Your message dated Tue, 9 Dec 2025 15:10:49 +0100
with message-id <[email protected]>
and subject line Bug was closed in 3.3.1+dfsg2-12
has caused the Debian Bug report #1108577,
regarding libgoby-java: FTBFS with default Java 25
to be marked as done.
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--
1108577: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108577
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libgoby-java
Version: 3.3.1+dfsg2-11
Severity: normal
Tags: ftbfs
Usertags: default-java25
Dear Maintainers,
The package libgoby-java ftbfs with default Java 25.
The relevant part of the build log:
---------------
[ERROR] Tests run: 512, Failures: 8, Errors: 0, Skipped: 46, Time elapsed:
60.705 s <<< FAILURE! - in TestSuite
[ERROR] testDiscoverSomaticVariation2 on
testDiscoverSomaticVariation2(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)
Time elapsed: 0.52 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.easymock.mocks.VCFWriter$$$EasyMock$2 must be defined in the same package
as org.easymock.internal.ClassProxyFactory
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation2(TestSomaticVariationOutputFormat.java:121)
[ERROR] testDiscoverSomaticVariation3 on
testDiscoverSomaticVariation3(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)
Time elapsed: 0.122 s <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testDiscoverSomaticVariation3(TestSomaticVariationOutputFormat.java:218)
Caused by: java.lang.IllegalArgumentException:
org.easymock.mocks.VCFWriter$$$EasyMock$4 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: 0.11 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.easymock.mocks.VCFWriter$$$EasyMock$6 must be defined in the same package
as org.easymock.internal.ClassProxyFactory
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue1(TestSomaticVariationOutputFormat.java:35)
[ERROR] testEstimateSomaticPValue2 on
testEstimateSomaticPValue2(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)
Time elapsed: 0.077 s <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue2(TestSomaticVariationOutputFormat.java:48)
Caused by: java.lang.IllegalArgumentException:
org.easymock.mocks.VCFWriter$$$EasyMock$8 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: 0.067 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.easymock.mocks.VCFWriter$$$EasyMock$10 must be defined in the same package
as org.easymock.internal.ClassProxyFactory
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue3(TestSomaticVariationOutputFormat.java:61)
[ERROR] testEstimateSomaticPValue4 on
testEstimateSomaticPValue4(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)(org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat)
Time elapsed: 0.07 s <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.assertPWithCounts(TestSomaticVariationOutputFormat.java:84)
at
org.campagnelab.goby.modes.formats.TestSomaticVariationOutputFormat.testEstimateSomaticPValue4(TestSomaticVariationOutputFormat.java:79)
Caused by: java.lang.IllegalArgumentException:
org.easymock.mocks.VCFWriter$$$EasyMock$12 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: 0.048 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.easymock.mocks.DiscoverVariantIterateSortedAlignments$$$EasyMock$14 must be
defined in the same package as org.easymock.internal.ClassProxyFactory
at
org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)
[ERROR] testIndelDifferences on
testIndelDifferences(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)(org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat)
Time elapsed: 0.041 s <<< FAILURE!
java.lang.IllegalArgumentException: Could not create type
at
org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)
Caused by: java.lang.IllegalArgumentException:
org.easymock.mocks.DiscoverVariantIterateSortedAlignments$$$EasyMock$16 must be
defined in the same package as org.easymock.internal.ClassProxyFactory
at
org.campagnelab.goby.modes.formats.TestCompareGroupsVCFOutputFormat.setUp(TestCompareGroupsVCFOutputFormat.java:80)
[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 [ 0.056 s]
[INFO] Goby I/O ........................................... SUCCESS [ 7.537 s]
[INFO] Goby Full Distribution ............................. FAILURE [01:36 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
--------------------------------------------------------------------------------
---------------
-- System Information:
Debian Release: trixie/sid
APT prefers plucky-updates
APT policy: (500, 'plucky-updates'), (500, 'plucky-security'), (500, 'plucky')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.14.0-22-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
--- End Message ---
--- Begin Message ---
Version: 3.3.1+dfsg2-12
Hi,
This bug was effectively closed by the last upload.
Best,
--
Pierre
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--- End Message ---
