[Debian-med-packaging] Bug#1116740: genomicsdb: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:genomicsdb
Version: 1.5.5-1
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:genomicsdb, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Building the Java part with Maven.
dh_auto_build --buildsystem=maven
	/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 -Dproperties.file.manual=/<<PKGBUILDDIR>>/debian/maven.properties 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 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...
[INFO] 
[INFO] ---------------------< org.genomicsdb:genomicsdb >----------------------
[INFO] Building org.genomicsdb:genomicsdb 1.5.5
[INFO]   from pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.testng:testng:jar:debian is missing, no dependency information available
[WARNING] The artifact com.googlecode.json-simple:json-simple:jar:debian has been relocated to com.github.cliftonlabs:json-simple:jar:debian
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.252 s
[INFO] Finished at: 2025-09-30T11:35:08Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project genomicsdb: Could not resolve dependencies for project org.genomicsdb:genomicsdb:jar:1.5.5
[ERROR] dependency: org.testng:testng:jar:debian (test)
[ERROR] 	Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.testng:testng: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=/<<PKGBUILDDIR>> -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/<<PKGBUILDDIR>>/debian/maven.properties 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 package -DskipTests -Dnotimestamp=true -Dlocale=en_US returned exit code 1
make[1]: *** [debian/rules:54: override_dh_auto_build-indep] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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