Testsuite: org.openscience.cdk.modulesuites.MioTests
Tests run: 596, Failures: 2, Errors: 3, Time elapsed: 10.954 sec
------------- Standard Output ---------------
io.PCCompoundXMLReader#read does not have a test method
io.PCCompoundXMLReader refers to a non-existing test class: org.openscience.cdk.io.PCCompounsXMLReaderTest
io.MDLRXNWriter#setWriter does not have a test method
io.MDLRXNWriter#setWriter does not have a test method
io.MDLRXNWriter#setRdFields does not have a test method
io.MDLRXNWriter#write does not have a test method
io.CMLReader#registerConvention does not have a test method
io.CMLReader#read does not have a test method
io.CMLReader refers to a non-existing test class: org.openscience.cdk.io.CMLReaderTest
io.random.DefaultRandomAccessChemObjectReader#getIOSettings does not have a test method
io.random.DefaultRandomAccessChemObjectReader#addChemObjectIOListener does not have a test method
io.random.DefaultRandomAccessChemObjectReader#removeChemObjectIOListener does not have a test method
io.random.DefaultRandomAccessChemObjectReader#setReaderMode does not have a test method
io.random.DefaultRandomAccessChemObjectReader#fireIOSettingQuestion does not have a test method
io.random.DefaultRandomAccessChemObjectReader did not have a TestClass annotation
io.random.RandomAccessReader#setChemObjectReader does not have a test method
io.random.RandomAccessReader#addChemObjectIOListener does not have a test method
io.random.RandomAccessReader#removeChemObjectIOListener does not have a test method
io.random.RandomAccessReader#readRecord does not have a test method
io.random.RandomAccessReader#readRecord does not have a test method
io.random.RandomAccessReader#readContent does not have a test method
io.random.RandomAccessReader#processContent does not have a test method
io.random.RandomAccessReader#isRecordEnd does not have a test method
io.random.RandomAccessReader#saveIndex does not have a test method
io.random.RandomAccessReader#loadIndex does not have a test method
io.random.RandomAccessReader#makeIndex does not have a test method
io.random.RandomAccessReader#getIndexFile does not have a test method
io.random.RandomAccessReader#getChemObjectReader does not have a test method
io.random.RandomAccessReader#createChemObjectReader does not have a test method
io.random.RandomAccessReader#getCurrentRecord does not have a test method
io.random.RandomAccessReader#isIndexCreated does not have a test method
io.random.RandomAccessReader#setIndexCreated does not have a test method
io.random.RandomAccessReader#add does not have a test method
io.random.RandomAccessReader#add does not have a test method
io.random.RandomAccessReader#finalize does not have a test method
io.random.RandomAccessReader#toString does not have a test method
io.random.RandomAccessReader#size does not have a test method
io.random.RandomAccessReader#first does not have a test method
io.random.RandomAccessReader#first does not have a test method
io.random.RandomAccessReader#hasNext does not have a test method
io.random.RandomAccessReader#next does not have a test method
io.random.RandomAccessReader#next does not have a test method
io.random.RandomAccessReader#last does not have a test method
io.random.RandomAccessReader#last does not have a test method
io.random.RandomAccessReader#set does not have a test method
io.random.RandomAccessReader#set does not have a test method
io.random.RandomAccessReader#previousIndex does not have a test method
io.random.RandomAccessReader#hasPrevious does not have a test method
io.random.RandomAccessReader#previous does not have a test method
io.random.RandomAccessReader#previous does not have a test method
io.random.RandomAccessReader#nextIndex does not have a test method
io.random.RandomAccessReader#resize does not have a test method
io.random.RandomAccessReader did not have a TestClass annotation
io.random.RandomAccessSDFReader#processContent does not have a test method
io.random.RandomAccessSDFReader#isRecordEnd does not have a test method
io.random.RandomAccessSDFReader#createChemObjectReader does not have a test method
io.random.RandomAccessSDFReader#remove does not have a test method
io.random.RandomAccessSDFReader did not have a TestClass annotation
io.GhemicalMMReader#read does not have a test method
io.GhemicalMMReader refers to a non-existing test class: org.openscience.cdk.io.GhemicalMMReaderTest
io.CDKSourceCodeWriter#getIOSettings does not have a test method
io.CDKSourceCodeWriter#setWriter does not have a test method
io.CDKSourceCodeWriter#setWriter does not have a test method
io.CDKSourceCodeWriter#getSupportedDataFeatures does not have a test method
io.CDKSourceCodeWriter#getRequiredDataFeatures does not have a test method
