[Debian-med-packaging] Bug#1043784: alter-sequence-alignment: Fails to build source after successful build

[Lucas Nussbaum]

Source: alter-sequence-alignment
Version: 1.3.4-6
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 alter-sequence-alignment
> dpkg-buildpackage: info: source version 1.3.4-6
> 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
> 	mh_patchpoms -palter-sequence-alignment --debian-build --keep-pom-version --maven-repo=/<<PKGBUILDDIR>>/debian/maven-repo
> 	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/<<PKGBUILDDIR>> -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<PKGBUILDDIR>>/debian -Dmaven.repo.local=/<<PKGBUILDDIR>>/debian/maven-repo --batch-mode clean
> OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
> [INFO] Scanning for projects...
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Build Order:
> [INFO] 
> [INFO] The ALTER Project                                                  [pom]
> [INFO] ALTER Core Library and Desktop app                                 [jar]
> [INFO] 
> [INFO] -------------------< es.uvigo.ei.sing:alter-project >-------------------
> [INFO] Building The ALTER Project 1.3.4                                   [1/2]
> [INFO] --------------------------------[ pom ]---------------------------------
> [WARNING] The artifact org.apache.maven.plugins:maven-clean-plugin:jar:2.5 has been relocated to org.apache.maven.plugins:maven-clean-plugin:jar:3.2.0
> [INFO] 
> [INFO] --- maven-clean-plugin:3.2.0:clean (default-clean) @ alter-project ---
> [INFO] Deleting /<<PKGBUILDDIR>>/target
> [INFO] 
> [INFO] ---------------------< es.uvigo.ei.sing:alter-lib >---------------------
> [INFO] Building ALTER Core Library and Desktop app 1.3.4                  [2/2]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO] 
> [INFO] --- maven-clean-plugin:3.2.0:clean (default-clean) @ alter-lib ---
> [INFO] Deleting /<<PKGBUILDDIR>>/alter-lib/target
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Summary for The ALTER Project 1.3.4:
> [INFO] 
> [INFO] The ALTER Project .................................. SUCCESS [  0.142 s]
> [INFO] ALTER Core Library and Desktop app ................. SUCCESS [  0.039 s]
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time:  0.301 s
> [INFO] Finished at: 2023-08-12T12:41:23Z
> [INFO] ------------------------------------------------------------------------
> 	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
> 	mh_unpatchpoms -palter-sequence-alignment
>    jh_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building alter-sequence-alignment using existing ./alter-sequence-alignment_1.3.4.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: info: local changes detected, the modified files are:
>  alter-sequence-alignment-1.3.4/README.html
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/alter-sequence-alignment_1.3.4-6.diff.iNr8Pw
> 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/alter-sequence-alignment_1.3.4-6_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.