Build log

The build generated 17,195 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log

01-Nov-2018 10:08:22	[testng] PASSED: testSetStatusReturnsNearestResiduePosition
01-Nov-2018 10:08:22	[testng] PASSED: testSeqFeatureAddition
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_DescEqualsType
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_colouredByAttribute
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_disulfideBond
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_noScore
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_status
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_stripHtml
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_withScore
01-Nov-2018 10:08:22	[testng] PASSED: testAppendFeature_withScoreStatusAttribute
01-Nov-2018 10:08:22	[testng] PASSED: testCreateSequenceAnnotationReport
01-Nov-2018 10:08:22	[testng] PASSED: testCreateSequenceAnnotationReport_withEllipsis
01-Nov-2018 10:08:22	[testng] PASSED: testBecome
01-Nov-2018 10:08:22	[testng] PASSED: testCopyConstructors
01-Nov-2018 10:08:22	[testng] PASSED: testEqualsAndHashCode
01-Nov-2018 10:08:22	[testng] PASSED: testGetDetailsReport
01-Nov-2018 10:08:22	[testng] PASSED: testGetStrand
01-Nov-2018 10:08:22	[testng] PASSED: testGetValue
01-Nov-2018 10:08:22	[testng] PASSED: testIsContactFeature
01-Nov-2018 10:08:22	[testng] PASSED: testConstructor
01-Nov-2018 10:08:22	[testng] PASSED: testDelete
01-Nov-2018 10:08:22	[testng] PASSED: testFindFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetAllFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetContactFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeatureCount
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeatureGroups
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeatureTypes
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeatureTypesForGroups
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeatureTypes_byOntology
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeaturesByOntology
01-Nov-2018 10:08:22	[testng] PASSED: testGetFeaturesForGroup
01-Nov-2018 10:08:22	[testng] PASSED: testGetMinimumScore_getMaximumScore
01-Nov-2018 10:08:22	[testng] PASSED: testGetNonPositionalFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetPositionalFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetTotalFeatureLength
01-Nov-2018 10:08:22	[testng] PASSED: testHasFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testIsOntologyTerm
01-Nov-2018 10:08:22	[testng] PASSED: testShiftFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testSortFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testVarargsToTypes
01-Nov-2018 10:08:22	[testng] PASSED: testAddOrRemove
01-Nov-2018 10:08:22	[testng] PASSED: testAddSequence
01-Nov-2018 10:08:22	[testng] PASSED: testContains
01-Nov-2018 10:08:22	[testng] PASSED: testCopyConstructor
01-Nov-2018 10:08:22	[testng] PASSED: testGetColourScheme
01-Nov-2018 10:08:22	[testng] PASSED: testSetContext
01-Nov-2018 10:08:22	[testng] PASSED: test_seqIdNameEquals
01-Nov-2018 10:08:22	[testng] PASSED: testIsA_sequenceVariant
01-Nov-2018 10:08:22	[testng] PASSED: testIsA
01-Nov-2018 10:08:22	[testng] PASSED: testIsCDS
01-Nov-2018 10:08:22	[testng] PASSED: testIsSequenceVariant
01-Nov-2018 10:08:22	[testng] PASSED: testGetResidueColour_WithGroup
01-Nov-2018 10:08:22	[testng] PASSED: testAddAlignmentAnnotation
01-Nov-2018 10:08:22	[testng] PASSED: testAddDBRef
01-Nov-2018 10:08:22	[testng] PASSED: testAddPDBId
01-Nov-2018 10:08:22	[testng] PASSED: testAddSequenceFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testCheckValidRange
01-Nov-2018 10:08:22	[testng] PASSED: testCopyConstructor_noDataset
01-Nov-2018 10:08:22	[testng] PASSED: testCopyConstructor_withDataset
01-Nov-2018 10:08:22	[testng] PASSED: testCreateDatasetSequence
01-Nov-2018 10:08:22	[testng] PASSED: testDeleteChars
01-Nov-2018 10:08:22	[testng] PASSED: testDeleteChars_withDbRefsAndFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testDeleteChars_withGaps
01-Nov-2018 10:08:22	[testng] PASSED: testDeriveSequence_existingDataset
01-Nov-2018 10:08:22	[testng] PASSED: testDeriveSequence_noDatasetGapped
01-Nov-2018 10:08:22	[testng] PASSED: testDeriveSequence_noDatasetUngapped
01-Nov-2018 10:08:22	[testng] PASSED: testFindFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testFindIndex
01-Nov-2018 10:08:22	[testng] PASSED: testFindIndex_withCursor
01-Nov-2018 10:08:22	[testng] PASSED: testFindPosition
01-Nov-2018 10:08:22	[testng] PASSED: testFindPositionMap
01-Nov-2018 10:08:22	[testng] PASSED: testFindPosition_withCursor
01-Nov-2018 10:08:22	[testng] PASSED: testFindPosition_withCursorAndEdits
01-Nov-2018 10:08:22	[testng] PASSED: testFindPositions
01-Nov-2018 10:08:22	[testng] PASSED: testGapBitset
01-Nov-2018 10:08:22	[testng] PASSED: testGapMap
01-Nov-2018 10:08:22	[testng] PASSED: testGetAlignmentAnnotations_forCalcIdAndLabel
01-Nov-2018 10:08:22	[testng] PASSED: testGetAnnotation
