Testsuite: org.openscience.cdk.modulesuites.MlibiocmlTests
Tests run: 87, Failures: 1, Errors: 4, Time elapsed: 5.083 sec
Testcase: testSFBug1085912_1(org.openscience.cdk.io.cml.CML2Test): Caused an ERROR
expected:<...="pdb:sequence" id="[PHEA105">
<atomArray>
<atom id="a3570711" elementType="N" x3="-3.504" y3="9.019" z3="-14.276" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a17624055" elementType="C" x3="-3.022" y3="7.654" z3="-14.09" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a22522046" elementType="C" x3="-4.179" y3="6.669" z3="-14.259" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a492511" elementType="O" x3="-5.32" y3="6.98" z3="-13.918" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a23250774" elementT]> but was:<...="pdb:sequence" id="[nullAnull">
<atomArray>
<atom id="a3570711" elementType="N" x3="-3.504" y3="9.019" z3="-14.276" formalCharge="0" isotopeNumber="14">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a17624055" elementType="C" x3="-3.022" y3="7.654" z3="-14.09" formalCharge="0" isotopeNumber="12">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a22522046" elementType="C" x3="-4.179" y3="6.669" z3="-14.259" formalCharge="0" isotopeNumber="12">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a492511" elementType="O" x3="-5.32" y3="6.98" z3="-13.918" formalCharge="0" isotopeNumber="16">
<scalar dictRef="cdk:partialCharge" dataType]>
<atomArray>
<atom id="a3570711" elementType="N" x3="-3.504" y3="9.019" z3="-14.276" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a17624055" elementType="C" x3="-3.022" y3="7.654" z3="-14.09" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a22522046" elementType="C" x3="-4.179" y3="6.669" z3="-14.259" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a492511" elementType="O" x3="-5.32" y3="6.98" z3="-13.918" formalCharge="0">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a23250774" elementT]> but was:<...="pdb:sequence" id="[nullAnull">
<atomArray>
<atom id="a3570711" elementType="N" x3="-3.504" y3="9.019" z3="-14.276" formalCharge="0" isotopeNumber="14">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a17624055" elementType="C" x3="-3.022" y3="7.654" z3="-14.09" formalCharge="0" isotopeNumber="12">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a22522046" elementType="C" x3="-4.179" y3="6.669" z3="-14.259" formalCharge="0" isotopeNumber="12">
<scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar>
</atom>
<atom id="a492511" elementType="O" x3="-5.32" y3="6.98" z3="-13.918" formalCharge="0" isotopeNumber="16">
<scalar dictRef="cdk:partialCharge" dataType]>
at org.openscience.cdk.io.cml.CML2Test.testSFBug1085912_1(CML2Test.java:747)
Testcase: testBug2697568(org.openscience.cdk.io.cml.CML2Test): Caused an ERROR
null
java.lang.NullPointerException
at org.openscience.cdk.io.cml.CMLCoreModule.storeData(CMLCoreModule.java:1141)
at org.openscience.cdk.io.cml.CMLReactionModule.endElement(CMLReactionModule.java:158)
at org.openscience.cdk.io.cml.CMLHandler.endElement(CMLHandler.java:95)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:604)
at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:183)
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:353)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2723)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:624)
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:486)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:810)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:740)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:110)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525)
at org.openscience.cdk.io.CMLReader.readChemFile(CMLReader.java:224)
at org.openscience.cdk.io.CMLReader.read(CMLReader.java:193)
at org.openscience.cdk.io.cml.CML2Test.testBug2697568(CML2Test.java:957)
Testcase: testIsotope_ExactMass(org.openscience.cdk.io.cml.CMLRoundTripTest): Caused an ERROR
null
java.lang.NullPointerException
at org.openscience.cdk.io.cml.CMLRoundTripTest.testIsotope_ExactMass(CMLRoundTripTest.java:308)
Testcase: testIsotope_Abundance(org.openscience.cdk.io.cml.CMLRoundTripTest): Caused an ERROR
null
java.lang.NullPointerException
at org.openscience.cdk.io.cml.CMLRoundTripTest.testIsotope_Abundance(CMLRoundTripTest.java:323)
Testcase: testAtomAromaticity(org.openscience.cdk.io.cml.CMLRoundTripTest): FAILED
junit.framework.AssertionFailedError:
at org.openscience.cdk.io.cml.CMLRoundTripTest.testAtomAromaticity(CMLRoundTripTest.java:606)