Build log

The build generated 17,166 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log

31-Oct-2018 15:15:46	[testng] PASSED: testFindPosition
31-Oct-2018 15:15:46	[testng] PASSED: testSomething
31-Oct-2018 15:15:46	[testng] PASSED: testAmbiguousAminoAcidGetsStatusMessage
31-Oct-2018 15:15:46	[testng] PASSED: testSetStatusReturnsNearestResiduePosition
31-Oct-2018 15:15:46	[testng] PASSED: testSeqFeatureAddition
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_DescEqualsType
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_colouredByAttribute
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_disulfideBond
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_noScore
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_status
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_stripHtml
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_withScore
31-Oct-2018 15:15:46	[testng] PASSED: testAppendFeature_withScoreStatusAttribute
31-Oct-2018 15:15:46	[testng] PASSED: testCreateSequenceAnnotationReport
31-Oct-2018 15:15:46	[testng] PASSED: testCreateSequenceAnnotationReport_withEllipsis
31-Oct-2018 15:15:46	[testng] PASSED: testBecome
31-Oct-2018 15:15:46	[testng] PASSED: testCopyConstructors
31-Oct-2018 15:15:46	[testng] PASSED: testEqualsAndHashCode
31-Oct-2018 15:15:46	[testng] PASSED: testGetDetailsReport
31-Oct-2018 15:15:46	[testng] PASSED: testGetStrand
31-Oct-2018 15:15:46	[testng] PASSED: testGetValue
31-Oct-2018 15:15:46	[testng] PASSED: testIsContactFeature
31-Oct-2018 15:15:46	[testng] PASSED: testConstructor
31-Oct-2018 15:15:46	[testng] PASSED: testDelete
31-Oct-2018 15:15:46	[testng] PASSED: testFindFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetAllFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetContactFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeatureCount
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeatureGroups
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeatureTypes
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeatureTypesForGroups
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeatureTypes_byOntology
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeaturesByOntology
31-Oct-2018 15:15:46	[testng] PASSED: testGetFeaturesForGroup
31-Oct-2018 15:15:46	[testng] PASSED: testGetMinimumScore_getMaximumScore
31-Oct-2018 15:15:46	[testng] PASSED: testGetNonPositionalFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetPositionalFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetTotalFeatureLength
31-Oct-2018 15:15:46	[testng] PASSED: testHasFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testIsOntologyTerm
31-Oct-2018 15:15:46	[testng] PASSED: testShiftFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testSortFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testVarargsToTypes
31-Oct-2018 15:15:46	[testng] PASSED: testAddOrRemove
31-Oct-2018 15:15:46	[testng] PASSED: testAddSequence
31-Oct-2018 15:15:46	[testng] PASSED: testContains
31-Oct-2018 15:15:46	[testng] PASSED: testCopyConstructor
31-Oct-2018 15:15:46	[testng] PASSED: testGetColourScheme
31-Oct-2018 15:15:46	[testng] PASSED: testSetContext
31-Oct-2018 15:15:46	[testng] PASSED: test_seqIdNameEquals
31-Oct-2018 15:15:46	[testng] PASSED: testIsA_sequenceVariant
31-Oct-2018 15:15:46	[testng] PASSED: testIsA
31-Oct-2018 15:15:46	[testng] PASSED: testIsCDS
31-Oct-2018 15:15:46	[testng] PASSED: testIsSequenceVariant
31-Oct-2018 15:15:46	[testng] PASSED: testGetResidueColour_WithGroup
31-Oct-2018 15:15:46	[testng] PASSED: testAddAlignmentAnnotation
31-Oct-2018 15:15:46	[testng] PASSED: testAddDBRef
31-Oct-2018 15:15:46	[testng] PASSED: testAddPDBId
31-Oct-2018 15:15:46	[testng] PASSED: testAddSequenceFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testCheckValidRange
31-Oct-2018 15:15:46	[testng] PASSED: testCopyConstructor_noDataset
31-Oct-2018 15:15:46	[testng] PASSED: testCopyConstructor_withDataset
31-Oct-2018 15:15:46	[testng] PASSED: testCreateDatasetSequence
31-Oct-2018 15:15:46	[testng] PASSED: testDeleteChars
31-Oct-2018 15:15:46	[testng] PASSED: testDeleteChars_withDbRefsAndFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testDeleteChars_withGaps
31-Oct-2018 15:15:46	[testng] PASSED: testDeriveSequence_existingDataset
31-Oct-2018 15:15:46	[testng] PASSED: testDeriveSequence_noDatasetGapped
