biojava 1.7.1 のテストを動かしてみた

実効結果。
BUILD SUCCESSFUL

unzip biojava-1.7.1-all.jar
cd biojava-1.7.1
ant
ant runtests

Buildfile: /home/hogehoge/work/biojava/1.7.1_stable/biojava-1.7.1/build.xml

init:
[echo] Building biojava-1.7.1
[echo] Java Home: /usr/lib/jvm/java-6-sun-1.6.0.20/jre
[echo] JUnit present: true
[echo] JUnit supported by Ant: true
[echo] HSQLDB driver present: ${sqlDriver.hsqldb}
[echo] XSLT support: true

prepare:

prepare-tests:

prepare-biojava:

compile-biojava:
[javac] /home/hogehoge/work/biojava/1.7.1_stable/biojava-1.7.1/build.xml:246: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds

package-biojava:

compile-tests:
[javac] /home/hogehoge/work/biojava/1.7.1_stable/biojava-1.7.1/build.xml:264: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds

runtests:
[echo] Running tests: **
[junit] Running org.biojava.bio.AnnotationTypeTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.058 sec
[junit] Running org.biojava.bio.MergeAnnotationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.dist.DistSerTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 0.074 sec
[junit] Running org.biojava.bio.dist.DistributionTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.dist.DistributionToolsTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.062 sec
[junit] Running org.biojava.bio.dist.TranslatedDistributionTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.dp.DPSerializationTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.034 sec
[junit] Running org.biojava.bio.dp.EmissionStateEventTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.dp.MarkovModelEventTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.043 sec
[junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.program.fastq.FastqBuilderTest
[junit] Tests run: 18, Failures: 0, Errors: 0, Time elapsed: 0.009 sec
[junit] Running org.biojava.bio.program.fastq.FastqTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.program.fastq.FastqVariantTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest
[junit] Tests run: 22, Failures: 0, Errors: 0, Time elapsed: 0.021 sec
[junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.044 sec
[junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest
[junit] Tests run: 27, Failures: 0, Errors: 0, Time elapsed: 0.022 sec
[junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest
[junit] Tests run: 22, Failures: 0, Errors: 0, Time elapsed: 0.016 sec
[junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.program.indexdb.IndexToolsTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.18 sec
[junit] Running org.biojava.bio.program.phred.PhredToolsTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.02 sec
[junit] Running org.biojava.bio.program.sax.BlastTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 0.185 sec
[junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.075 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.073 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.451 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.494 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.597 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.499 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.485 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.544 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.562 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.619 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 1.59 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.254 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.111 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.079 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.082 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 1.231 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.127 sec
[junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.proteomics.MassCalcTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.091 sec
[junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest
[junit] Tests run: 17, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.search.MaxMismatchPatternTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.search.SeqContentPatternTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.seq.CircularSequenceTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.01 sec
[junit] Running org.biojava.bio.seq.DNAToolsTest
[junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.seq.FeatureFilterTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.seq.FilterUtilsTest
[junit] Tests run: 23, Failures: 0, Errors: 0, Time elapsed: 0.014 sec
[junit] Running org.biojava.bio.seq.MergeFeatureHolderTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.073 sec
[junit] Running org.biojava.bio.seq.ProteinToolsTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.001 sec
[junit] Running org.biojava.bio.seq.RNAToolsTest
[junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 0.011 sec
[junit] Running org.biojava.bio.seq.SeqSerializationTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.066 sec
[junit] Running org.biojava.bio.seq.SimpleAssemblyTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
[junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 0.014 sec
[junit] Running org.biojava.bio.seq.db.HashSequenceDBTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.001 sec
[junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest
[junit] Tests run: 0, Failures: 0, Errors: 0, Time elapsed: 0 sec
[junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.001 sec
[junit] Running org.biojava.bio.seq.filter.FilterTransformerTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.021 sec
[junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.004 sec
[junit] Running org.biojava.bio.seq.impl.GappedSequenceTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.seq.impl.SubSequenceTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.016 sec
[junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.046 sec
[junit] Running org.biojava.bio.seq.impl.ViewSequenceTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.006 sec
[junit] Running org.biojava.bio.seq.io.LocationFormatterTest
[junit] Tests run: 26, Failures: 0, Errors: 0, Time elapsed: 0.098 sec
[junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.003 sec
[junit] Running org.biojava.bio.seq.io.SeqIOToolsTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.311 sec
[junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.519 sec
[junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest
[junit] Tests run: 12, Failures: 0, Errors: 0, Time elapsed: 0.034 sec
[junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.structure.MMcifTest
[junit] Tests run: 1, Failures: 1, Errors: 0, Time elapsed: 0.275 sec
[junit] Running org.biojava.bio.structure.PDBFileParserTest
[junit] Tests run: 5, Failures: 1, Errors: 0, Time elapsed: 0.014 sec
[junit] Running org.biojava.bio.structure.PdbFileFormat30Test
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.055 sec
[junit] Running org.biojava.bio.structure.SourceCompoundTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.553 sec
[junit] Running org.biojava.bio.structure.StructurePairAlignerTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.731 sec
[junit] Running org.biojava.bio.structure.StructureTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.056 sec
[junit] Running org.biojava.bio.structure.StructureToolsTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.012 sec
[junit] Running org.biojava.bio.symbol.AlphabetManagerTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.symbol.AlphabetSerializationTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.059 sec
[junit] Running org.biojava.bio.symbol.BetweenLocationTest
[junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 0.008 sec
[junit] Running org.biojava.bio.symbol.CircularLocationTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.005 sec
[junit] Running org.biojava.bio.symbol.CodonPrefToolsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.044 sec
[junit] Running org.biojava.bio.symbol.CompoundLocationTest
[junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 0.03 sec
[junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.732 sec
[junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.002 sec
[junit] Running org.biojava.bio.symbol.DoubleAlphabetTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.001 sec
[junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.003 sec