[Debian-med-packaging] Bug#1047580: ray: Fails to build source after successful build

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

Source: ray
Version: 2.3.1-7
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 ray
> dpkg-buildpackage: info: source version 2.3.1-7
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean -- CXXFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" HAVE_LIBZ=y HAVE_LIBBZ2=y
> 	make -j8 clean "CXXFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" HAVE_LIBZ=y HAVE_LIBBZ2=y
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make -w -j8 --jobserver-auth=3,4 -C RayPlatform clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: warning: -j8 forced in submake: resetting jobserver mode.
> echo CLEAN RayPlatform
> CLEAN RayPlatform
> rm -f libRayPlatform.a RayPlatform/memory/ReusableMemoryStore.o  RayPlatform/memory/MyAllocator.o RayPlatform/memory/RingAllocator.o  RayPlatform/memory/allocator.o RayPlatform/memory/DefragmentationGroup.o RayPlatform/memory/ChunkAllocatorWithDefragmentation.o RayPlatform/memory/DefragmentationLane.o RayPlatform/memory/DirtyBuffer.o RayPlatform/routing/ConnectionGraph.o RayPlatform/routing/GraphImplementation.o RayPlatform/routing/GraphImplementationRandom.o RayPlatform/routing/GraphImplementationComplete.o RayPlatform/routing/GraphImplementationDeBruijn.o RayPlatform/routing/GraphImplementationKautz.o RayPlatform/routing/GraphImplementationExperimental.o RayPlatform/routing/GraphImplementationGroup.o RayPlatform/routing/Polytope.o RayPlatform/routing/Torus.o RayPlatform/communication/mpi_tags.o 
> RayPlatform/communication/VirtualCommunicator.o RayPlatform/communication/BufferedData.o RayPlatform/communication/Message.o RayPlatform/communication/MessagesHandler.o RayPlatform/communication/MessageQueue.o RayPlatform/communication/MessageRouter.o RayPlatform/scheduling/VirtualProcessor.o RayPlatform/scheduling/TaskCreator.o RayPlatform/scheduling/SwitchMan.o RayPlatform/core/ComputeCore.o RayPlatform/core/MiniRank.o RayPlatform/core/slave_modes.o  RayPlatform/core/OperatingSystem.o RayPlatform/core/master_modes.o RayPlatform/core/statistics.o RayPlatform/plugins/CorePlugin.o RayPlatform/plugins/RegisteredPlugin.o RayPlatform/structures/StaticVector.o  RayPlatform/profiling/Profiler.o RayPlatform/profiling/Derivative.o RayPlatform/profiling/TickLogger.o RayPlatform/profiling/TimePrinter.o 
> RayPlatform/profiling/ProcessStatus.o RayPlatform/handlers/MasterModeExecutor.o RayPlatform/handlers/SlaveModeExecutor.o RayPlatform/handlers/MessageTagExecutor.o RayPlatform/cryptography/crypto.o RayPlatform/store/KeyValueStore.o RayPlatform/store/KeyValueStoreItem.o RayPlatform/store/KeyValueStoreRequest.o RayPlatform/actors/Actor.o RayPlatform/actors/Playground.o RayPlatform/files/FileReader.o
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/RayPlatform'
> echo CLEAN Ray plugins
> CLEAN Ray plugins
> rm -f Ray PREFIX code/Amos/Amos.o code/CoverageGatherer/CoverageGatherer.o  code/CoverageGatherer/CoverageDistribution.o  code/EdgePurger/EdgePurger.o code/EdgePurger/EdgePurgerWorker.o code/Example/Example.o code/FusionData/FusionData.o  code/FusionTaskCreator/FusionWorker.o  code/FusionTaskCreator/FusionTaskCreator.o  code/GeneOntology/KeyEncoder.o code/GeneOntology/GeneOntology.o code/GenomeNeighbourhood/GenomeNeighbourhood.o code/GenomeNeighbourhood/Neighbour.o code/GenomeNeighbourhood/NeighbourPair.o code/JoinerTaskCreator/JoinerWorker.o  code/JoinerTaskCreator/JoinerTaskCreator.o code/KmerAcademyBuilder/KmerAcademyBuilder.o code/KmerAcademyBuilder/BloomFilter.o code/KmerAcademyBuilder/Kmer.o code/Library/LibraryPeakFinder.o code/Library/LibraryWorker.o  code/Library/Library.o  code/MachineHelper/MachineHelper.o 