31-Oct-2018 15:15:46	[testng] PASSED: testDeriveSequence_noDatasetUngapped
31-Oct-2018 15:15:46	[testng] PASSED: testFindFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testFindIndex
31-Oct-2018 15:15:46	[testng] PASSED: testFindIndex_withCursor
31-Oct-2018 15:15:46	[testng] PASSED: testFindPosition
31-Oct-2018 15:15:46	[testng] PASSED: testFindPositionMap
31-Oct-2018 15:15:46	[testng] PASSED: testFindPosition_withCursor
31-Oct-2018 15:15:46	[testng] PASSED: testFindPosition_withCursorAndEdits
31-Oct-2018 15:15:46	[testng] PASSED: testFindPositions
31-Oct-2018 15:15:46	[testng] PASSED: testGapBitset
31-Oct-2018 15:15:46	[testng] PASSED: testGapMap
31-Oct-2018 15:15:46	[testng] PASSED: testGetAlignmentAnnotations_forCalcIdAndLabel
31-Oct-2018 15:15:46	[testng] PASSED: testGetAnnotation
31-Oct-2018 15:15:46	[testng] PASSED: testGetAnnotation_forLabel
31-Oct-2018 15:15:46	[testng] PASSED: testGetCharAt
31-Oct-2018 15:15:46	[testng] PASSED: testGetPrimaryDBRefs_nucleotide
31-Oct-2018 15:15:46	[testng] PASSED: testGetPrimaryDBRefs_peptide
31-Oct-2018 15:15:46	[testng] PASSED: testGetSequence
31-Oct-2018 15:15:46	[testng] PASSED: testGetSequenceFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetStartGetEnd
31-Oct-2018 15:15:46	[testng] PASSED: testGetSubsequence
31-Oct-2018 15:15:46	[testng] PASSED: testInsertCharAt
31-Oct-2018 15:15:46	[testng] PASSED: testInsertGapsAndGapmaps
31-Oct-2018 15:15:46	[testng] PASSED: testIsProtein
31-Oct-2018 15:15:46	[testng] PASSED: testLocateVisibleStartofSequence
31-Oct-2018 15:15:46	[testng] PASSED: testReplace
31-Oct-2018 15:15:46	[testng] PASSED: testSetDatasetSequence_cascading
31-Oct-2018 15:15:46	[testng] PASSED: testSetDatasetSequence_toSelf
31-Oct-2018 15:15:46	[testng] PASSED: testSetName
31-Oct-2018 15:15:46	[testng] PASSED: testUpdatePDBIds
31-Oct-2018 15:15:46	[testng] PASSED: testCountDisjunction
31-Oct-2018 15:15:46	[testng] PASSED: testParseMap
31-Oct-2018 15:15:46	[testng] PASSED: testShmmrService
31-Oct-2018 15:15:46	[testng] PASSED: testShmmrServiceDataprep
31-Oct-2018 15:15:46	[testng] PASSED: testAdd
31-Oct-2018 15:15:46	[testng] PASSED: testKeyAt_ValueAt
31-Oct-2018 15:15:46	[testng] PASSED: testOverflow
31-Oct-2018 15:15:46	[testng] PASSED: testPut
31-Oct-2018 15:15:46	[testng] PASSED: testUnderflow
31-Oct-2018 15:15:46	[testng] PASSED: testAdd
31-Oct-2018 15:15:46	[testng] PASSED: testCheckOverflow
31-Oct-2018 15:15:46	[testng] PASSED: testPut
31-Oct-2018 15:15:46	[testng] PASSED: testConstructor
31-Oct-2018 15:15:46	[testng] PASSED: testFillRatio
31-Oct-2018 15:15:46	[testng] PASSED: testPostMultiply
31-Oct-2018 15:15:46	[testng] PASSED: testPreMultiply
31-Oct-2018 15:15:46	[testng] PASSED: testPreMultiply_sparseProduct
31-Oct-2018 15:15:46	[testng] PASSED: testPreMultiply_tooFewColumns
31-Oct-2018 15:15:46	[testng] PASSED: testPreMultiply_tooManyColumns
31-Oct-2018 15:15:46	[testng] PASSED: testTqli_matchesMatrix
31-Oct-2018 15:15:46	[testng] PASSED: testTranspose
31-Oct-2018 15:15:46	[testng] PASSED: testTred_matchesMatrix
31-Oct-2018 15:15:46	[testng] PASSED: testTred_reproducible
31-Oct-2018 15:15:46	[testng] PASSED: testAdd
31-Oct-2018 15:15:46	[testng] PASSED: testPut
31-Oct-2018 15:15:46	[testng] PASSED: testBasicBoundsIterator
31-Oct-2018 15:15:46	[testng] PASSED: testBoundsIteratorUsingCursor
31-Oct-2018 15:15:46	[testng] PASSED: testBoundsIteratorUsingNullCursor
31-Oct-2018 15:15:46	[testng] PASSED: curlyWUSSsecondaryStructureForRNASequence
31-Oct-2018 15:15:46	[testng] PASSED: detectWussBrackets
31-Oct-2018 15:15:46	[testng] PASSED: fullWUSSsecondaryStructureForRNASequence
31-Oct-2018 15:15:46	[testng] PASSED: pfamFileDataExtraction
31-Oct-2018 15:15:46	[testng] PASSED: pfamFileIO
31-Oct-2018 15:15:46	[testng] PASSED: rfamFileIO
31-Oct-2018 15:15:46	[testng] PASSED: secondaryStructureForRNASequence
31-Oct-2018 15:15:46	[testng] PASSED: testAnnotationEquivalence
31-Oct-2018 15:15:46	[testng] PASSED: testFindColour
31-Oct-2018 15:15:46	[testng] PASSED: testArrayToSeparatorList
31-Oct-2018 15:15:46	[testng] PASSED: testCompareVersions
31-Oct-2018 15:15:46	[testng] PASSED: testDeleteChars
31-Oct-2018 15:15:46	[testng] PASSED: testGetLastToken
31-Oct-2018 15:15:46	[testng] PASSED: testInsertCharAt
31-Oct-2018 15:15:46	[testng] PASSED: testListToDelimitedString
31-Oct-2018 15:15:46	[testng] PASSED: testParseInt
