Your message dated Wed, 09 Apr 2025 12:05:09 +0000
with message-id <[email protected]>
and subject line Bug#1101085: fixed in toil 8.0.0-5
has caused the Debian Bug report #1101085,
regarding toil: FTBFS: toil.batchSystems.DeadlockException: Deadlock
encountered: The workflow is service deadlocked - all 1 running jobs have been
the same active services for at least 60 seconds
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1101085: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1101085
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:toil
Version: 8.0.0-4
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf docs/_build
find . -name "*.pyc" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
[... snipped ...]
[gw1] [ 47%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo
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[gw1] [ 47%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
[gw1] [ 47%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
[gw1] [ 48%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
[gw1] [ 48%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
[gw1] [ 48%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
[gw1] [ 49%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
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[gw1] [ 49%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo
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[gw1] [ 49%] SKIPPED
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[gw1] [ 49%] SKIPPED
toil/test/src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia
[gw1] [ 50%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes
[gw1] [ 50%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes
[gw1] [ 50%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet
[gw1] [ 50%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet
[gw1] [ 51%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse
[gw1] [ 51%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding
[gw1] [ 51%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large
[gw1] [ 52%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed
[gw1] [ 52%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small
[gw1] [ 52%] PASSED
toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows
[gw1] [ 52%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url
[gw1] [ 53%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip
[gw1] [ 53%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip
[gw1] [ 53%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip
[gw1] [ 54%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip
[gw1] [ 54%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip
[gw1] [ 54%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url
[gw1] [ 54%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw1] [ 55%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
[gw1] [ 55%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows
[gw1] [ 55%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url
[gw1] [ 55%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip
[gw1] [ 56%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip
[gw1] [ 56%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip
[gw1] [ 56%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip
[gw1] [ 57%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip
[gw1] [ 57%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url
[gw1] [ 57%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw1] [ 57%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
[gw1] [ 58%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows
[gw1] [ 58%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url
[gw1] [ 58%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip
[gw1] [ 59%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip
[gw1] [ 59%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip
[gw1] [ 59%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip
[gw1] [ 59%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip
[gw1] [ 60%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url
[gw1] [ 60%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw1] [ 60%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
[gw1] [ 60%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode
[gw1] [ 61%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime
[gw1] [ 61%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes
[gw1] [ 61%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs
[gw1] [ 62%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime
[gw1] [ 62%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape
[gw1] [ 62%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase
[gw1] [ 62%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testSorting
[gw1] [ 63%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testSorting
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs
[gw1] [ 63%] PASSED
toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs
toil/test/utils/utilsTest.py::UtilsTest::testGetPIDStatus
[gw1] [ 63%] PASSED toil/test/utils/utilsTest.py::UtilsTest::testGetPIDStatus
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedCWLWF
[gw1] [ 63%] SKIPPED
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedCWLWF
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedToilWF
[gw1] [ 64%] PASSED
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedToilWF
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusSuccessfulCWLWF
[gw1] [ 64%] SKIPPED
toil/test/utils/utilsTest.py::UtilsTest::testGetStatusSuccessfulCWLWF
toil/test/utils/utilsTest.py::UtilsTest::testPrintJobLog
[gw1] [ 64%] PASSED toil/test/utils/utilsTest.py::UtilsTest::testPrintJobLog
toil/test/utils/utilsTest.py::UtilsTest::testRestartAttribute
[gw1] [ 65%] PASSED