io.CDKSourceCodeWriter#writeMolecule does not have a test method
io.CDKSourceCodeWriter#writeAtomContainer does not have a test method
io.CDKSourceCodeWriter#writeAtom does not have a test method
io.CDKSourceCodeWriter#writeBond does not have a test method
io.CDKSourceCodeWriter#write does not have a test method
io.pubchemxml.PubChemXMLHelper#parseMolecule does not have a test method
io.pubchemxml.PubChemXMLHelper#parseCompoundsBlock does not have a test method
io.pubchemxml.PubChemXMLHelper#parseSubstance does not have a test method
io.pubchemxml.PubChemXMLHelper#getSID does not have a test method
io.pubchemxml.PubChemXMLHelper#getCID does not have a test method
io.pubchemxml.PubChemXMLHelper#parseAtomElements does not have a test method
io.pubchemxml.PubChemXMLHelper#parserAtomBlock does not have a test method
io.pubchemxml.PubChemXMLHelper#parserCompoundInfoData does not have a test method
io.pubchemxml.PubChemXMLHelper#parseAtomCharges does not have a test method
io.pubchemxml.PubChemXMLHelper#parserBondBlock does not have a test method
io.pubchemxml.PubChemXMLHelper#parserCoordBlock does not have a test method
io.pubchemxml.PubChemXMLHelper did not have a TestClass annotation
io.HINReader#read does not have a test method
io.Gaussian03Reader#read does not have a test method
io.Gaussian03Reader did not have a TestClass annotation
io.MDLRXNV2000Reader#read does not have a test method
io.ReaderFactory#createReader does not have a test method
io.ReaderFactory#createReader does not have a test method
io.ReaderFactory#createReader does not have a test method
io.ReaderFactory#registerFormat does not have a test method
io.ReaderFactory#getFormats does not have a test method
io.ReaderFactory did not have a TestClass annotation
io.WriterFactory#formatCount does not have a test method
io.WriterFactory#findChemFormats does not have a test method
io.WriterFactory#createWriter does not have a test method
io.WriterFactory#registerWriter does not have a test method
io.WriterFactory did not have a TestClass annotation
io.CTXReader#read does not have a test method
io.MDLWriter#getIOSettings does not have a test method
io.MDLWriter#customizeJob does not have a test method
io.MDLWriter#setWriter does not have a test method
io.MDLWriter#setWriter does not have a test method
io.MDLWriter#writeMolecule does not have a test method
io.MDLWriter#write does not have a test method
io.Gaussian98Reader#getIOSettings does not have a test method
io.Gaussian98Reader#read does not have a test method
io.ShelXReader#read does not have a test method
io.MDLV3000Reader#getIOSettings does not have a test method
io.MDLV3000Reader#readMolecule does not have a test method
io.MDLV3000Reader#readConnectionTable does not have a test method
io.MDLV3000Reader#readAtomBlock does not have a test method
io.MDLV3000Reader#readBondBlock does not have a test method
io.MDLV3000Reader#readSGroup does not have a test method
io.MDLV3000Reader#exhaustStringTokenizer does not have a test method
io.MDLV3000Reader#isReady does not have a test method
io.MDLV3000Reader#readLine does not have a test method
io.MDLV3000Reader#read does not have a test method
io.MDLV3000Reader#readHeader does not have a test method
io.cml.PDBConvention#characterData does not have a test method
io.cml.PDBConvention#newSequence does not have a test method
io.cml.PDBConvention#storeData does not have a test method
io.cml.PDBConvention#storeAtomData does not have a test method
io.cml.PDBConvention#endDocument does not have a test method
io.cml.PDBConvention#startElement does not have a test method
io.cml.PDBConvention#endElement does not have a test method
io.cml.PDBConvention did not have a TestClass annotation
io.cml.MDLMolConvention#characterData does not have a test method
io.cml.MDLMolConvention#startDocument does not have a test method
io.cml.MDLMolConvention#startElement does not have a test method
io.cml.MDLMolConvention did not have a TestClass annotation
io.cml.CMLReactionModule#startElement does not have a test method
io.cml.CMLReactionModule#endElement does not have a test method
io.cml.CMLReactionModule did not have a TestClass annotation
io.cml.CDKConvention#characterData does not have a test method
io.cml.CDKConvention#startDocument does not have a test method
io.cml.CDKConvention#startElement does not have a test method
io.cml.CDKConvention did not have a TestClass annotation
io.cml.CMLHandler#registerConvention does not have a test method
io.cml.CMLHandler#doctypeDecl does not have a test method
io.cml.CMLHandler#startDocument does not have a test method
io.cml.CMLHandler#endDocument does not have a test method
io.cml.CMLHandler#startElement does not have a test method