01-Nov-2018 10:08:22	[testng] PASSED: testGetAnnotation_forLabel
01-Nov-2018 10:08:22	[testng] PASSED: testGetCharAt
01-Nov-2018 10:08:22	[testng] PASSED: testGetPrimaryDBRefs_nucleotide
01-Nov-2018 10:08:22	[testng] PASSED: testGetPrimaryDBRefs_peptide
01-Nov-2018 10:08:22	[testng] PASSED: testGetSequence
01-Nov-2018 10:08:22	[testng] PASSED: testGetSequenceFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetStartGetEnd
01-Nov-2018 10:08:22	[testng] PASSED: testGetSubsequence
01-Nov-2018 10:08:22	[testng] PASSED: testInsertCharAt
01-Nov-2018 10:08:22	[testng] PASSED: testInsertGapsAndGapmaps
01-Nov-2018 10:08:22	[testng] PASSED: testIsProtein
01-Nov-2018 10:08:22	[testng] PASSED: testLocateVisibleStartofSequence
01-Nov-2018 10:08:22	[testng] PASSED: testReplace
01-Nov-2018 10:08:22	[testng] PASSED: testSetDatasetSequence_cascading
01-Nov-2018 10:08:22	[testng] PASSED: testSetDatasetSequence_toSelf
01-Nov-2018 10:08:22	[testng] PASSED: testSetName
01-Nov-2018 10:08:22	[testng] PASSED: testUpdatePDBIds
01-Nov-2018 10:08:22	[testng] PASSED: testCountDisjunction
01-Nov-2018 10:08:22	[testng] PASSED: testParseMap
01-Nov-2018 10:08:22	[testng] PASSED: testShmmrService
01-Nov-2018 10:08:22	[testng] PASSED: testShmmrServiceDataprep
01-Nov-2018 10:08:22	[testng] PASSED: testAdd
01-Nov-2018 10:08:22	[testng] PASSED: testKeyAt_ValueAt
01-Nov-2018 10:08:22	[testng] PASSED: testOverflow
01-Nov-2018 10:08:22	[testng] PASSED: testPut
01-Nov-2018 10:08:22	[testng] PASSED: testUnderflow
01-Nov-2018 10:08:22	[testng] PASSED: testAdd
01-Nov-2018 10:08:22	[testng] PASSED: testCheckOverflow
01-Nov-2018 10:08:22	[testng] PASSED: testPut
01-Nov-2018 10:08:22	[testng] PASSED: testConstructor
01-Nov-2018 10:08:22	[testng] PASSED: testFillRatio
01-Nov-2018 10:08:22	[testng] PASSED: testPostMultiply
01-Nov-2018 10:08:22	[testng] PASSED: testPreMultiply
01-Nov-2018 10:08:22	[testng] PASSED: testPreMultiply_sparseProduct
01-Nov-2018 10:08:22	[testng] PASSED: testPreMultiply_tooFewColumns
01-Nov-2018 10:08:22	[testng] PASSED: testPreMultiply_tooManyColumns
01-Nov-2018 10:08:22	[testng] PASSED: testTqli_matchesMatrix
01-Nov-2018 10:08:22	[testng] PASSED: testTranspose
01-Nov-2018 10:08:22	[testng] PASSED: testTred_matchesMatrix
01-Nov-2018 10:08:22	[testng] PASSED: testTred_reproducible
01-Nov-2018 10:08:22	[testng] PASSED: testAdd
01-Nov-2018 10:08:22	[testng] PASSED: testPut
01-Nov-2018 10:08:22	[testng] PASSED: testBasicBoundsIterator
01-Nov-2018 10:08:22	[testng] PASSED: testBoundsIteratorUsingCursor
01-Nov-2018 10:08:22	[testng] PASSED: testBoundsIteratorUsingNullCursor
01-Nov-2018 10:08:22	[testng] PASSED: curlyWUSSsecondaryStructureForRNASequence
01-Nov-2018 10:08:22	[testng] PASSED: detectWussBrackets
01-Nov-2018 10:08:22	[testng] PASSED: fullWUSSsecondaryStructureForRNASequence
01-Nov-2018 10:08:22	[testng] PASSED: pfamFileDataExtraction
01-Nov-2018 10:08:22	[testng] PASSED: pfamFileIO
01-Nov-2018 10:08:22	[testng] PASSED: rfamFileIO
01-Nov-2018 10:08:22	[testng] PASSED: secondaryStructureForRNASequence
01-Nov-2018 10:08:22	[testng] PASSED: testAnnotationEquivalence
01-Nov-2018 10:08:22	[testng] PASSED: testFindColour
01-Nov-2018 10:08:22	[testng] PASSED: testArrayToSeparatorList
01-Nov-2018 10:08:22	[testng] PASSED: testCompareVersions
01-Nov-2018 10:08:22	[testng] PASSED: testDeleteChars
01-Nov-2018 10:08:22	[testng] PASSED: testGetLastToken
01-Nov-2018 10:08:22	[testng] PASSED: testInsertCharAt
01-Nov-2018 10:08:22	[testng] PASSED: testListToDelimitedString
01-Nov-2018 10:08:22	[testng] PASSED: testParseInt
01-Nov-2018 10:08:22	[testng] PASSED: testSeparatorListToArray
01-Nov-2018 10:08:22	[testng] PASSED: testStripHtmlTags
01-Nov-2018 10:08:22	[testng] PASSED: testToSentenceCase
01-Nov-2018 10:08:22	[testng] PASSED: buildQueryTest
01-Nov-2018 10:08:22	[testng] PASSED: populateFilterComboBoxTest
01-Nov-2018 10:08:22	[testng] PASSED: sanitizeSeqNameTest
01-Nov-2018 10:08:22	[testng] PASSED: testEquals
01-Nov-2018 10:08:22	[testng] PASSED: testGetPDBResNumRanges
01-Nov-2018 10:08:22	[testng] PASSED: testRegisterMapping
01-Nov-2018 10:08:22	[testng] PASSED: testRegisterMappings
01-Nov-2018 10:08:22	[testng] PASSED: testSetMapping_seqFeatures
01-Nov-2018 10:08:22	[testng] PASSED: testGetSequencesForPdbs
01-Nov-2018 10:08:22	[testng] PASSED: testGetAsArray
01-Nov-2018 10:08:22	[testng] PASSED: testGetAsList
01-Nov-2018 10:08:22	[testng] PASSED: testHeightAndWidth
01-Nov-2018 10:08:22	[testng] PASSED: testHeightAndWidthWithResidueNumbers
01-Nov-2018 10:08:22	[testng] PASSED: testParse
01-Nov-2018 10:08:22	[testng] PASSED: testReadBlock
01-Nov-2018 10:08:22	[testng] PASSED: testReadHeader
01-Nov-2018 10:08:22	[testng] PASSED: testWrongFile
01-Nov-2018 10:08:22	[testng] PASSED: testExtractGaps
01-Nov-2018 10:08:22	[testng] PASSED: testGetMappingForS1
01-Nov-2018 10:08:22	[testng] PASSED: testPrintAlignment
01-Nov-2018 10:08:22	[testng] PASSED: testTrimLeft_noColumns
01-Nov-2018 10:08:22	[testng] PASSED: testTrimLeft_oneColumn