toil/test/utils/utilsTest.py::UtilsTest::testRestartAttribute
toil/test/utils/utilsTest.py::UtilsTest::testUnicodeSupport
[gw1] [ 65%] PASSED toil/test/utils/utilsTest.py::UtilsTest::testUnicodeSupport
toil/test/utils/utilsTest.py::UtilsTest::test_config_functionality
[gw1] [ 65%] PASSED
toil/test/utils/utilsTest.py::UtilsTest::test_config_functionality
toil/test/src/miscTests.py::MiscTests::testIDStability
[gw1] [ 65%] PASSED toil/test/src/miscTests.py::MiscTests::testIDStability
toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
[gw1] [ 66%] PASSED
toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
[gw1] [ 66%] PASSED
toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
toil/test/src/miscTests.py::MiscTests::test_atomic_install
[gw1] [ 66%] PASSED toil/test/src/miscTests.py::MiscTests::test_atomic_install
toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev
[gw1] [ 67%] PASSED
toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev
toil/test/src/miscTests.py::MiscTests::test_call_command_err
[gw1] [ 67%] PASSED
toil/test/src/miscTests.py::MiscTests::test_call_command_err
toil/test/src/miscTests.py::MiscTests::test_call_command_ok
[gw1] [ 67%] PASSED toil/test/src/miscTests.py::MiscTests::test_call_command_ok
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testAlways
[gw1] [ 67%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testAlways
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testNever
[gw1] [ 68%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testNever
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnErrorWithError
[gw1] [ 68%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnErrorWithError
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnErrorWithNoError
[gw1] [ 68%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnErrorWithNoError
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnSuccessWithError
[gw1] [ 68%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnSuccessWithError
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnSuccessWithSuccess
[gw1] [ 69%] PASSED
toil/test/src/retainTempDirTest.py::CleanWorkDirTest::testOnSuccessWithSuccess
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
[gw1] [ 69%] PASSED
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags
[gw1] [ 69%] PASSED
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags
[gw1] [ 70%] PASSED
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
[gw1] [ 70%] PASSED
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
[gw1] [ 70%] PASSED
toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility
[gw1] [ 70%] PASSED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw1] [ 71%] PASSED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw1] [ 71%] PASSED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
[gw1] [ 71%] PASSED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw1] [ 72%] PASSED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility
[gw1] [ 72%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
[gw1] [ 72%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
[gw1] [ 72%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw1] [ 73%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
[gw1] [ 73%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility
[gw1] [ 73%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
[gw1] [ 73%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
[gw1] [ 74%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw1] [ 74%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
[gw1] [ 74%] SKIPPED
toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
[gw1] [ 75%] PASSED toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
[gw1] [ 75%] PASSED
toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
toil/test/src/resourceTest.py::ResourceTest::testPackage
[gw1] [ 75%] PASSED toil/test/src/resourceTest.py::ResourceTest::testPackage
toil/test/src/resourceTest.py::ResourceTest::testStandAlone
[gw1] [ 75%] PASSED toil/test/src/resourceTest.py::ResourceTest::testStandAlone
toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
[gw1] [ 76%] PASSED
toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testBatchSystemCleanupCanHandleWorkerDeaths
[gw1] [ 76%] PASSED
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testBatchSystemCleanupCanHandleWorkerDeaths
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithClassMethod
[gw1] [ 76%] PASSED
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithClassMethod
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithLambda
[gw1] [ 77%] PASSED
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithLambda
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithMethod
[gw1] [ 77%] PASSED
toil/test/src/deferredFunctionTest.py::DeferredFunctionTest::testDeferredFunctionRunsWithMethod
toil/test/src/miscTests.py::TestPanic::test_nested_panic
[gw1] [ 77%] PASSED toil/test/src/miscTests.py::TestPanic::test_nested_panic
toil/test/src/miscTests.py::TestPanic::test_panic
[gw1] [ 77%] PASSED toil/test/src/miscTests.py::TestPanic::test_panic
toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
[gw1] [ 78%] PASSED toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
[gw1] [ 78%] PASSED
toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist
[gw1] [ 78%] PASSED
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists
[gw1] [ 78%] PASSED
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running
[gw1] [ 79%] PASSED
toil/test/batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running
toil/test/lib/test_conversions.py::ConversionTest::test_convert
[gw1] [ 79%] PASSED
toil/test/lib/test_conversions.py::ConversionTest::test_convert
toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
[gw1] [ 79%] PASSED
toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