io.cml.CMLHandler#endElement does not have a test method
io.cml.CMLHandler#characters does not have a test method
io.cml.CMLHandler did not have a TestClass annotation
io.cml.CMLCoreModule#newMolecule does not have a test method
io.cml.CMLCoreModule#characterData does not have a test method
io.cml.CMLCoreModule#returnChemFile does not have a test method
io.cml.CMLCoreModule#inherit does not have a test method
io.cml.CMLCoreModule#storeData does not have a test method
io.cml.CMLCoreModule#storeAtomData does not have a test method
io.cml.CMLCoreModule#storeBondData does not have a test method
io.cml.CMLCoreModule#newAtomData does not have a test method
io.cml.CMLCoreModule#newMoleculeData does not have a test method
io.cml.CMLCoreModule#newFormulaData does not have a test method
io.cml.CMLCoreModule#newBondData does not have a test method
io.cml.CMLCoreModule#newCrystalData does not have a test method
io.cml.CMLCoreModule#addArrayElementsTo does not have a test method
io.cml.CMLCoreModule#notify does not have a test method
io.cml.CMLCoreModule#startDocument does not have a test method
io.cml.CMLCoreModule#endDocument does not have a test method
io.cml.CMLCoreModule#startElement does not have a test method
io.cml.CMLCoreModule#endElement does not have a test method
io.cml.CMLCoreModule did not have a TestClass annotation
io.cml.QSARConvention#startElement does not have a test method
io.cml.QSARConvention#endElement does not have a test method
io.cml.QSARConvention did not have a TestClass annotation
io.cml.CMLStack#toString does not have a test method
io.cml.CMLStack#length does not have a test method
io.cml.PMPConvention#characterData does not have a test method
io.cml.PMPConvention#startDocument does not have a test method
io.cml.PMPConvention#startElement does not have a test method
io.cml.PMPConvention did not have a TestClass annotation
io.cml.CMLResolver#getExternalSubset does not have a test method
io.cml.CMLResolver#resolveEntity does not have a test method
io.cml.CMLResolver#resolveEntity does not have a test method
io.cml.CMLResolver did not have a TestClass annotation
io.cml.JMOLANIMATIONConvention#characterData does not have a test method
io.cml.JMOLANIMATIONConvention#startElement does not have a test method
io.cml.JMOLANIMATIONConvention#endElement does not have a test method
io.cml.JMOLANIMATIONConvention did not have a TestClass annotation
io.cml.CMLErrorHandler#error does not have a test method
io.cml.CMLErrorHandler#warning does not have a test method
io.cml.CMLErrorHandler#fatalError does not have a test method
io.cml.CMLErrorHandler did not have a TestClass annotation
io.PMPReader#read does not have a test method
io.MDLV2000Reader#getIOSettings does not have a test method
io.MDLV2000Reader#customizeJob does not have a test method
io.MDLV2000Reader#read does not have a test method
io.PCSubstanceXMLReader#read does not have a test method
io.MDLRXNReader#read does not have a test method
io.SDFWriter#getIOSettings does not have a test method
io.SDFWriter#customizeJob does not have a test method
io.SDFWriter#setWriter does not have a test method
io.SDFWriter#setWriter does not have a test method
io.SDFWriter#write does not have a test method
io.PCCompoundASNReader#read does not have a test method
io.Mol2Writer#setWriter does not have a test method
io.Mol2Writer#setWriter does not have a test method
io.Mol2Writer#writeMolecule does not have a test method
io.Mol2Writer#write does not have a test method
io.CIFReader#read does not have a test method
io.CIFReader#setReader has a test method annotation 'testSetReader_InputStream' which is not found in test class: org.openscience.cdk.io.CIFReaderTest
io.CIFReader#accepts has a test method annotation 'testAccepts' which is not found in test class: org.openscience.cdk.io.CIFReaderTest
io.XYZWriter#setWriter does not have a test method
io.XYZWriter#setWriter does not have a test method
io.XYZWriter#writeMolecule does not have a test method
io.XYZWriter#write does not have a test method
io.listener.TextGUIListener#processIOSettingQuestion does not have a test method
io.listener.TextGUIListener#frameRead does not have a test method
io.listener.TextGUIListener#setOutputWriter does not have a test method
io.listener.TextGUIListener#setInputReader does not have a test method
io.listener.TextGUIListener#setLevel does not have a test method
io.listener.TextGUIListener did not have a TestClass annotation
io.listener.SwingGUIListener#processIOSettingQuestion does not have a test method
io.listener.SwingGUIListener#frameRead does not have a test method
io.listener.SwingGUIListener#setLevel does not have a test method