01-Nov-2018 10:08:22	[testng] PASSED: testTrimLeft_withUndoAndRedo
01-Nov-2018 10:08:22	[testng] PASSED: testTrimRight_noColumns
01-Nov-2018 10:08:22	[testng] PASSED: testTrimRight_oneColumn
01-Nov-2018 10:08:22	[testng] PASSED: testTrimRight_withUndoAndRedo
01-Nov-2018 10:08:22	[testng] PASSED: testFindColour
01-Nov-2018 10:08:22	[testng] PASSED: testGetUniprotEntries
01-Nov-2018 10:08:22	[testng] PASSED: testGetUniprotEntryDescription
01-Nov-2018 10:08:22	[testng] PASSED: testGetUniprotEntryId
01-Nov-2018 10:08:22	[testng] PASSED: testGetUniprotSequence
01-Nov-2018 10:08:22	[testng] PASSED: getValue
01-Nov-2018 10:08:22	[testng] PASSED: testDescription
01-Nov-2018 10:08:22	[testng] PASSED: testDisplayColumnNames
01-Nov-2018 10:08:22	[testng] PASSED: testGetSetValue
01-Nov-2018 10:08:22	[testng] PASSED: testIsEditable
01-Nov-2018 10:08:22	[testng] PASSED: testName
01-Nov-2018 10:08:22	[testng] PASSED: testUrl
01-Nov-2018 10:08:22	[testng] PASSED: testColumns
01-Nov-2018 10:08:22	[testng] PASSED: testCounts
01-Nov-2018 10:08:22	[testng] PASSED: testDeletable
01-Nov-2018 10:08:22	[testng] PASSED: testEditable
01-Nov-2018 10:08:22	[testng] PASSED: testInitialisation
01-Nov-2018 10:08:22	[testng] PASSED: testRowDelete
01-Nov-2018 10:08:22	[testng] PASSED: testRowEditable
01-Nov-2018 10:08:22	[testng] PASSED: testRowInsert
01-Nov-2018 10:08:22	[testng] PASSED: testValues
01-Nov-2018 10:08:22	[testng] PASSED: testCreateLinksForNonDynamic
01-Nov-2018 10:08:22	[testng] PASSED: testCreateLinksFromNullSequence
01-Nov-2018 10:08:22	[testng] PASSED: testCreateLinksFromSequence
01-Nov-2018 10:08:22	[testng] PASSED: testLinksWithTargets
01-Nov-2018 10:08:22	[testng] PASSED: testMakeUrlNoRegex
01-Nov-2018 10:08:22	[testng] PASSED: testMakeUrlWithRegex
01-Nov-2018 10:08:22	[testng] PASSED: testUrlLinkCreationNoRegex
01-Nov-2018 10:08:22	[testng] PASSED: testUrlLinkCreationWithRegex
01-Nov-2018 10:08:22	[testng] PASSED: testInitUrlProvider
01-Nov-2018 10:08:22	[testng] PASSED: testSetDefaultUrl
01-Nov-2018 10:08:22	[testng] PASSED: testSetDefaultUrlWrongly
01-Nov-2018 10:08:22	[testng] PASSED: testConstructor_coloursArray
01-Nov-2018 10:08:22	[testng] PASSED: testParseAppletParameter
01-Nov-2018 10:08:22	[testng] PASSED: testToAppletParameter
01-Nov-2018 10:08:22	[testng] PASSED: testDoLoad
01-Nov-2018 10:08:22	[testng] PASSED: testDoLoad_reverseStrand
01-Nov-2018 10:08:22	[testng] PASSED: testDoLoad_vepCsq
01-Nov-2018 10:08:22	[testng] PASSED: testLoadVCFContig
01-Nov-2018 10:08:22	[testng] PASSED: testQuery_plain
01-Nov-2018 10:08:22	[testng] PASSED: testReadVcf_plain
01-Nov-2018 10:08:22	[testng] PASSED: testEventFiring
01-Nov-2018 10:08:22	[testng] PASSED: testGetAbsoluteAlignmentHeight
01-Nov-2018 10:08:22	[testng] PASSED: testGetAbsoluteAlignmentWidth
01-Nov-2018 10:08:22	[testng] PASSED: testGetWrappedMaxScroll
01-Nov-2018 10:08:22	[testng] PASSED: testGetWrappedScrollPosition
01-Nov-2018 10:08:22	[testng] PASSED: testPageUpDown
01-Nov-2018 10:08:22	[testng] PASSED: testPageUpDownWrapped
01-Nov-2018 10:08:22	[testng] PASSED: testScrollRight
01-Nov-2018 10:08:22	[testng] PASSED: testScrollRightWithHidden
01-Nov-2018 10:08:22	[testng] PASSED: testScrollToVisible
01-Nov-2018 10:08:22	[testng] PASSED: testScrollToWrappedVisible
01-Nov-2018 10:08:22	[testng] PASSED: testScrollUp
01-Nov-2018 10:08:22	[testng] PASSED: testScrollUpWithHidden
01-Nov-2018 10:08:22	[testng] PASSED: testScrollUp_wrapped
01-Nov-2018 10:08:22	[testng] PASSED: testSetEndSeq
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartEndRes
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartEndResWrapped
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartEndSeq
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartRes
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartResAndSeq
01-Nov-2018 10:08:22	[testng] PASSED: testSetStartSeq
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportHeight
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportLocation
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportStartAndHeight
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportStartAndWidth
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportStartAndWidthWrapped
01-Nov-2018 10:08:22	[testng] PASSED: testSetViewportWidth
01-Nov-2018 10:08:22	[testng] PASSED: testViewportRanges
01-Nov-2018 10:08:22	[testng] PASSED: testMultipleVisibleRegions
01-Nov-2018 10:08:22	[testng] PASSED: testSimpleVisibleRegions
01-Nov-2018 10:08:22	[testng] PASSED: testVisibleRegionsAtHiddenEdges
01-Nov-2018 10:08:22	[testng] PASSED: testHasNextAndNextEndHidden
01-Nov-2018 10:08:22	[testng] PASSED: testHasNextAndNextNoHidden
01-Nov-2018 10:08:22	[testng] PASSED: testHasNextAndNextStartHidden
01-Nov-2018 10:08:22	[testng] PASSED: testHasNextAndNextWithHidden
01-Nov-2018 10:08:22	[testng] PASSED: testLastNextEndHidden
01-Nov-2018 10:08:22	[testng] PASSED: testLastNextNoHidden
01-Nov-2018 10:08:22	[testng] PASSED: testLastNextStartHidden
01-Nov-2018 10:08:22	[testng] PASSED: testLastNextWithHidden
