[Debian-med-packaging] Bug#1048443: igv: Fails to build source after successful build

[Lucas Nussbaum]

Source: igv
Version: 2.16.1+dfsg-1
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 igv
> dpkg-buildpackage: info: source version 2.16.1+dfsg-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Pierre Gruet <pgt at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh  clean --buildsystem=gradle --with javahelper
>    dh_auto_clean -O--buildsystem=gradle
> 	sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
> 	sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
> 	rm -Rf /<<BUILDDIR>>/igv-2.16.1\+dfsg/.gradle /<<BUILDDIR>>/igv-2.16.1\+dfsg/buildSrc/.gradle .m2
>    dh_autoreconf_clean -O--buildsystem=gradle
>    jh_clean -O--buildsystem=gradle
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> if [ -e src/main/resources/log4j.xml ] ; then rm src/main/resources/log4j.xml ; fi
> if [ -e src/main/resources-icons ]; then \
>         rm -rf src/main/resources-icons ; \
> fi
> dh_clean
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building igv using existing ./igv_2.16.1+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file '.java/.userPrefs/.user.lock.debian' will not be represented in diff
> dpkg-source: warning: newly created empty file '.java/.userPrefs/.userRootModFile.debian' will not be represented in diff
> dpkg-source: warning: newly created empty file 'igv/prefs.properties' will not be represented in diff
> dpkg-source: info: local changes detected, the modified files are:
>  igv-2.16.1+dfsg/.java/.userPrefs/org/broad/igv/prefs.xml
>  igv-2.16.1+dfsg/.java/.userPrefs/org/broad/prefs.xml
>  igv-2.16.1+dfsg/.java/.userPrefs/org/prefs.xml
>  igv-2.16.1+dfsg/test/data/wig/test.bedgraph
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/igv_2.16.1+dfsg-1.diff.z_1iZA
> 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/igv_2.16.1+dfsg-1_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.