[Biojava-dev] [biojava-builder] BioJava nightly build report

Sun Aug 24 00:18:36 EDT 2003

BioJava automatic build system, run 20030824
This is an experimental system, contact Thomas Down if you see any problems.

Binary build: OK
Javadocs build: OK
Core test suite: OK (results attached)

A snapshot release has been made at:

      http://www.derkholm.net/autobuild/

No changes were made in the last 24 hours.
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Buildfile: build.xml

init:
     [echo] JUnit present:                   true
     [echo] JUnit supported by Ant:          true

prepare:

prepare-core:

prepare-src:

compile:

package:

compile-tests:
    [javac] Compiling 95 source files to /home/thomas/bjtemp/biojava-20030824/ant-build/classes/tests
    [javac] depend attribute is not supported by the modern compiler

runtests:
    [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.074 sec
    [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.075 sec
    [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.067 sec
    [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
    [junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 2.402 sec
    [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.588 sec
    [junit] Running org.biojava.bio.seq.CircularSequenceTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.268 sec
    [junit] Running org.biojava.bio.seq.SimpleAssemblyTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.328 sec
    [junit] Running org.biojava.bio.seq.io.LocationFormatterTest
    [junit] Tests run: 26, Failures: 0, Errors: 0, Time elapsed: 2.811 sec
    [junit] Running org.biojava.bio.seq.io.agave.AGAVEHandlerTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.442 sec
    [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.674 sec
    [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 6.211 sec
    [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest
    [junit] Tests run: 12, Failures: 0, Errors: 0, Time elapsed: 1.442 sec
    [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 6.401 sec
    [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest
    [junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 1.835 sec
    [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest
    [junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 2.332 sec
    [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.18 sec
    [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.217 sec
    [junit] Running org.biojava.bio.seq.impl.SubSequenceTest
    [junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 2.471 sec
    [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.444 sec
    [junit] Running org.biojava.bio.seq.RNAToolsTest
    [junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 2.999 sec
    [junit] Running org.biojava.bio.seq.DNAToolsTest
    [junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 1.615 sec
    [junit] Running org.biojava.bio.seq.FeatureFilterTest
    [junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 1.939 sec
    [junit] Running org.biojava.bio.seq.FilterUtilsTest
    [junit] Tests run: 23, Failures: 0, Errors: 0, Time elapsed: 0.378 sec
    [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.313 sec
    [junit] Running org.biojava.bio.seq.SeqSerializationTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.039 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 30.118 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.687 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 5.432 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.076 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.051 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 5.408 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 18.407 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.719 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 8.634 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.149 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 21.132 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.889 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.413 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 8.535 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.169 sec
    [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.58 sec
    [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest
    [junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 3.779 sec
    [junit] Running org.biojava.bio.program.phred.PhredToolsTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.65 sec
    [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest
    [junit] Tests run: 7, Failures: 0, Errors: 1, Time elapsed: 2.523 sec
    [junit] Running org.biojava.bio.symbol.MotifToolsTest
    [junit] Tests run: 13, Failures: 0, Errors: 0, Time elapsed: 1.637 sec
    [junit] Running org.biojava.bio.symbol.AlphabetManagerTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.181 sec
    [junit] Running org.biojava.bio.symbol.PackedDnaSymbolListTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.672 sec
    [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.619 sec
    [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 38.618 sec
    [junit] Running org.biojava.bio.symbol.NameTokenizationTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.608 sec
    [junit] Running org.biojava.bio.symbol.TranslationTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.856 sec
    [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 3.428 sec
    [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest
    [junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 1.61 sec
    [junit] Running org.biojava.bio.symbol.MergeLocationTest
    [junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.105 sec
    [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.552 sec
    [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 1.56 sec
    [junit] Running org.biojava.bio.symbol.BetweenLocationTest
    [junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 0.121 sec
    [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.45 sec
    [junit] Running org.biojava.bio.symbol.GappedSymbolListTest
    [junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 1.604 sec
    [junit] Running org.biojava.bio.symbol.PointLocationTest
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.1 sec
    [junit] Running org.biojava.bio.symbol.CompoundLocationTest
    [junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 0.3 sec
    [junit] Running org.biojava.bio.symbol.CircularLocationTest
    [junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.146 sec
    [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest
    [junit] Tests run: 5, Failures: 0, Errors: 2, Time elapsed: 1.882 sec
    [junit] Running org.biojava.bio.symbol.SymbolListTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 5.266 sec
    [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.448 sec
    [junit] Running org.biojava.bio.symbol.SymbolSerializationTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.724 sec
    [junit] Running org.biojava.bio.symbol.RangeLocationTest
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.091 sec
    [junit] Running org.biojava.bio.dist.DistributionTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.635 sec
    [junit] Running org.biojava.bio.dist.DistributionToolsTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.021 sec
    [junit] Running org.biojava.bio.dist.DistSerTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.346 sec
    [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest
    [junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 1.927 sec
    [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest
    [junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 1.919 sec
    [junit] Running org.biojava.bio.proteomics.MassCalcTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.114 sec
    [junit] Running org.biojava.bio.dp.EmissionStateEventTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.636 sec
    [junit] Running org.biojava.bio.dp.MarkovModelEventTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.684 sec
    [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest
    [junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 2.156 sec
    [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest
    [junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 2.252 sec
    [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest
    [junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 2.17 sec
    [junit] Running org.biojava.bio.MergeAnnotationTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.086 sec
    [junit] Running org.biojava.bio.AnnotationTypeTest
    [junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.173 sec
    [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.026 sec
    [junit] Running org.biojava.ontology.TermImplTest
    [junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.164 sec
    [junit] Running org.biojava.ontology.OntologyTest
    [junit] Tests run: 21, Failures: 0, Errors: 0, Time elapsed: 0.168 sec
    [junit] Running org.biojava.ontology.TripleImplTest
    [junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.137 sec
    [junit] Running org.biojava.ontology.ReasoningDomainTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 15.191 sec
    [junit] Running org.biojava.directory.SystemRegistryTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.648 sec
    [junit] Running org.biojava.directory.RegistryConfigurationTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.031 sec
    [junit] Running org.biojava.directory.OBDARegistryParserTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.067 sec
    [junit] Running org.biojava.utils.ListToolsTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.028 sec
    [junit] Running org.biojava.utils.walker.WalkerFactoryTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.405 sec
    [junit] Running org.biojava.utils.walker.WalkerTest
    [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.496 sec
    [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest
    [junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 0.122 sec

BUILD SUCCESSFUL
Total time: 6 minutes 51 seconds