Menu
▾
▴
Re: [Treebase-devel] Continuing to set up the development environment
|
From: youjun g. <you...@ya...> - 2009-12-14 22:13:46
|
Vladimir, The TreeBASE test suite may have some problem. You can skip the test for now by check the "skip test" boxes. Youjun On Mon, Dec 14, 2009 at 4:27 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 14, 2009, at 2:33 PM, youjun guo wrote: > > The TreeBASE is a whole Maven project with two modules treebase-core and > treebase-web, you need to run the "maven package" on project treebase > instead of treebase-web. > > To build treebase-web, the treebase-core need to be built first that's all > setup in the pom.xml, mesquite is one of the treebase-core's dependencies. > > Check your local .m2 directory see if there is a folder called mesquite. If > not then you can mannualy install it as maven dependency, our maven > dependency repository's url is: http://treebase.sourceforge.net/maven2/, > your Maven pom.xml have already pointed here every dependency should be > downloaded automaticly. > > > Ok, we are making some progress -- thanks Youjun! > > It turns out I did have ~/.m2/repository/mesquite/mesquite/2.6+SNAPSHOT. > So, after I *removed* the comment around the mesquite dependency in > treebase-core/pom.xml and did Run As > Maven package on the treebase > project, there was more progress: Maven started running tests. However, > there have been test failures and errors and the whole build failed. The > log's tail is copied below. Let me know if detailed info for any of the > failures or errors would be useful. > > --Vladimir > > > Results : > > Failed tests: > testValue_Study(org.cipres.treebase.auxdata.ValueStudyTest) > testDomainHome(org.cipres.treebase.service.admin.HelpServiceImplTest) > > Tests in error: > testFindColumnByIndices( > org.cipres.treebase.dao.matrix.MatrixElementDAOTest) > testCreateDelete(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testupdatePublishedFlagByStudy( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testfindKindByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindNodesByTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByAnyTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByStudy(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testfindQualityByDescription( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindTypeByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindTreeBlocksByNexusFileName( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByTopology3(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByTreeType(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testGetFormatInfo(org.cipres.treebase.domain.matrix.MatrixTest) > testGenerateNexusBlock(org.cipres.treebase.domain.matrix.MatrixTest) > testAddDelete(org.cipres.treebase.service.study.AnalysisServiceImplTest) > testFindTaxonLabelSets(org.cipres.treebase.dao.taxon.TaxonLabelDAOTest) > testJDBCConnection(org.cipres.treebase.core.CoreServiceLauncherTest) > testFindByDescription( > org.cipres.treebase.dao.matrix.MatrixDataTypeDAOTest) > testFindTaxonLabelSets( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindStudiesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTreesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindMatricesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testCreateFromUBIOService( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testExpandTaxonVariant( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testExpandTaxonVariantSet( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindByExactString( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTaxonVariantWithSubstring( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindByTaxonVariant( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTaxonVariantByFullName( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testMesqutieFolderDir( > org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest) > testFindStatusInProgress( > org.cipres.treebase.dao.study.StudyStatusDAOTest) > testFindStatusReady(org.cipres.treebase.dao.study.StudyStatusDAOTest) > testFindStatusPublished(org.cipres.treebase.dao.study.StudyStatusDAOTest > ) > testFindPredefinedItemDefinition( > org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) > testFindByDescription( > org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) > testGetHelp(org.cipres.treebase.domain.admin.HelpTest) > testChangeMessage(org.cipres.treebase.domain.admin.HelpTest) > testDelete(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByMatrix(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByTree(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindBySubmissionNumber( > org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByReadyState(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByCreateDateRange( > org.cipres.treebase.dao.study.SubmissionDAOTest) > testSetAuthors(org.cipres.treebase.domain.study.CitationTest) > testBuildNewickStringPerf(org.cipres.treebase.domain.tree.PhyloTreeTest) > testUpdateNewickString(org.cipres.treebase.domain.tree.PhyloTreeTest) > testDelete(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByID(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByExactMatch(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByLastName(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindCompleteEmailAddress(org.cipres.treebase.dao.admin.PersonDAOTest > ) > testFindDuplicateWithFirstAndLastNames( > org.cipres.treebase.dao.admin.PersonDAOTest) > testFindDuplicateWithLastNames( > org.cipres.treebase.dao.admin.PersonDAOTest) > testCreateDelete(org.cipres.treebase.dao.admin.UserDAOTest) > testDelete_Negative(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserName(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserRole(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByPerson(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByEmailAddress(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByEmailAddressNegative(org.cipres.treebase.dao.admin.UserDAOTest > ) > testFindByEmailAddressLike(org.cipres.treebase.dao.admin.UserDAOTest) > testMerge(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserName_Negative(org.cipres.treebase.dao.admin.UserDAOTest) > testAddDelete(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddAnalysisByUpdate( > org.cipres.treebase.service.study.StudyServiceImplTest) > testAddAnalysis(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddNexus(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddNexusFile(org.cipres.treebase.service.study.StudyServiceImplTest) > testGenerateReconstructedNexusFile( > org.cipres.treebase.service.study.StudyServiceImplTest) > testSetAuthors(org.cipres.treebase.domain.study.StudyTest) > testGetAnalyses(org.cipres.treebase.domain.study.StudyTest) > testfindByNexusFileName(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testfindRowAsString(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testupdatePublishedFlagByStudy( > org.cipres.treebase.dao.matrix.MatrixDAOTest) > testfindKindByDescription(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testgetInProgressSubmissions(org.cipres.treebase.domain.admin.UserTest) > testFindByMatrixID(org.cipres.treebase.dao.matrix.RowSegmentDAOTest) > testdeleteByMatrixAndColumnRange( > org.cipres.treebase.dao.matrix.RowSegmentDAOTest) > testFindBySubstring(org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindStudies(org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindMatricesByTaxonLabel( > org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindMatricesByTaxonVariant( > org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindByTopology3( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testFindSomethingByRangeExpression( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testupdateByRearrangeNodes( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testFindByTag(org.cipres.treebase.service.admin.HelpServiceImplTest) > testEnumRowSegmentField( > org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) > testCreateRowSegments( > org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) > testFindSomethingByRangeExpression( > org.cipres.treebase.service.matrix.MatrixServiceImplTest) > testAddDelete(org.cipres.treebase.service.matrix.MatrixServiceImplTest) > testNull(org.cipres.treebase.RangeExpressionTest) > testParsingErrors(org.cipres.treebase.RangeExpressionTest) > testParsing(org.cipres.treebase.RangeExpressionTest) > testFindByLabel(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testDeleteRows(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testDeleteRowsEmpty(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testAnalyzedDataDAO_1(org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testFindByMatrix_fixture_1( > org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testFindByTree_fixture_1( > org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testJDOMSerach(org.cipres.treebase.XMLTestCase) > testDOM4jSerach(org.cipres.treebase.XMLTestCase) > testTrivial(org.cipres.treebase.domain.search.SearchResultsTest) > testSearchService(org.cipres.treebase.domain.search.SearchResultsTest) > testQuickCheck(org.cipres.treebase.domain.search.SearchResultsTest) > testConvertToMatrices( > org.cipres.treebase.domain.search.SearchResultsTest) > testConvertFromMatrices( > org.cipres.treebase.domain.search.SearchResultsTest) > testConvertToTrees(org.cipres.treebase.domain.search.SearchResultsTest) > testConvertFromTrees(org.cipres.treebase.domain.search.SearchResultsTest > ) > testGetInfo(org.cipres.treebase.domain.matrix.SpecimenLabelTest) > testLoadPhyloDataSet(org.cipres.treebase.service.nexus.NexusParserTest) > testFinalAllUniqueAlgorithmDescriptions( > org.cipres.treebase.dao.study.AlgorithmDAOTest) > testNewickParsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testM1389Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testM12c11Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testGetMatrices(org.cipres.treebase.auxdata.AuxDataTest) > testGetTrees(org.cipres.treebase.auxdata.AuxDataTest) > testFindByAccessionNumber(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByAbstract(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByAuthor(org.cipres.treebase.dao.study.StudyDAOTest) > testFindBySubmitter(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByCriteria(org.cipres.treebase.dao.study.StudyDAOTest) > testPersistNexusClob(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByTBStudyID(org.cipres.treebase.dao.study.StudyDAOTest) > testC3p0(org.cipres.treebase.dao.EnvironmentTest) > testProperty(org.cipres.treebase.dao.EnvironmentTest) > testHibernateQueryStatement(org.cipres.treebase.dao.EnvironmentTest) > testGetGeneratedKey(org.cipres.treebase.dao.EnvironmentTest) > testSelectFromInsert(org.cipres.treebase.dao.EnvironmentTest) > testProcessNexusFile( > org.cipres.treebase.service.study.SubmissionServiceImplTest) > testGetSpecimenInfo(org.cipres.treebase.domain.matrix.RowSegmentTest) > > Tests run: 268, Failures: 2, Errors: 130, Skipped: 0 > > [INFO] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS > [1.133s] > [INFO] treebase-core ......................................... FAILED > [18.360s] > [INFO] treebase-web .......................................... NOT BUILT > [INFO] > ------------------------------------------------------------------------ > [ERROR] > > Mojo: > > org.apache.maven.plugins:maven-surefire-plugin:2.4.2:test > > FAILED for project: > > org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT > > Reason: > > There are test failures. > > Please refer to > /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/treebase-core/target/surefire-reports > for the individual test results. > > > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 19 seconds > [INFO] Finished at: Mon Dec 14 16:09:04 EST 2009 > [INFO] Final Memory: 2M/22M > [INFO] > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
