Testsuite: org.openscience.cdk.modulesuites.MsmartsTests
Tests run: 765, Failures: 14, Errors: 1, Time elapsed: 6.317 sec
------------- Standard Output ---------------
SMARTSQueryTool: missing the expected test method: testCountMatches
SMARTSQueryTool: missing the expected test method: testGetUniqueMatchingAtoms
SMARTSQueryTool: missing the expected test method: testSetSmarts_String
SMARTSQueryTool: missing the expected test method: testGetMatchingAtoms
SMARTSQueryTool: missing the expected test method: testGetSmarts
SMARTSQueryTool: missing the expected test method: testMatches_IAtomContainer
SMARTSQueryTool: missing the expected test method: testMatches_IAtomContainer_boolean
SMARTSQueryTool: missing the expected test method: testSMARTSQueryTool_String
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTOrBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTRingMembershipTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAliphaticTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTGroupTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTSmartsTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifierTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTStartTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.SimpleNodeTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumberTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTReactionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCountTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumberTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTChiralityTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTSimpleBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAromaticTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTElementTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTOrExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserStateTest
SmartsDumpVisitor: missing the expected test method: testVisit_ASTRingIdentifier_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAtom_Object
SmartsDumpVisitor: missing the expected test method: testVisit_SimpleNode_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTStart_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTReaction_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTGroup_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTSmarts_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTNotBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTSimpleBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTImplicitHighAndBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTLowAndBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTOrBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTExplicitHighAndBond_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTElement_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTRecursiveSmartsExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTPrimitiveAtomExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTTotalHCount_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTImplicitHCount_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTExplicitConnectivity_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAtomicNumber_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTHybrdizationNumber_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTCharge_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTRingConnectivity_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTPeriodicGroupNumber_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTTotalConnectivity_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTValence_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTRingMembership_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTSmallestRingSize_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAliphatic_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTNonCHHeavyAtom_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAromatic_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAnyAtom_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTAtomicMass_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTChirality_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTLowAndExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTOrExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTNotExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTExplicitHighAndExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTImplicitHighAndExpression_Object
SmartsDumpVisitor: missing the expected test method: testVisit_ASTExplicitAtom_Object
SmartsDumpVisitor: missing the expected test method: testSmartsDumpVisitor
Missing test class: org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitorTest
SmartsQueryVisitor: missing the expected test method: testVisit_ASTRingIdentifier_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAtom_Object
SmartsQueryVisitor: missing the expected test method: testVisit_SimpleNode_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTStart_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTReaction_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTGroup_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTSmarts_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTNotBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTImplicitHighAndBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTLowAndBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTOrBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTExplicitHighAndBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTSimpleBond_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTRecursiveSmartsExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTElement_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTTotalHCount_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTImplicitHCount_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTExplicitConnectivity_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAtomicNumber_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTHybrdizationNumber_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTCharge_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTRingConnectivity_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTPeriodicGroupNumber_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTTotalConnectivity_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTValence_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTRingMembership_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTSmallestRingSize_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAliphatic_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTNonCHHeavyAtom_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAromatic_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAnyAtom_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTAtomicMass_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTChirality_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTLowAndExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTOrExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTNotExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTExplicitHighAndExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTImplicitHighAndExpression_Object
SmartsQueryVisitor: missing the expected test method: testVisit_ASTExplicitAtom_Object
SmartsQueryVisitor: missing the expected test method: testGetRoot_Node
SmartsQueryVisitor: missing the expected test method: testSmartsQueryVisitor
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivityTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTNotBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivityTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtomTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSizeTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTNotExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTChargeTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAtomTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumberTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivityTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtomTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTLowAndBondTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAnyAtomTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpressionTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTValenceTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTAtomicMassTest
Missing test class: org.openscience.cdk.smiles.smarts.parser.ASTTotalHCountTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.DegreeAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.RingBondTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.StereoBondTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBondTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.MassAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBondTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtomTest
Missing test class: org.openscience.cdk.isomorphism.matchers.smarts.RingAtomTest
Cannot percieve atom type for the 10th atom: N
Cannot percieve atom type for the 10th atom: N
Cannot percieve atom type for the 10th atom: N
Cannot percieve atom type for the 9th atom: N
Cannot percieve atom type for the 8th atom: N
Cannot percieve atom type for the 8th atom: N
Cannot percieve atom type for the 18th atom: S
Cannot percieve atom type for the 5th atom: C
Cannot percieve atom type for the 5th atom: C
Cannot percieve atom type for the 18th atom: N
Cannot percieve atom type for the 7th atom: C
Cannot percieve atom type for the 10th atom: N
Cannot percieve atom type for the 9th atom: N
Cannot percieve atom type for the 6th atom: N
Cannot percieve atom type for the 8th atom: N
Cannot percieve atom type for the 8th atom: N
Cannot percieve atom type for the 22th atom: N
------------- ---------------- ---------------
Testcase: testCoverage(org.openscience.cdk.coverage.SmartsCoverageTest): FAILED
The smarts module is not fully tested! Missing number of method tests: 90 in number of classes: 3; Missing test classes: 71
junit.framework.AssertionFailedError: The smarts module is not fully tested! Missing number of method tests: 90 in number of classes: 3; Missing test classes: 71
at org.openscience.cdk.coverage.CoverageTest.runCoverageTest(CoverageTest.java:87)
at org.openscience.cdk.coverage.SmartsCoverageTest.testCoverage(SmartsCoverageTest.java:43)
Testcase: test2LetterSMARTS(org.openscience.cdk.smiles.smarts.parser.ParserTest): Caused an ERROR
The string Sc1ccccc1 is not a valid SMARTS string: Encountered "Sc" at line 1, column 1.