31-Oct-2018 15:15:46	[testng] PASSED: testSeparatorListToArray
31-Oct-2018 15:15:46	[testng] PASSED: testStripHtmlTags
31-Oct-2018 15:15:46	[testng] PASSED: testToSentenceCase
31-Oct-2018 15:15:46	[testng] PASSED: buildQueryTest
31-Oct-2018 15:15:46	[testng] PASSED: populateFilterComboBoxTest
31-Oct-2018 15:15:46	[testng] PASSED: sanitizeSeqNameTest
31-Oct-2018 15:15:46	[testng] PASSED: testEquals
31-Oct-2018 15:15:46	[testng] PASSED: testGetPDBResNumRanges
31-Oct-2018 15:15:46	[testng] PASSED: testRegisterMapping
31-Oct-2018 15:15:46	[testng] PASSED: testRegisterMappings
31-Oct-2018 15:15:46	[testng] PASSED: testSetMapping_seqFeatures
31-Oct-2018 15:15:46	[testng] PASSED: testGetSequencesForPdbs
31-Oct-2018 15:15:46	[testng] PASSED: testGetAsArray
31-Oct-2018 15:15:46	[testng] PASSED: testGetAsList
31-Oct-2018 15:15:46	[testng] PASSED: testHeightAndWidth
31-Oct-2018 15:15:46	[testng] PASSED: testHeightAndWidthWithResidueNumbers
31-Oct-2018 15:15:46	[testng] PASSED: testParse
31-Oct-2018 15:15:46	[testng] PASSED: testReadBlock
31-Oct-2018 15:15:46	[testng] PASSED: testReadHeader
31-Oct-2018 15:15:46	[testng] PASSED: testWrongFile
31-Oct-2018 15:15:46	[testng] PASSED: testExtractGaps
31-Oct-2018 15:15:46	[testng] PASSED: testGetMappingForS1
31-Oct-2018 15:15:46	[testng] PASSED: testPrintAlignment
31-Oct-2018 15:15:46	[testng] PASSED: testTrimLeft_noColumns
31-Oct-2018 15:15:46	[testng] PASSED: testTrimLeft_oneColumn
31-Oct-2018 15:15:46	[testng] PASSED: testTrimLeft_withUndoAndRedo
31-Oct-2018 15:15:46	[testng] PASSED: testTrimRight_noColumns
31-Oct-2018 15:15:46	[testng] PASSED: testTrimRight_oneColumn
31-Oct-2018 15:15:46	[testng] PASSED: testTrimRight_withUndoAndRedo
31-Oct-2018 15:15:46	[testng] PASSED: testFindColour
31-Oct-2018 15:15:46	[testng] PASSED: testGetUniprotEntries
31-Oct-2018 15:15:46	[testng] PASSED: testGetUniprotEntryDescription
31-Oct-2018 15:15:46	[testng] PASSED: testGetUniprotEntryId
31-Oct-2018 15:15:46	[testng] PASSED: testGetUniprotSequence
31-Oct-2018 15:15:46	[testng] PASSED: getValue
31-Oct-2018 15:15:46	[testng] PASSED: testDescription
31-Oct-2018 15:15:46	[testng] PASSED: testDisplayColumnNames
31-Oct-2018 15:15:46	[testng] PASSED: testGetSetValue
31-Oct-2018 15:15:46	[testng] PASSED: testIsEditable
31-Oct-2018 15:15:46	[testng] PASSED: testName
31-Oct-2018 15:15:46	[testng] PASSED: testUrl
31-Oct-2018 15:15:46	[testng] PASSED: testColumns
31-Oct-2018 15:15:46	[testng] PASSED: testCounts
31-Oct-2018 15:15:46	[testng] PASSED: testDeletable
31-Oct-2018 15:15:46	[testng] PASSED: testEditable
31-Oct-2018 15:15:46	[testng] PASSED: testInitialisation
31-Oct-2018 15:15:46	[testng] PASSED: testRowDelete
31-Oct-2018 15:15:46	[testng] PASSED: testRowEditable
31-Oct-2018 15:15:46	[testng] PASSED: testRowInsert
31-Oct-2018 15:15:46	[testng] PASSED: testValues
31-Oct-2018 15:15:46	[testng] PASSED: testCreateLinksForNonDynamic
31-Oct-2018 15:15:46	[testng] PASSED: testCreateLinksFromNullSequence
31-Oct-2018 15:15:46	[testng] PASSED: testCreateLinksFromSequence
31-Oct-2018 15:15:46	[testng] PASSED: testLinksWithTargets
31-Oct-2018 15:15:46	[testng] PASSED: testMakeUrlNoRegex
31-Oct-2018 15:15:46	[testng] PASSED: testMakeUrlWithRegex
31-Oct-2018 15:15:46	[testng] PASSED: testUrlLinkCreationNoRegex
31-Oct-2018 15:15:46	[testng] PASSED: testUrlLinkCreationWithRegex
31-Oct-2018 15:15:46	[testng] PASSED: testInitUrlProvider
31-Oct-2018 15:15:46	[testng] PASSED: testSetDefaultUrl
31-Oct-2018 15:15:46	[testng] PASSED: testSetDefaultUrlWrongly
31-Oct-2018 15:15:46	[testng] PASSED: testConstructor_coloursArray
31-Oct-2018 15:15:46	[testng] PASSED: testParseAppletParameter
31-Oct-2018 15:15:46	[testng] PASSED: testToAppletParameter
31-Oct-2018 15:15:46	[testng] PASSED: testDoLoad
31-Oct-2018 15:15:46	[testng] PASSED: testDoLoad_reverseStrand
31-Oct-2018 15:15:46	[testng] PASSED: testDoLoad_vepCsq
31-Oct-2018 15:15:46	[testng] PASSED: testLoadVCFContig
31-Oct-2018 15:15:46	[testng] PASSED: testQuery_plain
31-Oct-2018 15:15:46	[testng] PASSED: testReadVcf_plain
31-Oct-2018 15:15:46	[testng] PASSED: testEventFiring
31-Oct-2018 15:15:46	[testng] PASSED: testGetAbsoluteAlignmentHeight
31-Oct-2018 15:15:46	[testng] PASSED: testGetAbsoluteAlignmentWidth
31-Oct-2018 15:15:46	[testng] PASSED: testGetWrappedMaxScroll
31-Oct-2018 15:15:46	[testng] PASSED: testGetWrappedScrollPosition