> code/MessageProcessor/MessageProcessor.o code/Mock/Parameters.o code/Mock/common_functions.o code/Mock/Mock.o code/NetworkTest/NetworkTest.o code/Partitioner/Partitioner.o code/PathEvaluator/PathEvaluator.o code/Scaffolder/Scaffolder.o  code/Scaffolder/ScaffoldingLink.o code/Scaffolder/SummarizedLink.o code/Scaffolder/ScaffoldingAlgorithm.o code/Scaffolder/ScaffoldingVertex.o code/Scaffolder/ScaffoldingEdge.o code/Searcher/Searcher.o code/Searcher/SearchDirectory.o code/Searcher/ContigSearchEntry.o code/Searcher/ContigHit.o code/Searcher/ColorSet.o code/Searcher/VirtualKmerColor.o code/Searcher/QualityCaller.o code/Searcher/DistributionWriter.o code/Searcher/ColoredPeakFinder.o code/SeedExtender/SeedExtender.o  code/SeedExtender/Direction.o code/SeedExtender/VertexMessenger.o code/SeedExtender/ReadFetcher.o 
> code/SeedExtender/BubbleTool.o code/SeedExtender/Chooser.o code/SeedExtender/OpenAssemblerChooser.o code/SeedExtender/TipWatchdog.o code/SeedExtender/NovaEngine.o code/SeedExtender/ExtensionElement.o  code/SeedExtender/DepthFirstSearchData.o  code/SeedExtender/ExtensionData.o  code/SeedingData/GraphPath.o code/SeedingData/SeedWorker.o code/SeedingData/SeedingData.o  code/SeedingData/PathHandle.o  code/SequencesIndexer/SequencesIndexer.o  code/SequencesIndexer/IndexerWorker.o  code/SequencesIndexer/PairedRead.o code/SequencesIndexer/ReadAnnotation.o  code/SequencesLoader/SequencesLoader.o code/SequencesLoader/Read.o code/SequencesLoader/ArrayOfReads.o code/SequencesLoader/ColorSpaceDecoder.o code/SequencesLoader/ColorSpaceLoader.o code/SequencesLoader/FastaLoader.o code/SequencesLoader/FastaLoaderForReads.o 
> code/SequencesLoader/FastqLoader.o code/SequencesLoader/ExportLoader.o code/SequencesLoader/LoaderInterface.o code/SequencesLoader/LoaderFactory.o code/SequencesLoader/SffLoader.o code/SequencesLoader/Loader.o code/SequencesLoader/BufferedReader.o code/SequencesLoader/ReadHandle.o code/SequencesLoader/BzReader.o code/SequencesLoader/FastqBz2Loader.o code/SequencesLoader/FastaBz2Loader.o code/SequencesLoader/FastqGzLoader.o code/SequencesLoader/FastaGzLoader.o code/SequencesLoader/SequenceFileDetector.o code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.o code/SpuriousSeedAnnihilator/AnnihilationWorker.o code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.o code/SpuriousSeedAnnihilator/AttributeFetcher.o code/SpuriousSeedAnnihilator/AnnotationFetcher.o code/SpuriousSeedAnnihilator/NanoMerger.o 
> code/SpuriousSeedAnnihilator/SeedMergingWorkflow.o code/SpuriousSeedAnnihilator/GraphExplorer.o code/SpuriousSeedAnnihilator/GraphSearchResult.o code/SpuriousSeedAnnihilator/SeedGossipSolver.o code/SpuriousSeedAnnihilator/GossipAssetManager.o code/Surveyor/Mother.o code/Surveyor/StoreKeeper.o code/Surveyor/GenomeGraphReader.o code/Surveyor/CoalescenceManager.o code/Surveyor/ExperimentVertex.o code/Surveyor/MatrixOwner.o code/TaxonomyViewer/TaxonomyViewer.o code/TaxonomyViewer/GenomeToTaxonLoader.o code/TaxonomyViewer/TaxonomicTreeLoader.o code/TaxonomyViewer/TaxonNameLoader.o code/VerticesExtractor/VerticesExtractor.o  code/VerticesExtractor/GridTable.o code/VerticesExtractor/GridTableIterator.o code/VerticesExtractor/Vertex.o code/application_core/Machine.o  libRay.a libRayPlatform.a code/application_core/ray_main.o
