1s autopkgtest [16:07:42]: starting date and time: 2024-07-26 16:07:42+0000 1s autopkgtest [16:07:42]: git checkout: fd3bed09 nova: allow more retries for quota issues 1s autopkgtest [16:07:42]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xq43z4g1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml --apt-upgrade cwlformat --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-9.secgroup --name adt-oracular-arm64-cwlformat-20240726-160741-juju-7f2275-prod-proposed-migration-environment-2-5d37588f-32ad-4f65-af67-cbc3d268dd8b --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 118s autopkgtest [16:09:39]: testbed dpkg architecture: arm64 121s autopkgtest [16:09:42]: testbed apt version: 2.9.6 121s autopkgtest [16:09:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 128s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 128s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [436 kB] 128s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 128s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 128s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [88.6 kB] 128s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B] 128s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 128s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 128s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [482 kB] 129s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B] 129s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [8744 B] 129s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 130s Fetched 1261 kB in 4s (321 kB/s) 130s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 137s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 137s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 137s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 138s Reading package lists... 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s autopkgtest [16:10:06]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 146s autopkgtest [16:10:07]: @@@@@@@@@@@@@@@@@@@@ apt-source cwlformat 150s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cwlformat 2022.02.18-2 (dsc) [1560 B] 150s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cwlformat 2022.02.18-2 (tar) [98.8 kB] 150s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cwlformat 2022.02.18-2 (diff) [2180 B] 150s gpgv: Signature made Fri Dec 30 06:20:13 2022 UTC 150s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./cwlformat_2022.02.18-2.dsc: no acceptable signature found 150s autopkgtest [16:10:11]: testing package cwlformat version 2022.02.18-2 152s autopkgtest [16:10:13]: build not needed 153s autopkgtest [16:10:14]: test run-unit-test: preparing testbed 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 1 155s Starting 2 pkgProblemResolver with broken count: 1 155s Investigating (0) python3-ruamel.yaml:arm64 < none -> 0.18.6+ds-3 @un puN Ib > 155s Broken python3-ruamel.yaml:arm64 Depends on python3-ruamel.yaml.clib:arm64 < none | 0.2.8-1build1 @un uH > (>= 0.2.8-2) 155s Considering python3-ruamel.yaml.clib:arm64 0 as a solution to python3-ruamel.yaml:arm64 0 155s Re-Instated python3-ruamel.yaml.clib:arm64 155s Done 155s Some packages could not be installed. This may mean that you have 155s requested an impossible situation or if you are using the unstable 155s distribution that some required packages have not yet been created 155s or been moved out of Incoming. 155s The following information may help to resolve the situation: 155s 155s The following packages have unmet dependencies: 155s python3-ruamel.yaml : Depends: python3-ruamel.yaml.clib (>= 0.2.8-2) but 0.2.8-1build1 is to be installed 156s E: Unable to correct problems, you have held broken packages. 156s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from oracular-proposed 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s The following additional packages will be installed: 158s cwlformat libpython3-stdlib python3 python3-all python3-iniconfig 158s python3-minimal python3-packaging python3-pluggy python3-pytest 158s python3-ruamel.yaml python3-ruamel.yaml.clib 158s The following NEW packages will be installed: 158s autopkgtest-satdep cwlformat python3-all python3-iniconfig python3-packaging 158s python3-pluggy python3-pytest python3-ruamel.yaml python3-ruamel.yaml.clib 158s The following packages will be upgraded: 158s libpython3-stdlib python3 python3-minimal 158s 3 upgraded, 9 newly installed, 0 to remove and 40 not upgraded. 158s Need to get 641 kB/642 kB of archives. 158s After this operation, 2640 kB of additional disk space will be used. 158s Get:1 /tmp/autopkgtest.JuRSNr/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 158s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 python3-minimal arm64 3.12.4-1 [27.1 kB] 158s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 python3 arm64 3.12.4-1 [24.0 kB] 158s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libpython3-stdlib arm64 3.12.4-1 [9824 B] 158s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-1 [127 kB] 158s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 158s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 cwlformat all 2022.02.18-3 [7622 B] 158s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 python3-all arm64 3.12.4-1 [882 B] 158s Get:9 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 158s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.1-1 [41.4 kB] 158s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 158s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 159s Fetched 641 kB in 1s (995 kB/s) 159s (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 ... 78607 files and directories currently installed.) 159s Preparing to unpack .../python3-minimal_3.12.4-1_arm64.deb ... 159s Unpacking python3-minimal (3.12.4-1) over (3.12.3-0ubuntu1) ... 160s Setting up python3-minimal (3.12.4-1) ... 160s (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 ... 