[Debian-med-packaging] Bug#1046067: proalign: Fails to build source after successful build

[Lucas Nussbaum]

Source: proalign
Version: 0.603-5
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 proalign
> dpkg-buildpackage: info: source version 0.603-5
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: error: unwanted binary file: debian/_jh_build.javadoc/api/resources/x.png
> dpkg-source: error: unwanted binary file: debian/_jh_build.javadoc/api/resources/glass.png
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/MinimumProbWindow$1.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleAlignments.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$SplitListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/UserSettings.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/CheckSequence.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/NicePrint.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleAlignments$1.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintMinimumCurve$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/TraceBackException.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintNames$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$FileMenuListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/OutFile.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/NeighborJoining.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/Rule.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintData.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintData$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PixelRule.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/OpenFolderChooser.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/RunCommandLine.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/AlignmentLoop.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$AlignmentMenuListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$1.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$ScrollListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ParameterEstimates.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters$RadioListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SubstitutionModel.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleLoop.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintNames.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/OutOfMemoryException.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PwAlignment.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintTree.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/AlignmentNode.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleAlignments$CheckBoxListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$ProbabilityMenuListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/TransformLog.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintCurve.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/Viterbi.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SaveData.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/WinClustalw.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/InFile.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters$CheckBoxListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/TraceBackPath.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/CheckTrailing.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintTree$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PAFileFilter.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/QualityWindow.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/TreeReader.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/Rule$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters$ButtonListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/TreeNode.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ProAlign.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SequenceReader.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/OpenDialog.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/MinimumProbWindow.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/RunMultiple.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/RunClustalw.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/CheckTreeAndData.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/EstimateFrequencies.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PwSubstitutionMatrix.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleAlignments$RadioListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintCurve$MiceListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters$ComboBoxListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/QualityWindow$1.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SampleAlignments$ButtonL.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/SetParameters$1.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PwAlignmentLoop.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/PrintMinimumCurve.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ResultWindow$FontMenuListener.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/OpenFileChooser.class
> dpkg-source: error: unwanted binary file: debian/_jh_build.proalign/proalign/ReadArguments.class
> dpkg-source: error: detected 75 unwanted binary files (add them in debian/source/include-binaries to allow their inclusion).
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 255
> 
> 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/proalign_0.603-5_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.