31-Oct-2018 15:15:46	[testng] PASSED: testPageUpDown
31-Oct-2018 15:15:46	[testng] PASSED: testPageUpDownWrapped
31-Oct-2018 15:15:46	[testng] PASSED: testScrollRight
31-Oct-2018 15:15:46	[testng] PASSED: testScrollRightWithHidden
31-Oct-2018 15:15:46	[testng] PASSED: testScrollToVisible
31-Oct-2018 15:15:46	[testng] PASSED: testScrollToWrappedVisible
31-Oct-2018 15:15:46	[testng] PASSED: testScrollUp
31-Oct-2018 15:15:46	[testng] PASSED: testScrollUpWithHidden
31-Oct-2018 15:15:46	[testng] PASSED: testScrollUp_wrapped
31-Oct-2018 15:15:46	[testng] PASSED: testSetEndSeq
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartEndRes
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartEndResWrapped
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartEndSeq
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartRes
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartResAndSeq
31-Oct-2018 15:15:46	[testng] PASSED: testSetStartSeq
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportHeight
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportLocation
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportStartAndHeight
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportStartAndWidth
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportStartAndWidthWrapped
31-Oct-2018 15:15:46	[testng] PASSED: testSetViewportWidth
31-Oct-2018 15:15:46	[testng] PASSED: testViewportRanges
31-Oct-2018 15:15:46	[testng] PASSED: testMultipleVisibleRegions
31-Oct-2018 15:15:46	[testng] PASSED: testSimpleVisibleRegions
31-Oct-2018 15:15:46	[testng] PASSED: testVisibleRegionsAtHiddenEdges
31-Oct-2018 15:15:46	[testng] PASSED: testHasNextAndNextEndHidden
31-Oct-2018 15:15:46	[testng] PASSED: testHasNextAndNextNoHidden
31-Oct-2018 15:15:46	[testng] PASSED: testHasNextAndNextStartHidden
31-Oct-2018 15:15:46	[testng] PASSED: testHasNextAndNextWithHidden
31-Oct-2018 15:15:46	[testng] PASSED: testLastNextEndHidden
31-Oct-2018 15:15:46	[testng] PASSED: testLastNextNoHidden
31-Oct-2018 15:15:46	[testng] PASSED: testLastNextStartHidden
31-Oct-2018 15:15:46	[testng] PASSED: testLastNextWithHidden
31-Oct-2018 15:15:46	[testng] PASSED: testRemove
31-Oct-2018 15:15:46	[testng] FAILED: TestUpdateLayout_endRes
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected [156] but found [66]
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.fail(Assert.java:94)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:125)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:372)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:382)
31-Oct-2018 15:15:46	[testng] at jalview.gui.AlignmentPanelTest.__CLR4_2_1b5wha22x2p(AlignmentPanelTest.java:246)
31-Oct-2018 15:15:46	[testng] at jalview.gui.AlignmentPanelTest.TestUpdateLayout_endRes(AlignmentPanelTest.java:229)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testLaunchAndExit
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: Couldn't launch chimera
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24)
31-Oct-2018 15:15:46	[testng] at jalview.ext.rbvi.chimera.ChimeraConnect.testLaunchAndExit(ChimeraConnect.java:49)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testFindXrefSequences_forGeneAndTranscripts
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_16yj4942se0(CrossRefTest.java:535)
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_forGeneAndTranscripts(CrossRefTest.java:469)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testFindXrefSequences_uniprotEmblManyToMany
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_1nurnsm2ser(CrossRefTest.java:711)
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_uniprotEmblManyToMany(CrossRefTest.java:566)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testFindXrefSequences_withFetch
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.__CLR4_2_1ruxmrc2sde(CrossRefTest.java:452)
31-Oct-2018 15:15:46	[testng] at jalview.analysis.CrossRefTest.testFindXrefSequences_withFetch(CrossRefTest.java:415)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testCut_gappedWithFeatures
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected:<1> but was:<3>
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
31-Oct-2018 15:15:46	[testng] at jalview.commands.EditCommandTest.__CLR4_2_1b9p4i3axx(EditCommandTest.java:868)
