[Debichem-devel] Bug#1043799: comet-ms: Fails to build source after successful build

[Lucas Nussbaum]

Source: comet-ms
Version: 2019015+cleaned1-3
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 comet-ms
> dpkg-buildpackage: info: source version 2019015+cleaned1-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Filippo Rusconi <lopippo at debian.org>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean
> 	rm -f debian/comet-ms.debhelper.log
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -f debian/comet-ms.1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/comet-ms.substvars debian/files
> 	rm -fr -- debian/comet-ms/ debian/tmp/
> 	find .  \( \( \
> 		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> 	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> 		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> 		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> 		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> 		\) -exec rm -f {} + \) -o \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building comet-ms using existing ./comet-ms_2019015+cleaned1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to Comet.o: binary file contents changed
> dpkg-source: error: add Comet.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometCheckForUpdates.o: binary file contents changed
> dpkg-source: error: add CometCheckForUpdates.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometInterfaces.o: binary file contents changed
> dpkg-source: error: add CometInterfaces.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometMassSpecUtils.o: binary file contents changed
> dpkg-source: error: add CometMassSpecUtils.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometPostAnalysis.o: binary file contents changed
> dpkg-source: error: add CometPostAnalysis.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometPreprocess.o: binary file contents changed
> dpkg-source: error: add CometPreprocess.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch.o: binary file contents changed
> dpkg-source: error: add CometSearch.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometCheckForUpdates.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometCheckForUpdates.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometInterfaces.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometInterfaces.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometMassSpecUtils.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometMassSpecUtils.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometPostAnalysis.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometPostAnalysis.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometPreprocess.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometPreprocess.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometSearch.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometSearch.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometSearchManager.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometSearchManager.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometWriteOut.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometWriteOut.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometWritePepXML.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometWritePepXML.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometWritePercolator.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometWritePercolator.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometWriteSqt.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometWriteSqt.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/CometWriteTxt.o: binary file contents changed
> dpkg-source: error: add CometSearch/CometWriteTxt.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/Threading.o: binary file contents changed
> dpkg-source: error: add CometSearch/Threading.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearch/libcometsearch.a: binary file contents changed
> dpkg-source: error: add CometSearch/libcometsearch.a in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometSearchManager.o: binary file contents changed
> dpkg-source: error: add CometSearchManager.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometWriteOut.o: binary file contents changed
> dpkg-source: error: add CometWriteOut.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometWritePepXML.o: binary file contents changed
> dpkg-source: error: add CometWritePepXML.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometWritePercolator.o: binary file contents changed
> dpkg-source: error: add CometWritePercolator.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometWriteSqt.o: binary file contents changed
> dpkg-source: error: add CometWriteSqt.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to CometWriteTxt.o: binary file contents changed
> dpkg-source: error: add CometWriteTxt.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to Threading.o: binary file contents changed
> dpkg-source: error: add Threading.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to comet-ms: binary file contents changed
> dpkg-source: error: add comet-ms in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'comet-ms' will not be represented in diff
> 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/comet-ms_2019015+cleaned1-3_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.