Was expecting one of:
"c" ...
"n" ...
"o" ...
"s" ...
"p" ...
"as" ...
"se" ...
"B" ...
"C" ...
"N" ...
"O" ...
"F" ...
"P" ...
"S" ...
"Cl" ...
"Br" ...
"I" ...
"*" ...
"a" ...
"A" ...
"(" ...
"[" ...
">>" ...
">" ...
org.openscience.cdk.exception.CDKException: The string Sc1ccccc1 is not a valid SMARTS string: Encountered "Sc" at line 1, column 1.
Was expecting one of:
"c" ...
"n" ...
"o" ...
"s" ...
"p" ...
"as" ...
"se" ...
"B" ...
"C" ...
"N" ...
"O" ...
"F" ...
"P" ...
"S" ...
"Cl" ...
"Br" ...
"I" ...
"*" ...
"a" ...
"A" ...
"(" ...
"[" ...
">>" ...
">" ...
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.parse(SMARTSParser.java:88)
at org.openscience.cdk.smiles.smarts.parser.ParserTest.test2LetterSMARTS(ParserTest.java:147)
Caused by: org.openscience.cdk.smiles.smarts.parser.ParseException: Encountered "Sc" at line 1, column 1.
Was expecting one of:
"c" ...
"n" ...
"o" ...
"s" ...
"p" ...
"as" ...
"se" ...
"B" ...
"C" ...
"N" ...
"O" ...
"F" ...
"P" ...
"S" ...
"Cl" ...
"Br" ...
"I" ...
"*" ...
"a" ...
"A" ...
"(" ...
"[" ...
">>" ...
">" ...
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.generateParseException(SMARTSParser.java:3026)
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.jj_consume_token(SMARTSParser.java:2894)
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.ReactionExpression(SMARTSParser.java:243)
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.Start(SMARTSParser.java:137)
at org.openscience.cdk.smiles.smarts.parser.SMARTSParser.parse(SMARTSParser.java:83)
Testcase: testPropertyAromatic5(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<6> but was:<0>
junit.framework.AssertionFailedError: expected:<6> but was:<0>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testPropertyAromatic5(SMARTSSearchTest.java:294)
Testcase: testBondStereo1(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<0>
junit.framework.AssertionFailedError: expected:<1> but was:<0>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testBondStereo1(SMARTSSearchTest.java:936)
Testcase: testBondStereo2(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<0>
junit.framework.AssertionFailedError: expected:<1> but was:<0>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testBondStereo2(SMARTSSearchTest.java:941)
Testcase: testBondStereo3(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<0>
junit.framework.AssertionFailedError: expected:<1> but was:<0>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testBondStereo3(SMARTSSearchTest.java:946)
Testcase: testLogicalNot5(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<2> but was:<7>
junit.framework.AssertionFailedError: expected:<2> but was:<7>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testLogicalNot5(SMARTSSearchTest.java:981)
Testcase: testLogicalOr5(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<2>
junit.framework.AssertionFailedError: expected:<1> but was:<2>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testLogicalOr5(SMARTSSearchTest.java:1029)
Testcase: testLogicalOrLowAnd6(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<8>
junit.framework.AssertionFailedError: expected:<1> but was:<8>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testLogicalOrLowAnd6(SMARTSSearchTest.java:1150)
Testcase: testLactamRecursive(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest): FAILED
expected:<1> but was:<2>
junit.framework.AssertionFailedError: expected:<1> but was:<2>
at org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.testLactamRecursive(SMARTSSearchTest.java:1594)
Testcase: testRecursiveSmarts26(org.openscience.cdk.smiles.smarts.parser.RecursiveTest): FAILED
expected:<0> but was:<1>
junit.framework.AssertionFailedError: expected:<0> but was:<1>
at org.openscience.cdk.smiles.smarts.parser.RecursiveTest.testRecursiveSmarts26(RecursiveTest.java:290)
Testcase: testRecursiveSmarts27(org.openscience.cdk.smiles.smarts.parser.RecursiveTest): FAILED
expected:<0> but was:<1>
junit.framework.AssertionFailedError: expected:<0> but was:<1>
at org.openscience.cdk.smiles.smarts.parser.RecursiveTest.testRecursiveSmarts27(RecursiveTest.java:296)
Testcase: testRecursive28(org.openscience.cdk.smiles.smarts.parser.RecursiveTest): FAILED
expected:<0> but was:<1>
junit.framework.AssertionFailedError: expected:<0> but was:<1>
at org.openscience.cdk.smiles.smarts.parser.RecursiveTest.testRecursive28(RecursiveTest.java:302)
Testcase: testRecursive29(org.openscience.cdk.smiles.smarts.parser.RecursiveTest): FAILED
expected:<0> but was:<1>
junit.framework.AssertionFailedError: expected:<0> but was:<1>
at org.openscience.cdk.smiles.smarts.parser.RecursiveTest.testRecursive29(RecursiveTest.java:308)
Testcase: testBasicAmineOnDrugs(org.openscience.cdk.smiles.smarts.parser.RecursiveTest): FAILED
expected:<142> but was:<141>
junit.framework.AssertionFailedError: expected:<142> but was:<141>
at org.openscience.cdk.smiles.smarts.parser.RecursiveTest.testBasicAmineOnDrugs(RecursiveTest.java:331)