Bug#1078612: marked as done (biojava6-live: will FTBFS during trixie support period)

Debian Bug Tracking System Thu, 31 Oct 2024 10:06:36 -0700

Your message dated Thu, 31 Oct 2024 16:20:07 +0000
with message-id <[email protected]>
and subject line Bug#1078612: fixed in biojava6-live 6.1.0+dfsg-5
has caused the Debian Bug report #1078612,
regarding biojava6-live: will FTBFS during trixie support period
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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immediately.)


-- 
1078612: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1078612
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

Package: src:biojava6-live
Version: 6.1.0+dfsg-4
User: [email protected]
Usertags: ftbfs-during-trixie-support-period
Tags: ftbfs

Dear maintainer:

During a rebuild of all packages in unstable in the year 2028, your package 
failed to build:

--------------------------------------------------------------------------------
[...]
 debian/rules binary
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh binary  --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dpkg: warning: --compare-versions used with obsolete relation operator '>'
# Creating the directories for forester and jcolorbrewer, with symlinks.
mkdir -p biojava-forester/src/main/java/
cp -a forester/org biojava-forester/src/main/java/
mkdir -p biojava-jcolorbrewer/src/main/java/
cp -a jcolorbrewer/org biojava-jcolorbrewer/src/main/java/

[... snipped ...]

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s 
- in org.biojava.nbio.alignment.LocalAlignmentTest
[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s 
- in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s 
- in org.biojava.nbio.alignment.SmithWatermanTest
[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.135 
s - in org.biojava.nbio.alignment.TestSubOptimalMSA
[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s 
- in org.biojava.nbio.alignment.FractionalIdentityScorerTest
[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 s 
- in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s 
- in org.biojava.nbio.phylo.TestForesterWrapper
[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s 
- in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
[INFO]
[INFO] Results:
[INFO]
[WARNING] Tests run: 127, Failures: 0, Errors: 0, Skipped: 1
[INFO]
[INFO]
[INFO] -------------------< org.biojava:biojava-structure >--------------------
[INFO] Building biojava-structure 6.1.0                                  [5/15]
[INFO]   from biojava-structure/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to 
javax.vecmath:vecmath:jar:debian
[INFO]
[INFO] --- maven-resources-plugin:3.3.1:resources (default-resources) @ 
biojava-structure ---
[INFO] Copying 3 resources
[INFO] Copying 61 resources
[INFO] The encoding used to copy filtered properties files have not been set. 
This means that the same encoding will be used to copy filtered properties 
files as when copying other filtered resources. This might not be what you 
want! Run your build with --debug to see which files might be affected. Read 
more at 
https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ 
biojava-structure ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ 
biojava-structure ---
[INFO] Copying 55 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ 
biojava-structure ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure 
---
[INFO]
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 3.922 
s - in org.biojava.nbio.structure.TestEntityResIndexMapping
[INFO] Running org.biojava.nbio.structure.TestAtomIterator
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 
s - in org.biojava.nbio.structure.TestAtomIterator
[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.122 
s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.TestDNAAlignment
[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.015 
s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.851 s 
- in org.biojava.nbio.structure.geometry.TestSuperPosition
[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.026 
s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
[INFO] Running org.biojava.nbio.structure.Test2JA5
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 
s - in org.biojava.nbio.structure.Test2JA5
[INFO] Running org.biojava.nbio.structure.TestCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - 
in org.biojava.nbio.structure.TestCalc
[INFO] Running org.biojava.nbio.structure.Test4hhb
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.477 s 
- in org.biojava.nbio.structure.Test4hhb
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 
s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.516 s 
- in org.biojava.nbio.structure.xtal.TestSpaceGroup
[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 8.076 
s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s 
- in org.biojava.nbio.structure.xtal.TestCrystalCell
[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
Using PDB_DIR=/tmp as temporary file directory
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.677 
s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.955 
s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.91 s - 
in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 4.609 
s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.101 
s - in org.biojava.nbio.structure.io.TestMMCIFWriting
[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.TestSiftsParsing
[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 
8.583 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 
s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.TestParseOnAsymId
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 
0.085 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 5.743 
s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 
s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.51 s - 
in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 
s - in org.biojava.nbio.structure.io.TestTitleParsing
[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 4.629 
s - in org.biojava.nbio.structure.io.TestHeaderOnly
[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.io.TestHardBioUnits
[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.787 s 
- in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
[INFO] Running 
org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s 
- in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
[INFO] Running org.biojava.nbio.structure.io.TestShortLines
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.86 s - 
in org.biojava.nbio.structure.io.TestShortLines
[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s 
- in org.biojava.nbio.structure.io.TestDBRefParsing
[INFO] Running org.biojava.nbio.structure.TestStructureImpl
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s 
- in org.biojava.nbio.structure.TestStructureImpl
[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 
0.076 s - in org.biojava.nbio.structure.ResidueRangeTest
[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 
s - in org.biojava.nbio.structure.align.client.TestStructureName
[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s 
- in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
[INFO] Running 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.005 
s - in 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
[INFO] Running 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.007 
s - in 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
[INFO] Running 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s 
- in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
[INFO] Running 
org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s 
- in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 
0.061 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - 
in org.biojava.nbio.structure.align.util.RotationAxisTest
[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.035 
s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
Interface <A, B>
<CA R 0 3.0 3.0 3.0, CA R 0 7.0 3.0 3.0> - 4.0
Interface <A, C>
<CA R 0 3.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
Interface <B, C>
<CA R 0 7.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s 
- in org.biojava.nbio.structure.contact.TestInterfaceFinder
[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.contact.TestContactCalc
[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s 
- in org.biojava.nbio.structure.TestVeryLongFileName
[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[ERROR] Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 6.471 s 
<<< FAILURE! - in org.biojava.nbio.structure.TestURLIdentifier
[ERROR] testURLParameters  Time elapsed: 5.665 s  <<< ERROR!
javax.net.ssl.SSLHandshakeException: PKIX path validation failed: 
java.security.cert.CertPathValidatorException: validity check failed
        at 
org.biojava.nbio.structure.TestURLIdentifier.testURLParameters(TestURLIdentifier.java:107)
Caused by: sun.security.validator.ValidatorException: PKIX path validation 
failed: java.security.cert.CertPathValidatorException: validity check failed
        at 
org.biojava.nbio.structure.TestURLIdentifier.testURLParameters(TestURLIdentifier.java:107)
Caused by: java.security.cert.CertPathValidatorException: validity check failed
        at 
org.biojava.nbio.structure.TestURLIdentifier.testURLParameters(TestURLIdentifier.java:107)
Caused by: java.security.cert.CertificateExpiredException: NotAfter: Thu Jan 30 
23:59:59 UTC 2025
        at 
org.biojava.nbio.structure.TestURLIdentifier.testURLParameters(TestURLIdentifier.java:107)