01-Nov-2018 10:08:22	[testng] PASSED: testRemove
01-Nov-2018 10:08:22	[testng] FAILED: TestUpdateLayout_endRes
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected [156] but found [66]
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.fail(Assert.java:94)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:125)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:372)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:382)
01-Nov-2018 10:08:22	[testng] at jalview.gui.AlignmentPanelTest.__CLR4_2_1b5wha22x2p(AlignmentPanelTest.java:246)
01-Nov-2018 10:08:22	[testng] at jalview.gui.AlignmentPanelTest.TestUpdateLayout_endRes(AlignmentPanelTest.java:229)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testLaunchAndExit
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: Couldn't launch chimera
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24)
01-Nov-2018 10:08:22	[testng] at jalview.ext.rbvi.chimera.ChimeraConnect.testLaunchAndExit(ChimeraConnect.java:49)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testFindXrefSequences_forGeneAndTranscripts
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_16yj4942se0(CrossRefTest.java:535)
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_forGeneAndTranscripts(CrossRefTest.java:469)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testFindXrefSequences_uniprotEmblManyToMany
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_1nurnsm2ser(CrossRefTest.java:711)
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_uniprotEmblManyToMany(CrossRefTest.java:566)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testFindXrefSequences_withFetch
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_1ruxmrc2sde(CrossRefTest.java:452)
01-Nov-2018 10:08:22	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_withFetch(CrossRefTest.java:415)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testCut_gappedWithFeatures
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected:<1> but was:<3>
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
01-Nov-2018 10:08:22	[testng] at jalview.commands.EditCommandTest.__CLR4_2_1b9p4i3axx(EditCommandTest.java:868)
01-Nov-2018 10:08:22	[testng] at jalview.commands.EditCommandTest.testCut_gappedWithFeatures(EditCommandTest.java:848)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testCut_withFeatures
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected:<4> but was:<5>
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
01-Nov-2018 10:08:22	[testng] at jalview.commands.EditCommandTest.__CLR4_2_1l07oop3av8(EditCommandTest.java:699)
01-Nov-2018 10:08:22	[testng] at jalview.commands.EditCommandTest.testCut_withFeatures(EditCommandTest.java:661)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testIdentify("examples/rf00031_folded.stk", Stockholm)
01-Nov-2018 10:08:22	[testng] jalview.io.FileFormatException: Problem opening rf00031_folded.stk : FILE CANNOT BE OPENED FOR READING
01-Nov-2018 10:08:22	[testng] at jalview.io.IdentifyFile.identify(IdentifyFile.java:101)
01-Nov-2018 10:08:22	[testng] at jalview.io.IdentifyFileTest.__CLR4_2_163b86u3440(IdentifyFileTest.java:50)
01-Nov-2018 10:08:22	[testng] at jalview.io.IdentifyFileTest.testIdentify(IdentifyFileTest.java:47)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testAlignmentLoader
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at jalview.ext.jmol.JmolParserTest.__CLR4_2_1b9f5ij3usz(JmolParserTest.java:119)
01-Nov-2018 10:08:22	[testng] at jalview.ext.jmol.JmolParserTest.testAlignmentLoader(JmolParserTest.java:114)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testFileParser
01-Nov-2018 10:08:22	[testng] java.io.IOException: Problem opening 1GAQ.txt : FILE CANNOT BE OPENED FOR READING
01-Nov-2018 10:08:22	[testng] at jalview.io.FileParse.parse(FileParse.java:370)
01-Nov-2018 10:08:22	[testng] at jalview.io.FileParse.<init>(FileParse.java:329)
01-Nov-2018 10:08:22	[testng] at jalview.io.AlignFile.<init>(AlignFile.java:137)
01-Nov-2018 10:08:22	[testng] at jalview.io.StructureFile.<init>(StructureFile.java:104)
01-Nov-2018 10:08:22	[testng] at mc_view.PDBfile.<init>(PDBfile.java:53)
01-Nov-2018 10:08:22	[testng] at jalview.ext.jmol.JmolParserTest.__CLR4_2_19oqq383ut4(JmolParserTest.java:128)
01-Nov-2018 10:08:22	[testng] at jalview.ext.jmol.JmolParserTest.testFileParser(JmolParserTest.java:125)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: updateCacheTest
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError
01-Nov-2018 10:08:22	[testng] at org.junit.Assert.fail(Assert.java:86)
01-Nov-2018 10:08:22	[testng] at org.junit.Assert.assertTrue(Assert.java:41)
01-Nov-2018 10:08:22	[testng] at org.junit.Assert.assertTrue(Assert.java:52)
01-Nov-2018 10:08:22	[testng] at jalview.io.cache.JvCacheableInputBoxTest.__CLR4_2_1shislu3gio(JvCacheableInputBoxTest.java:68)
01-Nov-2018 10:08:22	[testng] at jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest(JvCacheableInputBoxTest.java:51)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testIsControlDown_mac
