[Debian-med-packaging] Bug#1116714: artemis: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:artemis
Version: 18.2.0+dfsg-4
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile

Dear maintainer:

During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:artemis, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean --with javahelper
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	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 -partemis
rm -f images/helix.png
rm -f -rf target/jarsBuild
rm -f -rf target/modifiedJars
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   jh_clean
Duplicate specification "unlink|u" for option "u"
   dh_clean
 debian/rules binary
dh binary --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	mh_patchpoms -partemis --debian-build --keep-pom-version --maven-repo=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian/maven-repo
   jh_linkjars
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
	/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=/<<BUILDDIR>>/artemis-18.2.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
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...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for uk.ac.sanger:artemis:jar:18.2.0
[WARNING] 'dependencies.dependency.systemPath' for org.emboss:jemboss:jar should use a variable instead of a hard-coded path /usr/share/EMBOSS/jemboss/lib/jemboss.jar @ line 200, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 253, column 16
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] 
[INFO] ------------------------< uk.ac.sanger:artemis >------------------------
[INFO] Building Artemis 18.2.0
[INFO]   from pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.mockito:mockito-core:jar:debian is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.219 s
[INFO] Finished at: 2025-09-30T11:29:00Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project artemis: Could not resolve dependencies for project uk.ac.sanger:artemis:jar:18.2.0
[ERROR] dependency: org.mockito:mockito-core:jar:debian (test)
[ERROR] 	Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.mockito:mockito-core:jar:debian has not been downloaded from it before.
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
dh_auto_build: error: /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=/<<BUILDDIR>>/artemis-18.2.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US returned exit code 1
make[1]: *** [debian/rules:9: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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