341s autopkgtest [21:57:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1341s run-unit-test FAIL non-zero exit status 1 1341s autopkgtest [21:57:42]: @@@@@@@@@@@@@@@@@@@@ summary 1341s command1 PASS 1341s run-unit-test FAIL non-zero exit status 1