[INFO] Running org.biojava.nbio.structure.TestNucleotides
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.009 
s - in org.biojava.nbio.structure.TestNucleotides
[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.053 s 
- in org.biojava.nbio.structure.PdbFileFormat30Test
[INFO] Running org.biojava.nbio.structure.SiteTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s 
- in org.biojava.nbio.structure.SiteTest
[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.544 s 
- in org.biojava.nbio.structure.TestEntityHeuristics
[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.TestParsingCalcium
[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.TestExperimentalTechniques
[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.141 s 
- in org.biojava.nbio.structure.SourceCompoundTest
[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s 
- in org.biojava.nbio.structure.ResidueNumberTest
[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.008 
s - in org.biojava.nbio.structure.AtomPositionMapTest
[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.48 s - 
in org.biojava.nbio.structure.TestStructureSerialization
[INFO] Running org.biojava.nbio.structure.HetatomImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s 
- in org.biojava.nbio.structure.HetatomImplTest
[INFO] Running org.biojava.nbio.structure.TestChargeAdder
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.008 
s - in org.biojava.nbio.structure.TestChargeAdder
[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s 
- in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s 
- in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
[INFO] Running 
org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in 
org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s 
- in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
[INFO] Running org.biojava.nbio.structure.ElementTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s 
- in org.biojava.nbio.structure.ElementTest
[INFO] Running org.biojava.nbio.structure.ChemCompTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.641 
s - in org.biojava.nbio.structure.ChemCompTest
[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 
s - in org.biojava.nbio.structure.TestLoadStructureFromURL
[INFO] Running org.biojava.nbio.structure.TestKeywords
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.077 s 
- in org.biojava.nbio.structure.TestKeywords
[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.616 
s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
[INFO] Running org.biojava.nbio.structure.TestAtomCache
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 1.281 
s - in org.biojava.nbio.structure.TestAtomCache
[INFO] Running org.biojava.nbio.structure.TestBond
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 
0.009 s - in org.biojava.nbio.structure.TestBond
[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
[INFO] Running org.biojava.nbio.structure.TestCloning
[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.TestCloning
[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.024 
s - in org.biojava.nbio.structure.asa.TestAsaCalc
[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 
s - in org.biojava.nbio.structure.TestStructureCrossReferences
[INFO] Running org.biojava.nbio.structure.TestAltLocs
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further 
details.
[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 
1.844 s - in org.biojava.nbio.structure.TestAltLocs
[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 
s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 
s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
[INFO] Running org.biojava.nbio.structure.PDBStatusTest
[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 
s - in org.biojava.nbio.structure.PDBStatusTest
[INFO] Running org.biojava.nbio.structure.TestPdbId
[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s 
- in org.biojava.nbio.structure.TestPdbId
[INFO]
[INFO] Results:
[INFO]
[ERROR] Errors:
[ERROR]   TestURLIdentifier.testURLParameters:107 » SSLHandshake PKIX path 
validation fa...
[INFO]
[ERROR] Tests run: 374, Failures: 0, Errors: 1, Skipped: 188
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
[INFO] biojava ............................................ SUCCESS [  0.005 s]
[INFO] biojava-core ....................................... SUCCESS [09:50 min]
[INFO] biojava-forester ................................... SUCCESS [  0.048 s]
[INFO] biojava-alignment .................................. SUCCESS [03:00 min]
[INFO] biojava-structure .................................. FAILURE [16:20 min]
[INFO] biojava-jcolorbrewer ............................... SKIPPED
[INFO] biojava-structure-gui .............................. SKIPPED
[INFO] biojava-genome ..................................... SKIPPED
[INFO] biojava-modfinder .................................. SKIPPED
[INFO] biojava-ws ......................................... SKIPPED
[INFO] biojava-protein-disorder ........................... SKIPPED
[INFO] biojava-aa-prop .................................... SKIPPED
[INFO] biojava-survival ................................... SKIPPED
[INFO] biojava-ontology ................................... SKIPPED
[INFO] biojava-protein-comparison-tool .................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  29:11 min
[INFO] Finished at: 2028-06-10T12:32:20Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal 
org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on 
project biojava-structure: There are test failures.
[ERROR]
[ERROR] Please refer to 
/<<PKGBUILDDIR>>/biojava-structure/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 :biojava-structure
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>>/biojava6-live-6.1.0\+dfsg 
-Dclassworlds.conf=/etc/maven/m2-debian.conf 
-Dproperties.file.manual=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian/maven.properties 
org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml 
-Ddebian.dir=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian 
-Dmaven.repo.local=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test returned exit code 1
make: *** [debian/rules:22: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