[gw1] [ 80%] PASSED
toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
[gw1] [ 80%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
[gw1] [ 80%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
[gw1] [ 80%] SKIPPED
toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
[gw1] [ 81%] PASSED
toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file
[gw1] [ 81%] PASSED
toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file
toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path
[gw1] [ 81%] PASSED
toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
[gw1] [ 81%] PASSED
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
[gw1] [ 82%] PASSED
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
[gw1] [ 82%] PASSED
toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
toil/test/src/jobTest.py::JobTest::testDAGConsistency
[gw1] [ 82%] PASSED toil/test/src/jobTest.py::JobTest::testDAGConsistency
toil/test/src/jobTest.py::JobTest::testDeadlockDetection
[gw1] [ 83%] PASSED toil/test/src/jobTest.py::JobTest::testDeadlockDetection
toil/test/src/jobTest.py::JobTest::testStatic2
[gw1] [ 83%] PASSED toil/test/src/jobTest.py::JobTest::testStatic2
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::testPromisesWithJobStoreFileObjects
[gw1] [ 83%] PASSED
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::testPromisesWithJobStoreFileObjects
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::testPromisesWithNonCachingFileStore
[gw1] [ 83%] PASSED
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::testPromisesWithNonCachingFileStore
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::test_omp_threads
<- toil/test/batchSystems/batchSystemTest.py
[gw1] [ 84%] PASSED
toil/test/src/promisedRequirementTest.py::SingleMachinePromisedRequirementsTest::test_omp_threads
<- toil/test/batchSystems/batchSystemTest.py
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::testPromisesWithJobStoreFileObjects
[gw1] [ 84%] SKIPPED
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::testPromisesWithJobStoreFileObjects
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::testPromisesWithNonCachingFileStore
[gw1] [ 84%] SKIPPED
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::testPromisesWithNonCachingFileStore
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::test_omp_threads
<- toil/test/batchSystems/batchSystemTest.py
[gw1] [ 85%] SKIPPED
toil/test/src/promisedRequirementTest.py::MesosPromisedRequirementsTest::test_omp_threads
<- toil/test/batchSystems/batchSystemTest.py
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
[gw1] [ 85%] PASSED
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
[gw1] [ 85%] PASSED
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
[gw1] [ 85%] PASSED
toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
[gw1] [ 86%] PASSED
toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
toil/test/utils/toilDebugTest.py::DebugJobTest::test_retrieve_task_directory
[gw1] [ 86%] SKIPPED
toil/test/utils/toilDebugTest.py::DebugJobTest::test_retrieve_task_directory
toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
[gw1] [ 86%] PASSED
toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
toil/test/__init__.py::toil.test.make_tests
[gw1] [ 86%] PASSED toil/test/__init__.py::toil.test.make_tests
toil/test/__init__.py::toil.test.timeLimit
[gw1] [ 87%] PASSED toil/test/__init__.py::toil.test.timeLimit
toil/test/options/options.py::OptionsTest::test_caching_option_priority
[gw1] [ 87%] PASSED
toil/test/options/options.py::OptionsTest::test_caching_option_priority
toil/test/options/options.py::OptionsTest::test_default_caching_slurm
[gw1] [ 87%] PASSED
toil/test/options/options.py::OptionsTest::test_default_caching_slurm
toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
[gw1] [ 88%] SKIPPED
toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
[gw1] [ 88%] SKIPPED
toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
[gw1] [ 88%] PASSED
toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false
[gw1] [ 88%] PASSED
toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false
toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
[gw1] [ 89%] PASSED
toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
[gw1] [ 89%] PASSED
toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
[gw1] [ 89%] PASSED
toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
[gw1] [ 90%] PASSED
toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
[gw1] [ 90%] PASSED
toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
[gw1] [ 90%] PASSED
toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
[gw1] [ 90%] PASSED
toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
[gw1] [ 91%] PASSED
toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
toil/test/batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable
[gw1] [ 91%] PASSED
toil/test/batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable
toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
[gw1] [ 91%] PASSED
toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
[gw1] [ 91%] SKIPPED
toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
[gw1] [ 92%] PASSED
toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
[gw1] [ 92%] PASSED
toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
[gw1] [ 92%] PASSED
toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
[gw1] [ 93%] PASSED
toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
[gw1] [ 93%] PASSED
toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
[gw1] [ 93%] SKIPPED
toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
[gw1] [ 93%] SKIPPED
toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
[gw1] [ 94%] SKIPPED
toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
[gw1] [ 94%] PASSED
toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
toil/test/src/environmentTest.py::EnvironmentTest::test_environment
[gw1] [ 94%] PASSED
toil/test/src/environmentTest.py::EnvironmentTest::test_environment
toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
[gw1] [ 95%] PASSED
toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
toil/test/src/jobServiceTest.py::JobServiceTest::testServiceWithCheckpoints
[gw1] [ 95%] SKIPPED
toil/test/src/jobServiceTest.py::JobServiceTest::testServiceWithCheckpoints
toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceWithCheckpoints
[gw1] [ 95%] SKIPPED
toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceWithCheckpoints
toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
[gw1] [ 95%] PASSED
toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
[gw1] [ 96%] PASSED
toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
[gw1] [ 96%] PASSED
toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
[gw1] [ 96%] PASSED
toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
[gw0] [ 96%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw1] [ 97%] PASSED
toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
[gw0] [ 97%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
[gw1] [ 97%] PASSED
toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
toil/test/src/workerTest.py::WorkerTests::testNextChainable
[gw1] [ 98%] PASSED toil/test/src/workerTest.py::WorkerTests::testNextChainable
toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
[gw0] [ 98%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore
[gw1] [ 98%] PASSED toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
toil/test/utils/toilKillTest.py::ToilKillTest::test_cwl_toil_kill
[gw0] [ 98%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore
[gw1] [ 99%] PASSED
toil/test/utils/toilKillTest.py::ToilKillTest::test_cwl_toil_kill
toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore::test_cwl_toil_kill
[gw1] [ 99%] SKIPPED
toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore::test_cwl_toil_kill
[gw0] [ 99%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw0] [100%] PASSED
toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
=================================== FAILURES ===================================
______________________ ToilDocumentationTest.testServices ______________________
[gw1] linux -- Python 3.13.2 /usr/bin/python3.13
Traceback (most recent call last):
File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.13/unittest/case.py", line 651, in run
self._callTestMethod(testMethod)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod
if method() is not None:
~~~~~~^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/test/docs/scriptsTest.py",
line 166, in testServices
self.checkExitCode("tutorial_services.py")
~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/test/docs/scriptsTest.py",
line 49, in checkExitCode
raise RuntimeError(stderr)
RuntimeError: [2025-03-23T00:22:27+0000] [MainThread] [I] [toil] Running Toil
version 8.0.0-d2ae0ea9ab49f238670dbf6aafd20de7afdd8514 on host
c7a-large-1742688931.
[2025-03-23T00:22:27+0000] [MainThread] [I] [toil.realtimeLogger] Starting
real-time logging.
[2025-03-23T00:22:27+0000] [MainThread] [I] [toil.leader] Issued job 'Job'
kind-Job/instance-d7r7bix5 v1 with job batch system ID: 1 and disk: 2.0 Gi,
memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:22:28+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0
jobs are issued and waiting to run
[2025-03-23T00:22:30+0000] [MainThread] [I] [toil.leader] Issued job
'DemoService' kind-DemoService/instance-g5shw13_ v1 with job batch system ID: 2
and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:22:34+0000] [MainThread] [I] [toil.leader] Issued job 'dbFn'
kind-dbFn/instance-6_ixslsk v1 with job batch system ID: 3 and disk: 2.0 Gi,
memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:23:00+0000] [MainThread] [W] [toil.leader] Potential deadlock
detected! All 1 running jobs are service jobs, with no normal jobs to use them!
The batch system reports: Not enough memory to run job 3
[2025-03-23T00:23:30+0000] [MainThread] [W] [toil.leader] Potentially
deadlocked for 30 seconds. Waiting at most 30 more seconds for any of 1 issued
non-service jobs to schedule and start. The batch system reports: Not enough
memory to run job 3
[2025-03-23T00:24:00+0000] [MainThread] [E] [toil.leader] We have been
deadlocked since 1742689380.054194 on these service jobs:
{'kind-DemoService/instance-g5shw13_'}
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.realtimeLogger] Stopping
real-time logging server.
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.realtimeLogger] Joining
real-time logging server thread.
[2025-03-23T00:24:01+0000] [MainThread] [W]
[toil.fileStores.nonCachingFileStore] Detected that job ('DemoService'
kind-DemoService/instance-g5shw13_ v1) prematurely terminated. Fixing the
state of the job on disk.
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.common] Successfully deleted
the job store: FileJobStore(/tmp/tmpodm70nnftutorial_services)
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/test/docs/scripts/tutorial_services.py",
line 45, in <module>
toil.start(j)
~~~~~~~~~~^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/common.py",
line 1055, in start
return self._runMainLoop(rootJobDescription)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/common.py",
line 1632, in _runMainLoop
).run()
~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 283, in run
self.innerLoop()
~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 943, in innerLoop
self.checkForDeadlocks()
~~~~~~~~~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 1044, in checkForDeadlocks
raise DeadlockException(
...<5 lines>...