31-Oct-2018 15:15:46	[testng] at jalview.commands.EditCommandTest.testCut_gappedWithFeatures(EditCommandTest.java:848)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testCut_withFeatures
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected:<4> but was:<5>
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
31-Oct-2018 15:15:46	[testng] at jalview.commands.EditCommandTest.__CLR4_2_1l07oop3av8(EditCommandTest.java:699)
31-Oct-2018 15:15:46	[testng] at jalview.commands.EditCommandTest.testCut_withFeatures(EditCommandTest.java:661)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testIdentify("examples/rf00031_folded.stk", Stockholm)
31-Oct-2018 15:15:46	[testng] jalview.io.FileFormatException: Problem opening rf00031_folded.stk : FILE CANNOT BE OPENED FOR READING
31-Oct-2018 15:15:46	[testng] at jalview.io.IdentifyFile.identify(IdentifyFile.java:101)
31-Oct-2018 15:15:46	[testng] at jalview.io.IdentifyFileTest.__CLR4_2_163b86u3440(IdentifyFileTest.java:50)
31-Oct-2018 15:15:46	[testng] at jalview.io.IdentifyFileTest.testIdentify(IdentifyFileTest.java:47)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testAlignmentLoader
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at jalview.ext.jmol.JmolParserTest.__CLR4_2_1b9f5ij3usz(JmolParserTest.java:119)
31-Oct-2018 15:15:46	[testng] at jalview.ext.jmol.JmolParserTest.testAlignmentLoader(JmolParserTest.java:114)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testFileParser
31-Oct-2018 15:15:46	[testng] java.io.IOException: Problem opening 1GAQ.txt : FILE CANNOT BE OPENED FOR READING
31-Oct-2018 15:15:46	[testng] at jalview.io.FileParse.parse(FileParse.java:370)
31-Oct-2018 15:15:46	[testng] at jalview.io.FileParse.<init>(FileParse.java:329)
31-Oct-2018 15:15:46	[testng] at jalview.io.AlignFile.<init>(AlignFile.java:137)
31-Oct-2018 15:15:46	[testng] at jalview.io.StructureFile.<init>(StructureFile.java:104)
31-Oct-2018 15:15:46	[testng] at mc_view.PDBfile.<init>(PDBfile.java:53)
31-Oct-2018 15:15:46	[testng] at jalview.ext.jmol.JmolParserTest.__CLR4_2_19oqq383ut4(JmolParserTest.java:128)
31-Oct-2018 15:15:46	[testng] at jalview.ext.jmol.JmolParserTest.testFileParser(JmolParserTest.java:125)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: updateCacheTest
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError
31-Oct-2018 15:15:46	[testng] at org.junit.Assert.fail(Assert.java:86)
31-Oct-2018 15:15:46	[testng] at org.junit.Assert.assertTrue(Assert.java:41)
31-Oct-2018 15:15:46	[testng] at org.junit.Assert.assertTrue(Assert.java:52)
31-Oct-2018 15:15:46	[testng] at jalview.io.cache.JvCacheableInputBoxTest.__CLR4_2_1shislu3gio(JvCacheableInputBoxTest.java:68)
31-Oct-2018 15:15:46	[testng] at jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest(JvCacheableInputBoxTest.java:51)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testIsControlDown_mac
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected [false] but found [true]
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.fail(Assert.java:94)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertFalse(Assert.java:63)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertFalse(Assert.java:73)
31-Oct-2018 15:15:46	[testng] at jalview.util.PlatformTest.__CLR4_2_16ar2hy3eu9(PlatformTest.java:65)
31-Oct-2018 15:15:46	[testng] at jalview.util.PlatformTest.testIsControlDown_mac(PlatformTest.java:53)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testAddFeatureLinks
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected:<5> but was:<6>
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:252)
31-Oct-2018 15:15:46	[testng] at jalview.gui.PopupMenuTest.__CLR4_2_1wjq27t33u7(PopupMenuTest.java:552)
31-Oct-2018 15:15:46	[testng] at jalview.gui.PopupMenuTest.testAddFeatureLinks(PopupMenuTest.java:503)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testCalculateWrappedGeometry_fromScrolled
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: expected [3] but found [13]
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.fail(Assert.java:94)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.failNotEquals(Assert.java:496)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:125)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:372)
31-Oct-2018 15:15:46	[testng] at org.testng.Assert.assertEquals(Assert.java:382)
31-Oct-2018 15:15:46	[testng] at jalview.gui.SeqCanvasTest.__CLR4_2_1ea6dhj47xn(SeqCanvasTest.java:334)
