Build #208

Build: #208 failed Changes by Mungo Carstairs

Build result summary

Details

Completed
Duration
14 minutes
Labels
None
Agent
Default Agent
Revision
f20ff42eac30f33cb69635ba3217a6224dbeb555 f20ff42eac30f33cb69635ba3217a6224dbeb555
Total tests
1253
Failing since
#207 (Changes by Mungo Carstairs – )

Responsible

This build has been failing since #207
No one has taken responsibility

Code commits

Author Commit Message Commit date
Mungo Carstairs Mungo Carstairs f20ff42eac30f33cb69635ba3217a6224dbeb555 f20ff42eac30f33cb69635ba3217a6224dbeb555 JAL-3048 JAL-3056 reinstate save/load project, colour scheme dialogs in JS

Tests

Existing test failures 19
Status Test Failing since View job Duration 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.CrossRefTest.__CLR4_2_1ruxmrc2sde(CrossRefTest.java:452)
	at jalview.analysis.CrossRefTest.testFindXrefSequences_withFetch(CrossRefTest.java:415)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
(21 more lines...)
 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.CrossRefTest.__CLR4_2_1nurnsm2ser(CrossRefTest.java:711)
	at jalview.analysis.CrossRefTest.testFindXrefSequences_uniprotEmblManyToMany(CrossRefTest.java:566)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
(21 more lines...)
 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.CrossRefTest.__CLR4_2_16yj4942se0(CrossRefTest.java:535)
	at jalview.analysis.CrossRefTest.testFindXrefSequences_forGeneAndTranscripts(CrossRefTest.java:469)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
(21 more lines...)
 
Classname: java.lang.AssertionError
Message: expected:<4> but was:<5>
Stacktrace:
java.lang.AssertionError: expected:<4> but was:<5>
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
(26 more lines...)
 
Classname: java.lang.AssertionError
Message: expected:<1> but was:<3>
Stacktrace:
java.lang.AssertionError: expected:<1> but was:<3>
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
(26 more lines...)
 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
	at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
	at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
	at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_14987dc2vb8(TestHtsContigDb.java:48)
(24 more lines...)
 
Classname: java.lang.NoSuchMethodError
Message: htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaIndexFileName(Ljava/nio/file/Path;)Ljava/nio/file/Path;
Stacktrace:
java.lang.NoSuchMethodError: htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaIndexFileName(Ljava/nio/file/Path;)Ljava/nio/file/Path;
	at htsjdk.samtools.reference.FastaSequenceIndexCreator.create(FastaSequenceIndexCreator.java:57)
	at jalview.ext.htsjdk.HtsContigDb.createFastaSequenceIndex(HtsContigDb.java:65)
	at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1fsv57j2vbn(TestHtsContigDb.java:101)
	at jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex(TestHtsContigDb.java:94)
(23 more lines...)
 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:69)
	at jalview.ext.htsjdk.HtsContigDb.initSource(HtsContigDb.java:104)
	at jalview.ext.htsjdk.HtsContigDb.<init>(HtsContigDb.java:79)
	at jalview.ext.htsjdk.TestHtsContigDb.__CLR4_2_1tl2la62vbj(TestHtsContigDb.java:77)
(24 more lines...)
 
Classname: java.io.IOException
Message: Problem opening 1GAQ.txt : FILE CANNOT BE OPENED FOR READING
Stacktrace:
java.io.IOException: Problem opening 1GAQ.txt : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.parse(FileParse.java:370)
	at jalview.io.FileParse.<init>(FileParse.java:329)
	at jalview.io.AlignFile.<init>(AlignFile.java:137)
	at jalview.io.StructureFile.<init>(StructureFile.java:104)
(26 more lines...)
 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.ext.jmol.JmolParserTest.__CLR4_2_1b9f5ij3usz(JmolParserTest.java:119)
	at jalview.ext.jmol.JmolParserTest.testAlignmentLoader(JmolParserTest.java:114)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
(21 more lines...)
 