)
toil.batchSystems.DeadlockException: Deadlock encountered: The workflow is
service deadlocked - all 1 running jobs have been the same active services for
at least 60 seconds
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testServices (Mar 22
2025 17:22:27:500313 PDT)
=========================== short test summary info ============================
FAILED toil/test/docs/scriptsTest.py::ToilDocumentationTest::testServices -
RuntimeError: [2025-03-23T00:22:27+0000] [MainThread] [I] [toil] Running Toil
version 8.0.0-d2ae0ea9ab49f238670dbf6aafd20de7afdd8514 on host
c7a-large-1742688931.
[2025-03-23T00:22:27+0000] [MainThread] [I] [toil.realtimeLogger] Starting
real-time logging.
[2025-03-23T00:22:27+0000] [MainThread] [I] [toil.leader] Issued job 'Job'
kind-Job/instance-d7r7bix5 v1 with job batch system ID: 1 and disk: 2.0 Gi,
memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:22:28+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0
jobs are issued and waiting to run
[2025-03-23T00:22:30+0000] [MainThread] [I] [toil.leader] Issued job
'DemoService' kind-DemoService/instance-g5shw13_ v1 with job batch system ID: 2
and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:22:34+0000] [MainThread] [I] [toil.leader] Issued job 'dbFn'
kind-dbFn/instance-6_ixslsk v1 with job batch system ID: 3 and disk: 2.0 Gi,
memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2025-03-23T00:23:00+0000] [MainThread] [W] [toil.leader] Potential deadlock
detected! All 1 running jobs are service jobs, with no normal jobs to use them!
The batch system reports: Not enough memory to run job 3
[2025-03-23T00:23:30+0000] [MainThread] [W] [toil.leader] Potentially
deadlocked for 30 seconds. Waiting at most 30 more seconds for any of 1 issued
non-service jobs to schedule and start. The batch system reports: Not enough
memory to run job 3
[2025-03-23T00:24:00+0000] [MainThread] [E] [toil.leader] We have been
deadlocked since 1742689380.054194 on these service jobs:
{'kind-DemoService/instance-g5shw13_'}
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.realtimeLogger] Stopping
real-time logging server.
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.realtimeLogger] Joining
real-time logging server thread.
[2025-03-23T00:24:01+0000] [MainThread] [W]
[toil.fileStores.nonCachingFileStore] Detected that job ('DemoService'
kind-DemoService/instance-g5shw13_ v1) prematurely terminated. Fixing the
state of the job on disk.
[2025-03-23T00:24:01+0000] [MainThread] [I] [toil.common] Successfully deleted
the job store: FileJobStore(/tmp/tmpodm70nnftutorial_services)
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/test/docs/scripts/tutorial_services.py",
line 45, in <module>
toil.start(j)
~~~~~~~~~~^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/common.py",
line 1055, in start
return self._runMainLoop(rootJobDescription)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/common.py",
line 1632, in _runMainLoop
).run()
~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 283, in run
self.innerLoop()
~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 943, in innerLoop
self.checkForDeadlocks()
~~~~~~~~~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build/toil/leader.py",
line 1044, in checkForDeadlocks
raise DeadlockException(
...<5 lines>...
)
toil.batchSystems.DeadlockException: Deadlock encountered: The workflow is
service deadlocked - all 1 running jobs have been the same active services for
at least 60 seconds
============ 1 failed, 205 passed, 155 skipped in 521.29s (0:08:41) ============
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_toil/build; python3.13 -m pytest -n 2
--dist loadscope -vv -W ignore -k "not (testVirtualEnv or DockstoreLookupTest
or testMultiplejobs)" -m "not slow" --ignore toil/test/lib/aws/test_s3.py
--ignore toil/test/provisioners/aws/awsProvisionerTest.py --ignore
toil/test/wdl/wdltoil_test.py --ignore toil/test/cwl/cwlTest.py --ignore
toil/test/lib/test_ec2.py --ignore toil/test/batchSystems/batchSystemTest.py
--ignore toil/test/lib/aws/test_iam.py --ignore
toil/test/provisioners/clusterTest.py --ignore
toil/test/wdl/wdltoil_test_kubernetes.py --ignore
toil/test/cactus/test_cactus_integration.py toil/test
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13
returned exit code 13
make[1]: *** [debian/rules:37: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:20: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202503/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:toil, so that this is still
visible in the BTS web page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: toil
Source-Version: 8.0.0-5
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
toil, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated toil package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 09 Apr 2025 13:42:27 +0200
Source: toil
Architecture: source
Version: 8.0.0-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1101085
Changes:
toil (8.0.0-5) unstable; urgency=medium
.
* d/rules: skip flaky testServices. Closes: #1101085
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