31-Oct-2018 15:15:46	[testng] at jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_fromScrolled(SeqCanvasTest.java:310)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testCreateFastaSequenceIndex
31-Oct-2018 15:15:46	[testng] java.lang.NoSuchMethodError: htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaIndexFileName(Ljava/nio/file/Path;)Ljava/nio/file/Path;
31-Oct-2018 15:15:46	[testng] at htsjdk.samtools.reference.FastaSequenceIndexCreator.create(FastaSequenceIndexCreator.java:57)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.HtsContigDb.createFastaSequenceIndex(HtsContigDb.java:65)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1fsv57j2vbn(TestHtsContigDb.java:101)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex(TestHtsContigDb.java:94)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testGetSequenceProxy
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_14987dc2vb8(TestHtsContigDb.java:48)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy(TestHtsContigDb.java:46)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testGetSequenceProxy_indexed
31-Oct-2018 15:15:46	[testng] java.lang.NullPointerException
31-Oct-2018 15:15:46	[testng] at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1tl2la62vbj(TestHtsContigDb.java:77)
31-Oct-2018 15:15:46	[testng] at jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexed(TestHtsContigDb.java:75)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testCopyConstructor
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1frqtvq3eoo(ViewStyleTest.java:73)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.testCopyConstructor(ViewStyleTest.java:65)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] FAILED: testEquals
31-Oct-2018 15:15:46	[testng] java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
31-Oct-2018 15:15:46	[testng] at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1s4e6083eqr(ViewStyleTest.java:215)
31-Oct-2018 15:15:46	[testng] at jalview.viewmodel.styles.ViewStyleTest.testEquals(ViewStyleTest.java:201)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
31-Oct-2018 15:15:46	[testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
31-Oct-2018 15:15:46	[testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
31-Oct-2018 15:15:46	[testng] at java.lang.reflect.Method.invoke(Method.java:498)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
31-Oct-2018 15:15:46	[testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
31-Oct-2018 15:15:46	[testng] at org.testng.TestRunner.run(TestRunner.java:621)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
31-Oct-2018 15:15:46	[testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.run(TestNG.java:1009)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
31-Oct-2018 15:15:46	[testng] at org.testng.TestNG.main(TestNG.java:1285)
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] ===============================================
31-Oct-2018 15:15:46	[testng] Ant test
31-Oct-2018 15:15:46	[testng] Tests run: 1255, Failures: 19, Skips: 0
31-Oct-2018 15:15:46	[testng] ===============================================
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:46	[testng] ===============================================
31-Oct-2018 15:15:46	[testng] Ant suite
31-Oct-2018 15:15:46	[testng] Total tests run: 1255, Failures: 19, Skips: 0
31-Oct-2018 15:15:46	[testng] ===============================================
31-Oct-2018 15:15:46	[testng]
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@3b192d32: 206 ms
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by org.testng.reporters.XMLReporter@6ed3ef1: 82 ms
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 36 ms
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by org.testng.reporters.jq.Main@ed17bee: 138 ms
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2@383534aa: 29 ms
31-Oct-2018 15:15:47	[testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@136432db: 70 ms
31-Oct-2018 15:15:48	[testng] The tests failed.
31-Oct-2018 15:15:48
31-Oct-2018 15:15:48	clover.save-history:
31-Oct-2018 15:15:48	[clover-historypoint] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
31-Oct-2018 15:15:48	[clover-historypoint] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
31-Oct-2018 15:15:48	[clover-historypoint] Clover free edition.
