Source: libgoby-java
Version: 3.3.1+dfsg2-9
Severity: important
Tags: ftbfs
User: debian-j...@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
[0m[0mdh_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
