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Re: [Treebase-devel] Continuing to set up the development environment
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From: Vladimir G. <vga...@ne...> - 2009-12-14 21:27:23
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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] ------------------------------------------------------------------------ |
