[Debian-med-packaging] Bug#1047298: toil: Fails to build source after successful build

Lucas Nussbaum lucas at debian.org
Sun Aug 13 20:21:30 BST 2023 

Source: toil
Version: 5.11.0-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> ----------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package toil
> dpkg-buildpackage: info: source version 5.11.0-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
>  dpkg-source --before-build .
> dpkg-source: info: using options from toil-5.11.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
>  debian/rules clean
> dh clean --with python3 --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .pybuild
> rm -rf docs/_build
> find . -name "*.pyc" -delete
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using options from toil-5.11.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building toil using existing ./toil_5.11.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file toil-5.11.0/docs/autoapi/index.rst has no final newline (either original or modified version)
> dpkg-source: warning: file toil-5.11.0/src/toil/test/utils/ABCWorkflowDebug/ABC.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  toil-5.11.0/docs/autoapi/debugWorkflow/index.rst
>  toil-5.11.0/docs/autoapi/example_alwaysfail/index.rst
>  toil-5.11.0/docs/autoapi/example_cachingbenchmark/index.rst
>  toil-5.11.0/docs/autoapi/fake_mpi_run/index.rst
>  toil-5.11.0/docs/autoapi/index.rst
>  toil-5.11.0/docs/autoapi/mkFile/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/abstractBatchSystem/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/abstractGridEngineBatchSystem/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/awsBatch/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/cleanup_support/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/contained_executor/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/gridengine/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/htcondor/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/kubernetes/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/local_support/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/lsf/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/lsfHelper/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/mesos/batchSystem/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/mesos/conftest/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/mesos/executor/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/mesos/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/mesos/test/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/options/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/parasol/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/registry/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/singleMachine/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/slurm/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/tes/index.rst
>  toil-5.11.0/docs/autoapi/toil/batchSystems/torque/index.rst
>  toil-5.11.0/docs/autoapi/toil/bus/index.rst
>  toil-5.11.0/docs/autoapi/toil/common/index.rst
>  toil-5.11.0/docs/autoapi/toil/cwl/conftest/index.rst
>  toil-5.11.0/docs/autoapi/toil/cwl/cwltoil/index.rst
>  toil-5.11.0/docs/autoapi/toil/cwl/index.rst
>  toil-5.11.0/docs/autoapi/toil/cwl/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/deferred/index.rst
>  toil-5.11.0/docs/autoapi/toil/exceptions/index.rst
>  toil-5.11.0/docs/autoapi/toil/fileStores/abstractFileStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/fileStores/cachingFileStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/fileStores/index.rst
>  toil-5.11.0/docs/autoapi/toil/fileStores/nonCachingFileStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/index.rst
>  toil-5.11.0/docs/autoapi/toil/job/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/abstractJobStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/aws/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/aws/jobStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/aws/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/conftest/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/fileJobStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/googleJobStore/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/index.rst
>  toil-5.11.0/docs/autoapi/toil/jobStores/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/leader/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/accelerators/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/aws/ami/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/aws/iam/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/aws/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/aws/session/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/aws/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/bioio/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/compatibility/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/conversions/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/docker/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/ec2/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/ec2nodes/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/encryption/_dummy/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/encryption/_nacl/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/encryption/conftest/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/encryption/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/exceptions/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/expando/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/generatedEC2Lists/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/humanize/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/io/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/iterables/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/memoize/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/misc/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/objects/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/resources/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/retry/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/threading/index.rst
>  toil-5.11.0/docs/autoapi/toil/lib/throttle/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/abstractProvisioner/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/aws/awsProvisioner/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/aws/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/clusterScaler/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/gceProvisioner/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/index.rst
>  toil-5.11.0/docs/autoapi/toil/provisioners/node/index.rst
>  toil-5.11.0/docs/autoapi/toil/realtimeLogger/index.rst
>  toil-5.11.0/docs/autoapi/toil/resource/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/api_spec/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/app/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/celery_app/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/cli/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/cli/wes_cwl_runner/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wes/abstract_backend/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wes/amazon_wes_utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wes/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wes/tasks/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wes/toil_backend/index.rst
>  toil-5.11.0/docs/autoapi/toil/server/wsgi_app/index.rst
>  toil-5.11.0/docs/autoapi/toil/serviceManager/index.rst
>  toil-5.11.0/docs/autoapi/toil/statsAndLogging/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/batchSystems/batchSystemTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/batchSystems/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/batchSystems/parasolTestSupport/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/batchSystems/test_lsf_helper/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/batchSystems/test_slurm/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/cwl/conftest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/cwl/cwlTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/cwl/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/docs/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/docs/scriptsTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/jobStores/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/jobStores/jobStoreTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/aws/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/aws/test_iam/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/aws/test_s3/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/aws/test_utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/dockerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/test_conversions/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/test_ec2/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/lib/test_misc/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/mesos/MesosDataStructuresTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/mesos/helloWorld/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/mesos/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/mesos/stress/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/aws/awsProvisionerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/aws/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/clusterScalerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/clusterTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/gceProvisionerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/provisionerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/provisioners/restartScript/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/server/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/server/serverTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/sort/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/sort/restart_sort/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/sort/sort/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/sort/sortTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/autoDeploymentTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/busTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/checkpointTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/deferredFunctionTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/dockerCheckTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/fileStoreTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/helloWorldTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/importExportFileTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/jobDescriptionTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/jobEncapsulationTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/jobFileStoreTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/jobServiceTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/jobTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/miscTests/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/promisedRequirementTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/promisesTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/realtimeLoggerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/regularLogTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/resourceTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/restartDAGTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/resumabilityTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/retainTempDirTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/systemTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/threadingTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/toilContextManagerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/userDefinedJobArgTypeTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/src/workerTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/utils/toilDebugTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/utils/toilKillTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/utils/utilsTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/wdl/builtinTest/index.rst
>  toil-5.11.0/docs/autoapi/toil/test/wdl/conftest/index.rst
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>  toil-5.11.0/docs/autoapi/toil/toilState/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilClean/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilDebugFile/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilDebugJob/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilDestroyCluster/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilKill/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilLaunchCluster/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilMain/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilRsyncCluster/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilServer/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilSshCluster/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilStats/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilStatus/index.rst
>  toil-5.11.0/docs/autoapi/toil/utils/toilUpdateEC2Instances/index.rst
>  toil-5.11.0/docs/autoapi/toil/version/index.rst
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>  toil-5.11.0/docs/autoapi/toil/wdl/utils/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/versions/dev/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/versions/draft2/index.rst
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>  toil-5.11.0/docs/autoapi/toil/wdl/versions/v1/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/wdl_analysis/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/wdl_functions/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/wdl_synthesis/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/wdl_types/index.rst
>  toil-5.11.0/docs/autoapi/toil/wdl/wdltoil/index.rst
>  toil-5.11.0/docs/autoapi/toil/worker/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_arguments/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_cwlexample/index.rst
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>  toil-5.11.0/docs/autoapi/tutorial_encapsulation/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_encapsulation2/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_helloworld/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_invokeworkflow/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_invokeworkflow2/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_jobfunctions/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_managing/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_managing2/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_multiplejobs/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_multiplejobs2/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_multiplejobs3/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_promises/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_promises2/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_quickstart/index.rst
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>  toil-5.11.0/docs/autoapi/tutorial_services/index.rst
>  toil-5.11.0/docs/autoapi/tutorial_staging/index.rst
>  toil-5.11.0/src/toil/test/utils/ABCWorkflowDebug/ABC.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/toil_5.11.0-2.diff.8Z6YPN
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/13/toil_5.11.0-2_unstable.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

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