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected [false] but found [true]
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.fail(Assert.java:94)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertFalse(Assert.java:63)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertFalse(Assert.java:73)
01-Nov-2018 10:08:22	[testng] at jalview.util.PlatformTest.__CLR4_2_16ar2hy3eu9(PlatformTest.java:65)
01-Nov-2018 10:08:22	[testng] at jalview.util.PlatformTest.testIsControlDown_mac(PlatformTest.java:53)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testAddFeatureLinks
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected:<5> but was:<6>
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
01-Nov-2018 10:08:22	[testng] at jalview.gui.PopupMenuTest.__CLR4_2_1wjq27t33u7(PopupMenuTest.java:552)
01-Nov-2018 10:08:22	[testng] at jalview.gui.PopupMenuTest.testAddFeatureLinks(PopupMenuTest.java:503)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testCalculateWrappedGeometry_fromScrolled
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: expected [3] but found [13]
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.fail(Assert.java:94)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:125)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:372)
01-Nov-2018 10:08:22	[testng] at org.testng.Assert.assertEquals(Assert.java:382)
01-Nov-2018 10:08:22	[testng] at jalview.gui.SeqCanvasTest.__CLR4_2_1ea6dhj47xn(SeqCanvasTest.java:334)
01-Nov-2018 10:08:22	[testng] at jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_fromScrolled(SeqCanvasTest.java:310)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testCreateFastaSequenceIndex
01-Nov-2018 10:08:22	[testng] java.lang.NoSuchMethodError: htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaIndexFileName(Ljava/nio/file/Path;)Ljava/nio/file/Path;
01-Nov-2018 10:08:22	[testng] at htsjdk.samtools.reference.FastaSequenceIndexCreator.create(FastaSequenceIndexCreator.java:57)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.HtsContigDb.createFastaSequenceIndex(HtsContigDb.java:65)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1fsv57j2vbn(TestHtsContigDb.java:101)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex(TestHtsContigDb.java:94)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testGetSequenceProxy
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_14987dc2vb8(TestHtsContigDb.java:48)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy(TestHtsContigDb.java:46)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testGetSequenceProxy_indexed
01-Nov-2018 10:08:22	[testng] java.lang.NullPointerException
01-Nov-2018 10:08:22	[testng] at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1tl2la62vbj(TestHtsContigDb.java:77)
01-Nov-2018 10:08:22	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexed(TestHtsContigDb.java:75)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testCopyConstructor
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1frqtvq3eoo(ViewStyleTest.java:73)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.testCopyConstructor(ViewStyleTest.java:65)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] FAILED: testEquals
01-Nov-2018 10:08:22	[testng] java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
01-Nov-2018 10:08:22	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1s4e6083eqr(ViewStyleTest.java:215)
01-Nov-2018 10:08:22	[testng] at jalview.viewmodel.styles.ViewStyleTest.testEquals(ViewStyleTest.java:201)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
01-Nov-2018 10:08:22	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
01-Nov-2018 10:08:22	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
01-Nov-2018 10:08:22	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
01-Nov-2018 10:08:22	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
01-Nov-2018 10:08:22	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
01-Nov-2018 10:08:22	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.run(TestNG.java:1009)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
01-Nov-2018 10:08:22	[testng] at org.testng.TestNG.main(TestNG.java:1285)
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] ===============================================
01-Nov-2018 10:08:22	[testng] Ant test
01-Nov-2018 10:08:22	[testng] Tests run: 1255, Failures: 19, Skips: 0
01-Nov-2018 10:08:22	[testng] ===============================================
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:22	[testng] ===============================================
01-Nov-2018 10:08:22	[testng] Ant suite
01-Nov-2018 10:08:22	[testng] Total tests run: 1255, Failures: 19, Skips: 0
01-Nov-2018 10:08:22	[testng] ===============================================
01-Nov-2018 10:08:22	[testng]
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@3b192d32: 217 ms
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by org.testng.reporters.XMLReporter@6ed3ef1: 75 ms
