[Debian-med-packaging] Bug#1057518: libgoby-java: FTBFS with default Java 21

Vladimir Petko vpa1977 at gmail.com
Tue Dec 5 21:04:57 GMT 2023 

Source: libgoby-java
Version: 3.3.1+dfsg2-9
Severity: important
Tags: ftbfs
User: debian-java at lists.debian.org
Usertags: default-java21

Dear Maintainers,

The package libgoby-java ftbfs with default Java 21.
The relevant part of the build log:
---------------
[ERROR] Tests run: 512, Failures: 8, Errors: 0, Skipped: 46, Time elapsed: 51.615 s <<< FAILURE! - in TestSuite
[ERROR] testDiscoverSomaticVariation2 on testDiscoverSomaticVariation2(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.344 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation2(TestSomaticVariationOutputFormat.java:121)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$1 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation2(TestSomaticVariationOutputFormat.java:121)

[ERROR] testDiscoverSomaticVariation3 on testDiscoverSomaticVariation3(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.056 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation3(TestSomaticVariationOutputFormat.java:218)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$2 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation3(TestSomaticVariationOutputFormat.java:218)

[ERROR] testEstimateSomaticPValue1 on testEstimateSomaticPValue1(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.05 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue1(TestSomaticVariationOutputFormat.java:35)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$3 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue1(TestSomaticVariationOutputFormat.java:35)

[ERROR] testEstimateSomaticPValue2 on testEstimateSomaticPValue2(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.04 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue2(TestSomaticVariationOutputFormat.java:48)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$4 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue2(TestSomaticVariationOutputFormat.java:48)

[ERROR] testEstimateSomaticPValue3 on testEstimateSomaticPValue3(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.035 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue3(TestSomaticVariationOutputFormat.java:61)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$5 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue3(TestSomaticVariationOutputFormat.java:61)

[ERROR] testEstimateSomaticPValue4 on testEstimateSomaticPValue4(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)  Time elapsed: 0.033 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue4(TestSomaticVariationOutputFormat.java:79)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.stats.VCFWriter$$$EasyMock$6 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
	at org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue4(TestSomaticVariationOutputFormat.java:79)

[ERROR] testAlignIndels on testAlignIndels(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)  Time elapsed: 0.037 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.modes.dsv.DiscoverVariantIterateSortedAlignments$$$EasyMock$7 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)

[ERROR] testIndelDifferences on testIndelDifferences(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)  Time elapsed: 0.02 s  <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
	at org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)
Caused by: java.lang.IllegalArgumentException: org.campagnelab.goby.modes.dsv.DiscoverVariantIterateSortedAlignments$$$EasyMock$8 must be defined in the same package as org.easymock.internal.ClassProxyFactory
	at org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)

[GobyRengine-ShutdownHook] INFO org.campagnelab.goby.R.GobyRengine - Shutdown hook is terminating R
[INFO]
[INFO] Results:
[INFO]
[ERROR] Failures:
[ERROR]   TestCompareGroupsVCFOutputFormat.setUp:80 » IllegalArgument Could not create t...
[ERROR]   TestCompareGroupsVCFOutputFormat.setUp:80 » IllegalArgument Could not create t...
[ERROR]   TestSomaticVariationOutputFormat.testDiscoverSomaticVariation2:121 » IllegalArgument
[ERROR]   TestSomaticVariationOutputFormat.testDiscoverSomaticVariation3:218 » IllegalArgument
[ERROR]   TestSomaticVariationOutputFormat.testEstimateSomaticPValue1:35->assertPWithCounts:84 » IllegalArgument
[ERROR]   TestSomaticVariationOutputFormat.testEstimateSomaticPValue2:48->assertPWithCounts:84 » IllegalArgument
[ERROR]   TestSomaticVariationOutputFormat.testEstimateSomaticPValue3:61->assertPWithCounts:84 » IllegalArgument
[ERROR]   TestSomaticVariationOutputFormat.testEstimateSomaticPValue4:79->assertPWithCounts:84 » IllegalArgument
[INFO]
[ERROR] Tests run: 512, Failures: 8, Errors: 0, Skipped: 46
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO]
[INFO] Goby Framework ..................................... SUCCESS [  0.029 s]
[INFO] Goby I/O ........................................... SUCCESS [  5.270 s]
[INFO] Goby Full Distribution ............................. FAILURE [01:03 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:09 min
[INFO] Finished at: 2023-12-04T09:47:58Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on project goby-distribution: There are test failures.
[ERROR]
[ERROR] Please refer to /<<PKGBUILDDIR>>/goby-distribution/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
[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/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :goby-distribution
dh_auto_test: 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>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test returned exit code 1
make[1]: *** [debian/rules:22: override_dh_auto_test] 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
---------------


-- System Information:
Debian Release: trixie/sid
  APT prefers mantic-updates
  APT policy: (500, 'mantic-updates'), (500, 'mantic-security'), (500, 'mantic')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.5.0-13-generic (SMP w/32 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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