Build #207

Build: #207 failed Changes by Mungo Carstairs

Build result summary

Details

Completed
Duration
11 minutes
Labels
None
Agent
Default Agent
Revision
7434a5c8bf464bf806a6e88a17bae3f217a5ec68 7434a5c8bf464bf806a6e88a17bae3f217a5ec68
Total tests
1253

Responsible

No one has taken responsibility for this failure

Code commits

Author Commit Message Commit date
Mungo Carstairs Mungo Carstairs 7434a5c8bf464bf806a6e88a17bae3f217a5ec68 7434a5c8bf464bf806a6e88a17bae3f217a5ec68 JAL-3026 skip unsupported HttpURLConnection methods 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-3026Could not obtain issue details from JIRA

Shared artifacts

Artifact File size
jalview-jars 36 MB