31-Oct-2018 15:15:51	[clover-historypoint] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.cloverhistory/jalviewX/clover-20181031151547.xml.gz'
31-Oct-2018 15:15:52
31-Oct-2018 15:15:52	clover.report:
31-Oct-2018 15:15:52	[clover-report] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
31-Oct-2018 15:15:52	[clover-report] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
31-Oct-2018 15:15:52	[clover-report] Clover free edition.
31-Oct-2018 15:15:52	[clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'
31-Oct-2018 15:15:52	[clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'
31-Oct-2018 15:15:52	[clover-report] Loading historical coverage data from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.cloverhistory/jalviewX'
31-Oct-2018 15:15:54	[clover-report] Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX'
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBChain.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBCanvas.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/AppletPDBViewer.java (No such file or directory)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Zsort.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Bond.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBCanvas.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/PDBfile.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/MCMatrix.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Residue.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/src/MCview/Atom.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBfileTest.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/BondTest.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/ResidueTest.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/PDBChainTest.java (No such file or directory)
31-Oct-2018 15:16:08	[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)
31-Oct-2018 15:16:08	[clover-report] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/test/MCview/AtomTest.java (No such file or directory)
31-Oct-2018 15:16:26	[clover-report] Done. Processed 106 packages in 31700ms (299ms per package).
31-Oct-2018 15:16:27	[clover-report] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX/clover.xml'
31-Oct-2018 15:16:27	[clover-report] Writing historical report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX'
31-Oct-2018 15:16:32	[clover-report] Read 29 history points.
31-Oct-2018 15:16:32	[clover-report] using movers interval of 2 days
31-Oct-2018 15:16:32	[clover-report] using movers interval of 2 days
31-Oct-2018 15:16:32	[clover-report] Writing JSON historical-data to: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/clover/jalviewX/historical-json.js
31-Oct-2018 15:16:32	[clover-report] Done.
31-Oct-2018 15:16:32
31-Oct-2018 15:16:32	BUILD SUCCESSFUL
31-Oct-2018 15:16:32	Total time: 3 minutes 8 seconds
31-Oct-2018 15:16:33	Finished task 'Clover TestNG Suite' with result: Success
31-Oct-2018 15:16:33	Starting task 'Process Jalview TestNG Suite' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
31-Oct-2018 15:16:33	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1...
31-Oct-2018 15:16:36	Failing task since 19 failing test cases were found.
31-Oct-2018 15:16:36	Finished task 'Process Jalview TestNG Suite' with result: Failed
31-Oct-2018 15:16:36	Starting task 'build' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
31-Oct-2018 15:16:36	Beginning to execute external process for build 'Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job #207 (JB-JDB1-JOB1-207)' ... 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=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-207 bamboo_repository_2228226_revision_number=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 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=207 bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-207 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=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 bamboo_buildTimeStamp=2018-10-31T15:13:19.425Z bamboo_repository_previous_revision_number=b11a3470c5ccd9eeb4e80c1e85b282dcc8111b4a bamboo_planRepository_previousRevision=b11a3470c5ccd9eeb4e80c1e85b282dcc8111b4a bamboo_repository_git_branch=Jalview-BH/JAL-3026 bamboo_buildResultKey=JB-JDB1-JOB1-207 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=7434a5c8bf464bf806a6e88a17bae3f217a5ec68 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=b11a3470c5ccd9eeb4e80c1e85b282dcc8111b4a 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=b11a3470c5ccd9eeb4e80c1e85b282dcc8111b4a 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
31-Oct-2018 15:16:36	Buildfile: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml
31-Oct-2018 15:16:37
31-Oct-2018 15:16:37	init:
31-Oct-2018 15:16:37
31-Oct-2018 15:16:37	prepare:
31-Oct-2018 15:16:37
31-Oct-2018 15:16:37	build:
31-Oct-2018 15:16:37	[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