io.listener.SwingGUIListener did not have a TestClass annotation
io.listener.PropertiesListener#processIOSettingQuestion does not have a test method
io.listener.PropertiesListener#frameRead does not have a test method
io.listener.PropertiesListener#setOutputWriter does not have a test method
io.listener.PropertiesListener did not have a TestClass annotation
io.Mol2Reader#read does not have a test method
io.iterator.event.EventCMLReader#getAtomContainer does not have a test method
io.iterator.event.EventCMLReader#process does not have a test method
io.iterator.event.EventCMLReader did not have a TestClass annotation
io.iterator.event.EventCMLHandler#getAtomContainer does not have a test method
io.iterator.event.EventCMLHandler#setDocumentProperty does not have a test method
io.iterator.event.EventCMLHandler#startObject does not have a test method
io.iterator.event.EventCMLHandler#endObject does not have a test method
io.iterator.event.EventCMLHandler#setObjectProperty does not have a test method
io.iterator.event.EventCMLHandler#startDocument does not have a test method
io.iterator.event.EventCMLHandler#endDocument does not have a test method
io.iterator.event.EventCMLHandler did not have a TestClass annotation
io.iterator.event.DefaultEventChemObjectReader#accepts does not have a test method
io.iterator.event.DefaultEventChemObjectReader#accepts does not have a test method
io.iterator.event.DefaultEventChemObjectReader#getIOSettings does not have a test method
io.iterator.event.DefaultEventChemObjectReader#addChemObjectIOListener does not have a test method
io.iterator.event.DefaultEventChemObjectReader#removeChemObjectIOListener does not have a test method
io.iterator.event.DefaultEventChemObjectReader#fireIOSettingQuestion does not have a test method
io.iterator.event.DefaultEventChemObjectReader#fireFrameRead does not have a test method
io.iterator.event.DefaultEventChemObjectReader#remove does not have a test method
io.iterator.event.DefaultEventChemObjectReader did not have a TestClass annotation
io.iterator.IteratingPCSubstancesXMLReader#hasNext does not have a test method
io.iterator.IteratingPCSubstancesXMLReader#next does not have a test method
io.iterator.IteratingPCSubstancesXMLReader#next does not have a test method
io.iterator.IteratingPCSubstancesXMLReader#remove does not have a test method
io.iterator.IteratingPCSubstancesXMLReader did not have a TestClass annotation
io.iterator.IteratingMDLReader#getIOSettings does not have a test method
io.iterator.IteratingMDLReader#customizeJob does not have a test method
io.iterator.IteratingMDLReader#processIOSettingQuestion does not have a test method
io.iterator.IteratingMDLReader#hasNext does not have a test method
io.iterator.IteratingMDLReader#next does not have a test method
io.iterator.IteratingMDLReader#next does not have a test method
io.iterator.IteratingMDLReader#remove does not have a test method
io.iterator.IteratingMDLReader did not have a TestClass annotation
io.iterator.IteratingPCCompoundASNReader#hasNext does not have a test method
io.iterator.IteratingPCCompoundASNReader#next does not have a test method
io.iterator.IteratingPCCompoundASNReader#next does not have a test method
io.iterator.IteratingPCCompoundASNReader#remove does not have a test method
io.iterator.IteratingPCCompoundASNReader did not have a TestClass annotation
io.iterator.DefaultIteratingChemObjectReader#accepts does not have a test method
io.iterator.DefaultIteratingChemObjectReader#getIOSettings does not have a test method
io.iterator.DefaultIteratingChemObjectReader#addChemObjectIOListener does not have a test method
io.iterator.DefaultIteratingChemObjectReader#removeChemObjectIOListener does not have a test method
io.iterator.DefaultIteratingChemObjectReader#setReaderMode does not have a test method
io.iterator.DefaultIteratingChemObjectReader#fireIOSettingQuestion does not have a test method
io.iterator.DefaultIteratingChemObjectReader#remove does not have a test method
io.iterator.DefaultIteratingChemObjectReader did not have a TestClass annotation
io.iterator.IteratingPCCompoundXMLReader#hasNext does not have a test method
io.iterator.IteratingPCCompoundXMLReader#next does not have a test method
io.iterator.IteratingPCCompoundXMLReader#next does not have a test method
io.iterator.IteratingPCCompoundXMLReader#remove does not have a test method
io.iterator.IteratingPCCompoundXMLReader did not have a TestClass annotation
io.MDLReader#getIOSettings does not have a test method
io.MDLReader#customizeJob does not have a test method
io.MDLReader#read does not have a test method
io.MDLRXNV3000Reader#getIOSettings does not have a test method
io.DefaultChemObjectWriter#getIOSettings does not have a test method