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 30 ms
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by org.testng.reporters.jq.Main@ed17bee: 164 ms
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2@383534aa: 30 ms
01-Nov-2018 10:08:23	[testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@136432db: 95 ms
01-Nov-2018 10:08:24	[testng] The tests failed.
01-Nov-2018 10:08:24
01-Nov-2018 10:08:24	clover.save-history:
01-Nov-2018 10:08:24	[clover-historypoint] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
01-Nov-2018 10:08:24	[clover-historypoint] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
01-Nov-2018 10:08:24	[clover-historypoint] Clover free edition.
01-Nov-2018 10:08:33	[clover-historypoint] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.cloverhistory/jalviewX/clover-20181101100823.xml.gz'
01-Nov-2018 10:08:34
01-Nov-2018 10:08:34	clover.report:
01-Nov-2018 10:08:34	[clover-report] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
01-Nov-2018 10:08:34	[clover-report] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
01-Nov-2018 10:08:34	[clover-report] Clover free edition.
01-Nov-2018 10:08:34	[clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'
01-Nov-2018 10:08:34	[clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'
01-Nov-2018 10:08:34	[clover-report] Loading historical coverage data from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.cloverhistory/jalviewX'
01-Nov-2018 10:08:37	[clover-report] Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX'
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBChain.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBChain.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBChain.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBCanvas.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBCanvas.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBCanvas.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBViewer.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBViewer.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBViewer.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Zsort.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Zsort.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Zsort.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBCanvas.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBCanvas.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBCanvas.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Bond.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Bond.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Bond.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBfile.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBfile.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBfile.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/MCMatrix.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/MCMatrix.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/MCMatrix.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Residue.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Residue.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Residue.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Atom.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Atom.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Atom.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBfileTest.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBfileTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBfileTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/ResidueTest.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/ResidueTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/ResidueTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/BondTest.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/BondTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/BondTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBChainTest.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBChainTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBChainTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] Failed to render syntax highlights for /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/AtomTest.java: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/AtomTest.java (No such file or directory)
01-Nov-2018 10:08:54	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/AtomTest.java (No such file or directory)
01-Nov-2018 10:09:13	[clover-report] Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/jalview/schemes/ResidueProperties.java
01-Nov-2018 10:09:20	[clover-report] Done. Processed 106 packages in 42658ms (402ms per package).
01-Nov-2018 10:09:22	[clover-report] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX/clover.xml'
01-Nov-2018 10:09:23	[clover-report] Writing historical report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX'
01-Nov-2018 10:09:27	[clover-report] Read 30 history points.
