[Debian-med-packaging] Bug#1045547: ipig: Fails to build source after successful build

Lucas Nussbaum lucas at debian.org
Sun Aug 13 20:20:48 BST 2023 

Source: ipig
Version: 0.0.r5-4
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 ipig
> dpkg-buildpackage: info: source version 0.0.r5-4
> 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 --with javahelper
>    dh_auto_clean
> 	ant clean
> Buildfile: /<<PKGBUILDDIR>>/build.xml
> 
> clean:
>      [echo] Cleaning build directories
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/GeneControl.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/Ipig.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/Exporter.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/Gene.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/GeneSet.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/MzIdentML$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/MzIdentML$Peptide.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/MzIdentML$Protein.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/MzIdentML$Result.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/MzIdentML.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/Peptide.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/PeptideSet$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/PeptideSet$PeptideComparator.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data/PeptideSet.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/exceptions/ExitException.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/exceptions/FormatException.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$10.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$11.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$12.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$13.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$14.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$15.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$16.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$17.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$18.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$2.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$3.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$4.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$5.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$6.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$7.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$8.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$9.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$Loader.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader$Organism.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/Downloader.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$10.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$11.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$12.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$2.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$3.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$4.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$5.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$6.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$7.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$8.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$9.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui$Control.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/GeneControlGui.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$10.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$11.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$12.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$13.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$14.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$15.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$16.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$17.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$18.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$19.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$2.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$20.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$21.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$22.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$23.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$3.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$4.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$5.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$6.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$7.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$8.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$9.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui$Mapper.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/IpigGui.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/OutputJTextArea$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/OutputJTextArea$2.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/OutputJTextArea.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/ProxyDialog$1.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/ProxyDialog$2.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/ProxyDialog$3.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui/ProxyDialog.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping/Mapper.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping/Position$PositionComparator.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping/Position.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping/Validator.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping/WuManber.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools/Configurator.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools/Info.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools/Logger.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools/MascotCSV2TXT.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools/Translator.class
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/help/downloader_help.txt
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/help/genecontrolgui_help.txt
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/help/ipig_help.txt
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/help/ipiggui_help.txt
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/images/rki.png
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/organisms
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/xsd/FuGElightv1.0.0.xsd
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/xsd/mzIdentML1.0.0.xsd
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/xsd
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/images
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/help
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/tools
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/mapping
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/gui
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/exceptions
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig/data
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4/ipig
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki/ng4
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de/rki
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes/de
>    [delete] Deleting /<<PKGBUILDDIR>>/build/classes
>    [delete] Deleting /<<PKGBUILDDIR>>/build
> 
> BUILD SUCCESSFUL
> Total time: 0 seconds
>    jh_clean
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f build.xml
> dh_clean
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building ipig using existing ./ipig_0.0.r5.orig.tar.xz
> dpkg-source: error: cannot represent change to dist/iPiG.jar: binary file contents changed
> dpkg-source: error: add dist/iPiG.jar in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> 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/ipig_0.0.r5-4_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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