io.DefaultChemObjectWriter#addChemObjectIOListener does not have a test method
io.DefaultChemObjectWriter#removeChemObjectIOListener does not have a test method
io.DefaultChemObjectWriter#fireIOSettingQuestion does not have a test method
io.DefaultChemObjectWriter did not have a TestClass annotation
io.HINWriter#setWriter does not have a test method
io.HINWriter#setWriter does not have a test method
io.HINWriter#write does not have a test method
io.HINWriter refers to a non-existing test class: org.openscience.cdk.io.HINWriterTest
io.program.GaussianInputWriter#getIOSettings does not have a test method
io.program.GaussianInputWriter#setWriter does not have a test method
io.program.GaussianInputWriter#setWriter does not have a test method
io.program.GaussianInputWriter#writeMolecule does not have a test method
io.PDBWriter#setWriter does not have a test method
io.PDBWriter#setWriter does not have a test method
io.PDBWriter#writeMolecule does not have a test method
io.PDBWriter#writeCrystal does not have a test method
io.PDBWriter#write does not have a test method
io.PDBWriter#accepts has a test method annotation 'testAccepts' which is not found in test class: org.openscience.cdk.io.PDBWriterTest
io.setting.OptionIOSetting#setSetting does not have a test method
io.setting.OptionIOSetting#setSetting does not have a test method
io.setting.OptionIOSetting#getOptions does not have a test method
io.setting.OptionIOSetting did not have a TestClass annotation
io.setting.BooleanIOSetting#setSetting does not have a test method
io.setting.BooleanIOSetting#isSet does not have a test method
io.setting.BooleanIOSetting did not have a TestClass annotation
io.setting.IntegerIOSetting#setSetting does not have a test method
io.setting.IntegerIOSetting#getSettingValue does not have a test method
io.setting.IntegerIOSetting did not have a TestClass annotation
io.setting.StringIOSetting#setSetting does not have a test method
io.setting.StringIOSetting did not have a TestClass annotation
io.setting.IOSetting#getDefaultSetting does not have a test method
io.setting.IOSetting#getQuestion does not have a test method
io.setting.IOSetting#setSetting does not have a test method
io.setting.IOSetting#getName does not have a test method
io.setting.IOSetting#getLevel does not have a test method
io.setting.IOSetting#getSetting does not have a test method
io.setting.IOSetting did not have a TestClass annotation
io.DefaultChemObjectReader#getIOSettings does not have a test method
io.DefaultChemObjectReader#addChemObjectIOListener does not have a test method
io.DefaultChemObjectReader#removeChemObjectIOListener does not have a test method
io.DefaultChemObjectReader#setReaderMode does not have a test method
io.DefaultChemObjectReader#fireIOSettingQuestion does not have a test method
io.DefaultChemObjectReader#fireFrameRead does not have a test method
io.DefaultChemObjectReader did not have a TestClass annotation
geometry.ZMatrixTools#zmatrixToCartesian does not have a test method
geometry.ZMatrixTools did not have a TestClass annotation
CDK 11/18/09,21:19
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
> <foo>
bar
$$$$
CDK 11/18/09,21:19
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
> <toys>
r-us
$$$$
HEADER created with the CDK (http://cdk.sf.net/)
CRYST1 1.0001.0002.00090.00090.00090.000
HETATM 1 C MOL 0.100 0.100 0.300
TER
HEADER created with the CDK (http://cdk.sf.net/)
CRYST1 1.0001.0002.00090.00090.00090.000
HETATM 1 C MOL 0.100 0.100 0.600
TER
------------- ---------------- ---------------
------------- Standard Error -----------------
java.lang.StringIndexOutOfBoundsException: String index out of range: 80
at java.lang.String.substring(String.java:1946)
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:504)
at org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:212)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:179)
at org.openscience.cdk.io.MDLV2000ReaderTest.testMassNumber(MDLV2000ReaderTest.java:157)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:73)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:46)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at org.junit.runners.Suite.runChild(Suite.java:115)
at org.junit.runners.Suite.runChild(Suite.java:23)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at junit.framework.JUnit4TestAdapter.run(JUnit4TestAdapter.java:39)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.run(JUnitTestRunner.java:420)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.launch(JUnitTestRunner.java:911)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.main(JUnitTestRunner.java:768)
java.lang.StringIndexOutOfBoundsException: String index out of range: 80