01-Nov-2018 10:09:27	[clover-report] using movers interval of 18 hours
01-Nov-2018 10:09:27	[clover-report] using movers interval of 18 hours
01-Nov-2018 10:09:28	[clover-report] Writing JSON historical-data to: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX/historical-json.js
01-Nov-2018 10:09:28	[clover-report] Done.
01-Nov-2018 10:09:28
01-Nov-2018 10:09:28	BUILD SUCCESSFUL
01-Nov-2018 10:09:28	Total time: 3 minutes 31 seconds
01-Nov-2018 10:09:29	Finished task 'Clover TestNG Suite' with result: Success
01-Nov-2018 10:09:29	Starting task 'Process Jalview TestNG Suite' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
01-Nov-2018 10:09:29	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1...
01-Nov-2018 10:09:33	Failing task since 19 failing test cases were found.
01-Nov-2018 10:09:33	Finished task 'Process Jalview TestNG Suite' with result: Failed
01-Nov-2018 10:09:33	Starting task 'build' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
01-Nov-2018 10:09:33	Beginning to execute external process for build 'Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job #208 (JB-JDB1-JOB1-208)' ... running command line: /usr/share/ant/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDB1-JOB1 -f build.xml makedist ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=Jalview-BH/JAL-3026 bamboo_planRepository_1_branchDisplayName=Jalview-BH/JAL-3026 bamboo_repository_revision_number=f20ff42eac30f33cb69635ba3217a6224dbeb555 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-208 bamboo_repository_2228226_revision_number=f20ff42eac30f33cb69635ba3217a6224dbeb555 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-JDB1-JOB1 bamboo_capability_system_jdk_JDK_1_8_0_171=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_shortPlanName=Jalview-BH-JAL-3026 bamboo_planRepository_name=Jalview Git bamboo_repository_2228226_git_username= bamboo_buildNumber=208 bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-208 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 bamboo_shortPlanKey=JDB1 bamboo_repository_2228226_branch_name=Jalview-BH/JAL-3026 bamboo_shortJobKey=JOB1 bamboo_planRepository_revision=f20ff42eac30f33cb69635ba3217a6224dbeb555 bamboo_buildTimeStamp=2018-11-01T10:04:19.982Z bamboo_repository_previous_revision_number=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_planRepository_previousRevision=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_repository_git_branch=Jalview-BH/JAL-3026 bamboo_buildResultKey=JB-JDB1-JOB1-208 bamboo_repository_branch_name=Jalview-BH/JAL-3026 bamboo_buildPlanName=Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job bamboo_planRepository_1_revision=f20ff42eac30f33cb69635ba3217a6224dbeb555 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_2228226_git_branch=Jalview-BH/JAL-3026 bamboo_repository_name=Jalview Git bamboo_repository_2228226_previous_revision_number=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_repository_2228226_name=Jalview Git JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_buildFailed=true bamboo_build_commandline_com_atlassian_bamboo_plugins_ant_task_builder_ant_3=/home/bamboo/buildtools/x11-ant/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDB1-JOB1 -f build.xml -Dclover.jar=/home/bamboo/buildtools/clover/lib/clover.jar clean with.clover testng clover.report ANT_HOME=/usr/share/ant bamboo_planRepository_branch=Jalview-BH/JAL-3026 bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_planRepository_branchDisplayName=Jalview-BH/JAL-3026 bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=Jalview-BH/JAL-3026 bamboo_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_plan_storageTag=plan-2031619 bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_2228226_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1 bamboo_planKey=JB-JDB1 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_planRepository_1_branchName=Jalview-BH/JAL-3026 PATH=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
01-Nov-2018 10:09:34	Buildfile: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml
01-Nov-2018 10:09:34
01-Nov-2018 10:09:34	init:
01-Nov-2018 10:09:34
01-Nov-2018 10:09:34	prepare:
01-Nov-2018 10:09:34
01-Nov-2018 10:09:34	build:
01-Nov-2018 10:09:34	[javac] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml:279: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
01-Nov-2018 10:09:35	[javac] Compiling 5 source files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes
01-Nov-2018 10:09:39	[javac] Note: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/jalview/gui/Desktop.java uses unchecked or unsafe operations.
01-Nov-2018 10:09:39	[javac] Note: Recompile with -Xlint:unchecked for details.
