[R-pkg-team] Bug#1043632: cdkr: Fails to build source after successful build

[Lucas Nussbaum]

Source: cdkr
Version: 3.6.0+dfsg-3
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 cdkr
> dpkg-buildpackage: info: source version 3.6.0+dfsg-3
> 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
>    jh_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building cdkr using existing ./cdkr_3.6.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/app/OSXHelper.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/app/OSXHelper.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/descriptors/DescriptorUtilities.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/descriptors/DescriptorUtilities.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/formula/FormulaTools.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/formula/FormulaTools.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/util/Misc.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/util/Misc.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/util/TablePacker.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/util/TablePacker.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ImageSelection.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ImageSelection.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/MoleculeDisplay.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/MoleculeDisplay.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/MoleculeImage.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/MoleculeImage.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/MoleculeImageToClipboard.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/MoleculeImageToClipboard.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$1.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$1.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$CobColorer.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$CobColorer.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$NobColorer.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor$NobColorer.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/RcdkDepictor.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/RowLabelRenderer.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/RowLabelRenderer.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/StructureTable2D.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/StructureTable2D.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2D$ApplicationCloser.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2D$ApplicationCloser.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2D.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2D.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$ApplicationCloser.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$ApplicationCloser.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DColumnModelListener.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DColumnModelListener.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DPanelCellRenderer.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DPanelCellRenderer.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DPanelJTableModel.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$Render2DPanelJTableModel.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$RowLabelRenderer.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable$RowLabelRenderer.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DDataTable.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DTable.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/ViewMolecule2DTable.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/panels/MoleculeCell.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/panels/MoleculeCell.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/table/MyTable.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/table/MyTable.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellEditor.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellEditor.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellEditor2D.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellEditor2D.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellRenderer2D.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/table/StructureTableCellRenderer2D.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/classes/org/guha/rcdk/view/table/StructureTableModel.class: binary file contents changed
> dpkg-source: error: add rcdkjar/classes/org/guha/rcdk/view/table/StructureTableModel.class in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to rcdkjar/rcdk.jar: binary file contents changed
> dpkg-source: error: add rcdkjar/rcdk.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/cdkr_3.6.0+dfsg-3_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.