at java.lang.String.substring(String.java:1946)
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:504)
at org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:212)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:179)
at org.openscience.cdk.io.MDLV2000ReaderTest.testHisotopes_Strict(MDLV2000ReaderTest.java:490)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:73)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:46)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at org.junit.runners.Suite.runChild(Suite.java:115)
at org.junit.runners.Suite.runChild(Suite.java:23)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at junit.framework.JUnit4TestAdapter.run(JUnit4TestAdapter.java:39)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.run(JUnitTestRunner.java:420)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.launch(JUnitTestRunner.java:911)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.main(JUnitTestRunner.java:768)
java.lang.StringIndexOutOfBoundsException: String index out of range: 80
at java.lang.String.substring(String.java:1946)
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:504)
at org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:212)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:179)
at org.openscience.cdk.io.MDLV2000ReaderTest.testHisotopes_Relaxed(MDLV2000ReaderTest.java:505)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:73)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:46)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at org.junit.runners.Suite.runChild(Suite.java:115)
at org.junit.runners.Suite.runChild(Suite.java:23)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at junit.framework.JUnit4TestAdapter.run(JUnit4TestAdapter.java:39)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.run(JUnitTestRunner.java:420)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.launch(JUnitTestRunner.java:911)
at org.apache.tools.ant.taskdefs.optional.junit.JUnitTestRunner.main(JUnitTestRunner.java:768)
------------- ---------------- ---------------
Testcase: testCoverage(org.openscience.cdk.coverage.IoCoverageTest): FAILED
The io module is not fully tested! Missing number of method tests: 363 in number of classes: 65
junit.framework.AssertionFailedError: The io module is not fully tested! Missing number of method tests: 363 in number of classes: 65
at org.openscience.cdk.coverage.CoverageAnnotationTest.runCoverageTest(CoverageAnnotationTest.java:83)
at org.openscience.cdk.coverage.IoCoverageTest.testCoverage(IoCoverageTest.java:42)
Testcase: testIsotopeRef(org.openscience.cdk.io.cml.CML25FragmentsTest): FAILED
junit.framework.AssertionFailedError:
at org.openscience.cdk.io.cml.CML25FragmentsTest.testIsotopeRef(CML25FragmentsTest.java:75)
Testcase: testMassNumber(org.openscience.cdk.io.MDLV2000ReaderTest): Caused an ERROR
Error while parsing line 5: 2.5369 -0.1550 0.0000 O 0 0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 -> String index out of range: 80
org.openscience.cdk.exception.CDKException: Error while parsing line 5: 2.5369 -0.1550 0.0000 O 0 0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 -> String index out of range: 80
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:731)
at org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:212)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:179)
at org.openscience.cdk.io.MDLV2000ReaderTest.testMassNumber(MDLV2000ReaderTest.java:157)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 80
at java.lang.String.substring(String.java:1946)
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:504)
Testcase: testHisotopes_Relaxed(org.openscience.cdk.io.MDLV2000ReaderTest): Caused an ERROR
Error while parsing line 5: 2.5369 -0.1550 0.0000 O 0 0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 -> String index out of range: 80
org.openscience.cdk.exception.CDKException: Error while parsing line 5: 2.5369 -0.1550 0.0000 O 0 0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 ??0 -> String index out of range: 80
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:731)
at org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:212)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:179)
at org.openscience.cdk.io.MDLV2000ReaderTest.testHisotopes_Relaxed(MDLV2000ReaderTest.java:505)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 80
at java.lang.String.substring(String.java:1946)
at org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:504)
Testcase: testDataFromSDFReading(org.openscience.cdk.io.SDFReaderTest): Caused an ERROR
expected:<[1]> but was:<[]>
at org.openscience.cdk.io.SDFReaderTest.testDataFromSDFReading(SDFReaderTest.java:90)