01-Nov-2018 10:09:39
01-Nov-2018 10:09:39	buildPropertiesFile:
01-Nov-2018 10:09:40	[properties] write property file /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes/.build_properties
01-Nov-2018 10:09:40
01-Nov-2018 10:09:40	linkcheck:
01-Nov-2018 10:09:40	[javac] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml:991: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
01-Nov-2018 10:09:40	[java] Checking help file links
01-Nov-2018 10:09:41	[java]
01-Nov-2018 10:09:41	[java] Results:
01-Nov-2018 10:09:41	[java] 132 distinct help targets
01-Nov-2018 10:09:41	[java] 132 help mappings
01-Nov-2018 10:09:41	[java] 0 invalid targets
01-Nov-2018 10:09:41	[java] 21 unused targets
01-Nov-2018 10:09:41	[java] uniprotfetcher: html/features/uniprotsequencefetcher.html
01-Nov-2018 10:09:41	[java] overviewprefs: html/features/preferences.html#overview
01-Nov-2018 10:09:41	[java] cdnafeatures: html/features/codingfeatures.html
01-Nov-2018 10:09:41	[java] ensemblfetch: html/features/ensemblsequencefetcher.html
01-Nov-2018 10:09:41	[java] io.modellerpir: html/io/modellerpir.html
01-Nov-2018 10:09:41	[java] pdbmcviewer: html/features/pdbviewer.html
01-Nov-2018 10:09:41	[java] groovy.colours: html/features/groovy.html#groovyColours
01-Nov-2018 10:09:41	[java] seqmappings: html/features/seqmappings.html
01-Nov-2018 10:09:41	[java] splitframe.mirrorfonts: html/features/splitView.html#mirror
01-Nov-2018 10:09:41	[java] subtMatrices.pam250: html/calculations/scorematrices.html#pam250
01-Nov-2018 10:09:41	[java] search: html/features/search.html
01-Nov-2018 10:09:41	[java] viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
01-Nov-2018 10:09:41	[java] alformats: html/io/fileformats.html
01-Nov-2018 10:09:41	[java] strucprefs: html/features/preferences.html#structure
01-Nov-2018 10:09:41	[java] siftsmapping: html/features/siftsmapping.html
01-Nov-2018 10:09:41	[java] newkeys: html/features/newkeystrokes.html
01-Nov-2018 10:09:41	[java] seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
01-Nov-2018 10:09:41	[java] jalarchive: html/features/jalarchive.html
01-Nov-2018 10:09:41	[java] newsreader: html/webServices/newsreader.html
01-Nov-2018 10:09:41	[java] popMenuAddref: html/menus/popupMenu.html#addrefannot
01-Nov-2018 10:09:41	[java] overview: html/features/overview.html
01-Nov-2018 10:09:41	[java] 0 invalid map urls
01-Nov-2018 10:09:41	[java] 0 invalid image attributes
01-Nov-2018 10:09:41	[java] 352 internal href links (62 with anchors)
01-Nov-2018 10:09:41	[java] 0 invalid internal href links
01-Nov-2018 10:09:41	[java] 0 invalid internal anchor links
01-Nov-2018 10:09:41	[java] 83 external href links
01-Nov-2018 10:09:41	[java] External links not verified as internet not available
01-Nov-2018 10:09:41	[java] * Success *
01-Nov-2018 10:09:41
01-Nov-2018 10:09:41	buildindices:
01-Nov-2018 10:09:43
01-Nov-2018 10:09:43	makedist:
01-Nov-2018 10:09:44	[jar] Building jar: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/dist/jalview.jar
01-Nov-2018 10:09:48	[copy] Copying 52 files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/dist
01-Nov-2018 10:09:49
01-Nov-2018 10:09:49	BUILD SUCCESSFUL
01-Nov-2018 10:09:49	Total time: 14 seconds
01-Nov-2018 10:09:49	Finished task 'build' with result: Success
01-Nov-2018 10:09:49	Running post build plugin 'NCover Results Collector'
01-Nov-2018 10:09:49	Running post build plugin 'Artifact Copier'
01-Nov-2018 10:09:49	Publishing an artifact: jalview-jars
01-Nov-2018 10:09:49	Finished publishing of artifact Shared artifact: [jalview-jars], pattern: [*/.*] anchored at: [dist] in 60.05 ms
01-Nov-2018 10:09:49	Publishing an artifact: Clover Report (System)
01-Nov-2018 10:18:26	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [*/.*] anchored at: [clover] in 8.610 min
01-Nov-2018 10:18:26	Running post build plugin 'npm Cache Cleanup'
01-Nov-2018 10:18:26	Running post build plugin 'Clover Results Collector'
01-Nov-2018 10:18:26	Running post build plugin 'Docker Container Cleanup'
01-Nov-2018 10:18:26	Finalising the build...
01-Nov-2018 10:18:26	Stopping timer.
01-Nov-2018 10:18:26	Build JB-JDB1-JOB1-208 completed.
01-Nov-2018 10:18:26	Running on server: post build plugin 'NCover Results Collector'
01-Nov-2018 10:18:26	Running on server: post build plugin 'Build Hanging Detection Configuration'
01-Nov-2018 10:18:26	Running on server: post build plugin 'Clover Delta Calculator'
01-Nov-2018 10:18:26	Running on server: post build plugin 'Maven Dependencies Postprocessor'
01-Nov-2018 10:18:26	All post build plugins have finished
01-Nov-2018 10:18:26	Generating build results summary...
01-Nov-2018 10:18:26	Saving build results to disk...
01-Nov-2018 10:18:26	Logging substituted variables...
01-Nov-2018 10:18:26	Indexing build results...
01-Nov-2018 10:18:26	Finished building JB-JDB1-JOB1-208.

Build #208

Build: #208 failed

Job: Default Job failed

Stages & jobs

Default Stage

Build log