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

About the archive rebuild: This is an effort to keep trixie free from FTBFS bugs
during its lifetime as a supported distribution, as explained here:

https://lists.debian.org/debian-devel/2024/05/msg00414.html

(While they are not yet, please note that the bugs will be RC for trixie)

The build was made 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 affects, so that this is still visible in the BTS web
page for this package.

Thanks.

--- End Message ---

--- Begin Message ---

Source: biojava6-live
Source-Version: 6.1.0+dfsg-5
Done: Pierre Gruet <[email protected]>

We believe that the bug you reported is fixed in the latest version of
biojava6-live, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated biojava6-live package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Thu, 31 Oct 2024 08:16:17 +0100
Source: biojava6-live
Architecture: source
Version: 6.1.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1078612
Changes:
 biojava6-live (6.1.0+dfsg-5) unstable; urgency=medium
 .
   * Raising Standards version to 4.7.0, no change
   * Skipping test depending on certificate with foreseeable expiration
     (Closes: #1078612)
   * Updating the path to the javadoc files to install
Checksums-Sha1:
 bab1210d3b4f2a116829dd3344759c9a1d918d4a 3360 biojava6-live_6.1.0+dfsg-5.dsc
 4ec7bffefbb9f1d455660790776c8dde12dc9e93 27540 
biojava6-live_6.1.0+dfsg-5.debian.tar.xz
 66224aea1c323cebb2d69e4eba818db964a06c11 19668 
biojava6-live_6.1.0+dfsg-5_amd64.buildinfo
Checksums-Sha256:
 4253e527024ab7a151540e6ae80d9bbbb11b0cd514d83bbc8c2845645de904f6 3360 
biojava6-live_6.1.0+dfsg-5.dsc
 352d378215ef762c6c4cf1b6f6cbe0e443024a881c3c642a88040c7b71859914 27540 
biojava6-live_6.1.0+dfsg-5.debian.tar.xz
 f373ca74e43717174f04c6b0973883b03ba31fdd04177ae0bc3e47c11617844c 19668 
biojava6-live_6.1.0+dfsg-5_amd64.buildinfo
Files:
 a188f7b3d03a45afa55475c59018c747 3360 java optional 
biojava6-live_6.1.0+dfsg-5.dsc
 68a54cefe36ba83b2dcfa57a53e5188b 27540 java optional 
biojava6-live_6.1.0+dfsg-5.debian.tar.xz
 7e7b5839d1cffe7d2d6afe630303f911 19668 java optional 
biojava6-live_6.1.0+dfsg-5_amd64.buildinfo

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Bug#1078612: marked as done (biojava6-live: will FTBFS during trixie support period)

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