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -rf install-prefix
> rm -f README.Ray  README.RayPlatform
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building ray using existing ./ray_2.3.1.orig.tar.bz2
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: executable mode 0755 of 'REFIX/Build-Link-Time-Optimization.sh' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/Create-Taxon-Names.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/CreateRayInputStructures.sh' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/GenerateTaxonNames.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/generateTrees.sh' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/getName.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/NCBI-Taxonomy/getNameInFile.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/ShipProduct.sh' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/dump-ChangeLog.sh' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/getSeq.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/illumina-split-linked-sequences-fastq.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/interleave-fasta.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/interleave-fastq.py' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/plot-color-distributions.R' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/plot-coverage-distribution.R' will not be represented in diff
> dpkg-source: warning: executable mode 0755 of 'REFIX/plot-library-distribution.R' will not be represented in diff
> dpkg-source: info: local changes detected, the modified files are:
>  ray-2.3.1/REFIX/Build-Link-Time-Optimization.sh
>  ray-2.3.1/REFIX/GenerateRayCommand.sh
>  ray-2.3.1/REFIX/NCBI-Taxonomy/Create-Taxon-Names.py
>  ray-2.3.1/REFIX/NCBI-Taxonomy/CreateRayInputStructures.sh
>  ray-2.3.1/REFIX/NCBI-Taxonomy/GenerateTaxonNames.py
>  ray-2.3.1/REFIX/NCBI-Taxonomy/README
>  ray-2.3.1/REFIX/NCBI-Taxonomy/generateTrees.sh
>  ray-2.3.1/REFIX/NCBI-Taxonomy/getName.py
>  ray-2.3.1/REFIX/NCBI-Taxonomy/getNameInFile.py
>  ray-2.3.1/REFIX/ShipProduct.sh
>  ray-2.3.1/REFIX/dump-ChangeLog.sh
>  ray-2.3.1/REFIX/getSeq.py
>  ray-2.3.1/REFIX/illumina-split-linked-sequences-fastq.py
>  ray-2.3.1/REFIX/interleave-fasta.py
>  ray-2.3.1/REFIX/interleave-fastq.py
>  ray-2.3.1/REFIX/plot-color-distributions.R
>  ray-2.3.1/REFIX/plot-coverage-distribution.R
>  ray-2.3.1/REFIX/plot-library-distribution.R
>  ray-2.3.1/REFIX/xsl-xml/SequenceAbundances-assembled.xsl
>  ray-2.3.1/REFIX/xsl-xml/SequenceAbundances-to-html-tables.xsl
>  ray-2.3.1/REFIX/xsl-xml/SequenceAbundances-to-html.xsl
>  ray-2.3.1/REFIX/xsl-xml/SequenceAbundances-to-tsv.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-html-tables.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-html.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-any-rank.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-class.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-family.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-genus.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-order.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-phylum.xsl
>  ray-2.3.1/REFIX/xsl-xml/Taxons-to-tsv-species.xsl
>  ray-2.3.1/REFIX/xsl-xml/Terms-to-tsv.xsl
>  ray-2.3.1/RayPlatform/README
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/ray_2.3.1-7.diff._5phb0
> 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/ray_2.3.1-7_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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