78607 files and directories currently installed.) 160s Preparing to unpack .../00-python3_3.12.4-1_arm64.deb ... 160s Unpacking python3 (3.12.4-1) over (3.12.3-0ubuntu1) ... 160s Preparing to unpack .../01-libpython3-stdlib_3.12.4-1_arm64.deb ... 160s Unpacking libpython3-stdlib:arm64 (3.12.4-1) over (3.12.3-0ubuntu1) ... 160s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 161s Preparing to unpack .../02-python3-ruamel.yaml.clib_0.2.8+ds-1_arm64.deb ... 161s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 161s Selecting previously unselected package python3-ruamel.yaml. 161s Preparing to unpack .../03-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 161s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 161s Selecting previously unselected package cwlformat. 161s Preparing to unpack .../04-cwlformat_2022.02.18-3_all.deb ... 161s Unpacking cwlformat (2022.02.18-3) ... 161s Selecting previously unselected package python3-all. 161s Preparing to unpack .../05-python3-all_3.12.4-1_arm64.deb ... 161s Unpacking python3-all (3.12.4-1) ... 161s Selecting previously unselected package python3-iniconfig. 161s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 161s Unpacking python3-iniconfig (1.1.1-2) ... 161s Selecting previously unselected package python3-packaging. 161s Preparing to unpack .../07-python3-packaging_24.1-1_all.deb ... 161s Unpacking python3-packaging (24.1-1) ... 161s Selecting previously unselected package python3-pluggy. 161s Preparing to unpack .../08-python3-pluggy_1.5.0-1_all.deb ... 161s Unpacking python3-pluggy (1.5.0-1) ... 161s Selecting previously unselected package python3-pytest. 161s Preparing to unpack .../09-python3-pytest_8.2.2-1ubuntu1_all.deb ... 161s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 161s Selecting previously unselected package autopkgtest-satdep. 162s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 162s Unpacking autopkgtest-satdep (0) ... 162s Setting up libpython3-stdlib:arm64 (3.12.4-1) ... 162s Setting up python3 (3.12.4-1) ... 163s Setting up python3-packaging (24.1-1) ... 163s Setting up python3-pluggy (1.5.0-1) ... 163s Setting up python3-iniconfig (1.1.1-2) ... 163s Setting up python3-pytest (8.2.2-1ubuntu1) ... 164s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 164s Setting up python3-all (3.12.4-1) ... 164s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 164s Setting up cwlformat (2022.02.18-3) ... 164s Setting up autopkgtest-satdep (0) ... 164s Processing triggers for man-db (2.12.1-2) ... 168s (Reading database ... 78861 files and directories currently installed.) 168s Removing autopkgtest-satdep (0) ... 169s autopkgtest [16:10:30]: test run-unit-test: [----------------------- 170s /tmp/autopkgtest.JuRSNr/build.kt5/src/tests /tmp/autopkgtest.JuRSNr/build.kt5/src 170s Testing with python3.12 in /tmp/autopkgtest.JuRSNr/build.kt5/src/tests: 170s ============================= test session starts ============================== 170s platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0 -- /usr/bin/python3.12 170s cachedir: .pytest_cache 170s rootdir: /tmp/autopkgtest.JuRSNr/build.kt5/src 170s collecting ... collected 3 items 170s 171s test_battery.py::test_formatting_battery FAILED [ 33%] 171s test_battery.py::test_node_conservation PASSED [ 66%] 172s test_explode.py::test_explode PASSED [100%] 172s 172s =================================== FAILURES =================================== 172s ___________________________ test_formatting_battery ____________________________ 172s 172s def test_formatting_battery(): 172s 172s path = current_path / "cwl" 172s for raw_name in path.glob("original-*"): 172s expected_name = raw_name.parent / pathlib.Path("formatted-" + "-".join(raw_name.stem.split("-")[1:]) + ".cwl") 172s formatted_cwl = cwl_format(raw_name.open("r").read()) 172s expected_raw_cwl = expected_name.open("r").read() 172s 172s > assert formatted_cwl == expected_raw_cwl 172s E assert "#!/usr/bin/e...nome_sizes'\n" == "#!/usr/bin/e...nome_sizes'\n" 172s E 172s E #!/usr/bin/env cwl-runner 172s E 172s E cwlVersion: v1.0 172s E class: Workflow 172s E label: ATAC-seq-pipeline-se 172s E doc: 'ATAC-seq pipeline - reads: SE'... 172s E 172s E ...Full output truncated (4516 lines hidden), use '-vv' to show 172s 172s test_battery.py:19: AssertionError 172s =============================== warnings summary =============================== 172s ../../../../../usr/lib/python3/dist-packages/cwlformat/formatter.py:23 172s /usr/lib/python3/dist-packages/cwlformat/formatter.py:23: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice. 172s key_order_dict = yaml.load(read_text("cwlformat", "keyorder.yml")) 172s 172s ../../../../../usr/lib/python3.12/importlib/resources/_legacy.py:79 172s /usr/lib/python3.12/importlib/resources/_legacy.py:79: DeprecationWarning: open_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice. 172s with open_text(package, resource, encoding, errors) as fp: 172s 172s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 172s =========================== short test summary info ============================ 172s FAILED test_battery.py::test_formatting_battery - assert "#!/usr/bin/e...nome... 172s =================== 1 failed, 2 passed, 2 warnings in 1.79s ==================== 173s autopkgtest [16:10:34]: test run-unit-test: -----------------------] 174s autopkgtest [16:10:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 174s run-unit-test FAIL non-zero exit status 1 175s autopkgtest [16:10:36]: @@@@@@@@@@@@@@@@@@@@ summary 175s run-unit-test FAIL non-zero exit status 1 188s nova [W] Skipping flock in bos03-arm64 188s Creating nova instance adt-oracular-arm64-cwlformat-20240726-160741-juju-7f2275-prod-proposed-migration-environment-2-5d37588f-32ad-4f65-af67-cbc3d268dd8b from image adt/ubuntu-oracular-arm64-server-20240726.img (UUID 33caccb7-bc3b-4ecc-9e17-59d67995dc9e)...