31-Oct-2018 15:16:37	[javac] Compiling 1 source file to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes
31-Oct-2018 15:16:39
31-Oct-2018 15:16:39	buildPropertiesFile:
31-Oct-2018 15:16:40	[properties] write property file /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes/.build_properties
31-Oct-2018 15:16:40
31-Oct-2018 15:16:40	linkcheck:
31-Oct-2018 15:16:40	[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
31-Oct-2018 15:16:40	[java] Checking help file links
31-Oct-2018 15:16:41	[java]
31-Oct-2018 15:16:41	[java] Results:
31-Oct-2018 15:16:41	[java] 132 distinct help targets
31-Oct-2018 15:16:41	[java] 132 help mappings
31-Oct-2018 15:16:41	[java] 0 invalid targets
31-Oct-2018 15:16:41	[java] 21 unused targets
31-Oct-2018 15:16:41	[java] uniprotfetcher: html/features/uniprotsequencefetcher.html
31-Oct-2018 15:16:41	[java] overviewprefs: html/features/preferences.html#overview
31-Oct-2018 15:16:41	[java] cdnafeatures: html/features/codingfeatures.html
31-Oct-2018 15:16:41	[java] ensemblfetch: html/features/ensemblsequencefetcher.html
31-Oct-2018 15:16:41	[java] io.modellerpir: html/io/modellerpir.html
31-Oct-2018 15:16:41	[java] pdbmcviewer: html/features/pdbviewer.html
31-Oct-2018 15:16:41	[java] groovy.colours: html/features/groovy.html#groovyColours
31-Oct-2018 15:16:41	[java] seqmappings: html/features/seqmappings.html
31-Oct-2018 15:16:41	[java] splitframe.mirrorfonts: html/features/splitView.html#mirror
31-Oct-2018 15:16:41	[java] subtMatrices.pam250: html/calculations/scorematrices.html#pam250
31-Oct-2018 15:16:41	[java] search: html/features/search.html
31-Oct-2018 15:16:41	[java] viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
31-Oct-2018 15:16:41	[java] alformats: html/io/fileformats.html
31-Oct-2018 15:16:41	[java] strucprefs: html/features/preferences.html#structure
31-Oct-2018 15:16:41	[java] siftsmapping: html/features/siftsmapping.html
31-Oct-2018 15:16:41	[java] newkeys: html/features/newkeystrokes.html
31-Oct-2018 15:16:41	[java] seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
31-Oct-2018 15:16:41	[java] jalarchive: html/features/jalarchive.html
31-Oct-2018 15:16:41	[java] newsreader: html/webServices/newsreader.html
31-Oct-2018 15:16:41	[java] popMenuAddref: html/menus/popupMenu.html#addrefannot
31-Oct-2018 15:16:41	[java] overview: html/features/overview.html
31-Oct-2018 15:16:41	[java] 0 invalid map urls
31-Oct-2018 15:16:41	[java] 0 invalid image attributes
31-Oct-2018 15:16:41	[java] 352 internal href links (62 with anchors)
31-Oct-2018 15:16:41	[java] 0 invalid internal href links
31-Oct-2018 15:16:41	[java] 0 invalid internal anchor links
31-Oct-2018 15:16:41	[java] 83 external href links
31-Oct-2018 15:16:41	[java] External links not verified as internet not available
31-Oct-2018 15:16:41	[java] * Success *
31-Oct-2018 15:16:42
31-Oct-2018 15:16:42	buildindices:
31-Oct-2018 15:16:44
31-Oct-2018 15:16:44	makedist:
31-Oct-2018 15:16:44	[jar] Building jar: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/dist/jalview.jar
31-Oct-2018 15:16:48	[copy] Copying 52 files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/dist
31-Oct-2018 15:16:49
31-Oct-2018 15:16:49	BUILD SUCCESSFUL
31-Oct-2018 15:16:49	Total time: 13 seconds
31-Oct-2018 15:16:49	Finished task 'build' with result: Success
31-Oct-2018 15:16:49	Running post build plugin 'NCover Results Collector'
31-Oct-2018 15:16:49	Running post build plugin 'Artifact Copier'
31-Oct-2018 15:16:49	Publishing an artifact: jalview-jars
31-Oct-2018 15:16:50	Finished publishing of artifact Shared artifact: [jalview-jars], pattern: [*/.*] anchored at: [dist] in 62.17 ms
31-Oct-2018 15:16:50	Publishing an artifact: Clover Report (System)
31-Oct-2018 15:24:29	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [*/.*] anchored at: [clover] in 7.651 min
31-Oct-2018 15:24:29	Running post build plugin 'npm Cache Cleanup'
31-Oct-2018 15:24:29	Running post build plugin 'Clover Results Collector'
31-Oct-2018 15:24:29	Running post build plugin 'Docker Container Cleanup'
31-Oct-2018 15:24:29	Finalising the build...
31-Oct-2018 15:24:29	Stopping timer.
31-Oct-2018 15:24:29	Build JB-JDB1-JOB1-207 completed.
31-Oct-2018 15:24:29	Running on server: post build plugin 'NCover Results Collector'
31-Oct-2018 15:24:29	Running on server: post build plugin 'Build Hanging Detection Configuration'
31-Oct-2018 15:24:29	Running on server: post build plugin 'Clover Delta Calculator'
31-Oct-2018 15:24:29	Running on server: post build plugin 'Maven Dependencies Postprocessor'
31-Oct-2018 15:24:29	All post build plugins have finished
31-Oct-2018 15:24:29	Generating build results summary...
31-Oct-2018 15:24:29	Saving build results to disk...
31-Oct-2018 15:24:29	Logging substituted variables...
31-Oct-2018 15:24:29	Indexing build results...
31-Oct-2018 15:24:29	Finished building JB-JDB1-JOB1-207.

Build #207

Build: #207 failed

Job: Default Job failed

Stages & jobs

Default Stage

Build log