Classname: java.lang.AssertionError
Message: Couldn't launch chimera
Stacktrace:
java.lang.AssertionError: Couldn't launch chimera
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24)
	at jalview.ext.rbvi.chimera.ChimeraConnect.testLaunchAndExit(ChimeraConnect.java:49)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
(22 more lines...)
 
Classname: java.lang.AssertionError
Message: expected [156] but found [66]
Stacktrace:
java.lang.AssertionError: expected [156] but found [66]
	at org.testng.Assert.fail(Assert.java:94)
	at org.testng.Assert.failNotEquals(Assert.java:496)
	at org.testng.Assert.assertEquals(Assert.java:125)
	at org.testng.Assert.assertEquals(Assert.java:372)
(26 more lines...)
 
Classname: java.lang.AssertionError
Message: expected:<5> but was:<6>
Stacktrace:
java.lang.AssertionError: expected:<5> but was:<6>
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
	at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
(26 more lines...)
 
Classname: java.lang.AssertionError
Message: expected [3] but found [13]
Stacktrace:
java.lang.AssertionError: expected [3] but found [13]
	at org.testng.Assert.fail(Assert.java:94)
	at org.testng.Assert.failNotEquals(Assert.java:496)
	at org.testng.Assert.assertEquals(Assert.java:125)
	at org.testng.Assert.assertEquals(Assert.java:372)
(26 more lines...)
 
Classname: java.lang.AssertionError
Message: null
Stacktrace:
java.lang.AssertionError
	at org.junit.Assert.fail(Assert.java:86)
	at org.junit.Assert.assertTrue(Assert.java:41)
	at org.junit.Assert.assertTrue(Assert.java:52)
	at jalview.io.cache.JvCacheableInputBoxTest.__CLR4_2_1shislu3gio(JvCacheableInputBoxTest.java:68)
(24 more lines...)
 
Classname: jalview.io.FileFormatException
Message: Problem opening rf00031_folded.stk : FILE CANNOT BE OPENED FOR READING
Stacktrace:
jalview.io.FileFormatException: Problem opening rf00031_folded.stk : FILE CANNOT BE OPENED FOR READING
	at jalview.io.IdentifyFile.identify(IdentifyFile.java:101)
	at jalview.io.IdentifyFileTest.__CLR4_2_163b86u3440(IdentifyFileTest.java:50)
	at jalview.io.IdentifyFileTest.testIdentify(IdentifyFileTest.java:47)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
(22 more lines...)
 
Classname: java.lang.AssertionError
Message: expected [false] but found [true]
Stacktrace:
java.lang.AssertionError: expected [false] but found [true]
	at org.testng.Assert.fail(Assert.java:94)
	at org.testng.Assert.failNotEquals(Assert.java:496)
	at org.testng.Assert.assertFalse(Assert.java:63)
	at org.testng.Assert.assertFalse(Assert.java:73)
(25 more lines...)
 
Classname: java.lang.AssertionError
Message: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
Stacktrace:
java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
	at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1s4e6083eqr(ViewStyleTest.java:215)
	at jalview.viewmodel.styles.ViewStyleTest.testEquals(ViewStyleTest.java:201)
(23 more lines...)
 
Classname: java.lang.AssertionError
Message: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
Stacktrace:
java.lang.AssertionError: Unhandled field type (add to test): __CLR4_2_1_TEST_NAME_SNIFFER:interface com_atlassian_clover.TestNameSniffer
	at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
	at jalview.viewmodel.styles.ViewStyleTest.changeValue(ViewStyleTest.java:170)
	at jalview.viewmodel.styles.ViewStyleTest.__CLR4_2_1frqtvq3eoo(ViewStyleTest.java:73)
	at jalview.viewmodel.styles.ViewStyleTest.testCopyConstructor(ViewStyleTest.java:65)
(23 more lines...)

JIRA issues

IssueDescriptionStatus
Unknown Issue TypeJAL-3048Could not obtain issue details from JIRA
Unknown Issue TypeJAL-3056Could not obtain issue details from JIRA

Shared artifacts

Artifact File size
jalview-jars 36 MB