PMD Results

The following document contains the results of PMD 6.29.0.

Violations By Priority

Priority 2

ubic/basecode/io/reader/AbstractMatrixReader.java

Rule Violation Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 66

ubic/basecode/math/DescriptiveWithMissing.java

Rule Violation Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 228

ubic/basecode/util/StringUtil.java

Rule Violation Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 149

Priority 3

ubic/basecode/dataStructure/graph/Graph.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'addNode': the method is declared in an interface type 27
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsKey': the method is declared in an interface type 29
UnnecessaryModifier Unnecessary modifier 'public' on method 'get': the method is declared in an interface type 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getNodeContents': the method is declared in an interface type 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'unmarkAll': the method is declared in an interface type 35

ubic/basecode/dataStructure/graph/GraphNode.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getGraph': the method is declared in an interface type 30
UnnecessaryModifier Unnecessary modifier 'public' on method 'getItem': the method is declared in an interface type 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'getKey': the method is declared in an interface type 40
UnnecessaryModifier Unnecessary modifier 'public' on method 'setItem': the method is declared in an interface type 47
UnnecessaryModifier Unnecessary modifier 'public' on method 'setValue': the method is declared in an interface type 55

ubic/basecode/dataStructure/matrix/Matrix2D.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'abstract' on interface 'Matrix2D': interface types are implicitly abstract 31–218
UnnecessaryModifier Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type 38
UnnecessaryModifier Unnecessary modifier 'public' on method 'asDoubles': the method is declared in an interface type 49
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 56
UnnecessaryModifier Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type 63
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type 69
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type 75
UnnecessaryModifier Unnecessary modifier 'public' on method 'getByKeys': the method is declared in an interface type 81
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type 89
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type 97
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type 102
UnnecessaryModifier Unnecessary modifier 'public' on method 'getEntry': the method is declared in an interface type 109
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type 117
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type 125
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNameMapIterator': the method is declared in an interface type 130
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type 135
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type 142
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type 148
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type 153
UnnecessaryModifier Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type 162
UnnecessaryModifier Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type 169
UnnecessaryModifier Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type 176
UnnecessaryModifier Unnecessary modifier 'public' on method 'set': the method is declared in an interface type 183
UnnecessaryModifier Unnecessary modifier 'public' on method 'setByKeys': the method is declared in an interface type 190
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnName': the method is declared in an interface type 198
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type 203
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowName': the method is declared in an interface type 211
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type 216

ubic/basecode/dataStructure/matrix/Matrix3D.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'addRowName': the method is declared in an interface type 43
UnnecessaryModifier Unnecessary modifier 'public' on method 'addSliceName': the method is declared in an interface type 51
UnnecessaryModifier Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type 58
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type 66
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type 74
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsSliceName': the method is declared in an interface type 82
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type 90
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type 98
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNameIterator': the method is declared in an interface type 100
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type 105
UnnecessaryModifier Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type 107
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type 115
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type 123
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNameIterator': the method is declared in an interface type 128
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type 133
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceIndexByName': the method is declared in an interface type 141
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceName': the method is declared in an interface type 149
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceNameIterator': the method is declared in an interface type 151
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceNames': the method is declared in an interface type 153
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type 160
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type 166
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type 171
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasSliceNames': the method is declared in an interface type 173
UnnecessaryModifier Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type 183
UnnecessaryModifier Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type 190
UnnecessaryModifier Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type 197
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type 202
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type 207
UnnecessaryModifier Unnecessary modifier 'public' on method 'setSliceNames': the method is declared in an interface type 209
UnnecessaryModifier Unnecessary modifier 'public' on method 'slices': the method is declared in an interface type 211

ubic/basecode/dataStructure/matrix/ObjectMatrix.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'get': the method is declared in an interface type 29
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColumn': the method is declared in an interface type 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRow': the method is declared in an interface type 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'subset': the method is declared in an interface type 42
UnnecessaryModifier Unnecessary modifier 'public' on method 'subsetColumns': the method is declared in an interface type 48

ubic/basecode/dataStructure/matrix/PrimitiveMatrix.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColObj': the method is declared in an interface type 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type 40
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowObj': the method is declared in an interface type 46

ubic/basecode/dataStructure/matrix/RCDoubleMatrix1D.java

Rule Violation Line
UnusedFormalParameter Avoid unused constructor parameters such as 'length'. 53

ubic/basecode/datafilter/Filter.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'filter': the method is declared in an interface type 39

ubic/basecode/io/excel/CreateSpreadSheet.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 45–47

ubic/basecode/io/reader/AbstractMatrixReader.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 103–106
EmptyIfStmt Avoid empty if statements 109–111

ubic/basecode/io/reader/DoubleMatrixReader.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 85–87
EmptyIfStmt Avoid empty if statements 311–313

ubic/basecode/io/reader/SparseDoubleMatrixReader.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 78–80
EmptyIfStmt Avoid empty if statements 91–93
UnnecessaryConversionTemporary Avoid unnecessary temporaries when converting primitives to Strings 183
UnnecessaryConversionTemporary Avoid unnecessary temporaries when converting primitives to Strings 184

ubic/basecode/io/reader/StringMatrixReader.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 101–103

ubic/basecode/math/MatrixStats.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 186–188
EmptyIfStmt Avoid empty if statements 196–198
EmptyIfStmt Avoid empty if statements 206–208
EmptyIfStmt Avoid empty if statements 216–218

ubic/basecode/math/Wilcoxon.java

Rule Violation Line
CollapsibleIfStatements These nested if statements could be combined 135–138

ubic/basecode/math/distribution/DensityGenerator.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'density': the method is declared in an interface type 33

ubic/basecode/math/distribution/ProbabilityComputer.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type 44

ubic/basecode/math/linalg/Blas.java

Rule Violation Line
UnnecessaryReturn Avoid unnecessary return statements 178
UnnecessaryReturn Avoid unnecessary return statements 419
UnnecessaryReturn Avoid unnecessary return statements 468
UnnecessaryReturn Avoid unnecessary return statements 522
UnnecessaryReturn Avoid unnecessary return statements 576
UnnecessaryReturn Avoid unnecessary return statements 685
UnnecessaryReturn Avoid unnecessary return statements 759
UnnecessaryReturn Avoid unnecessary return statements 833
UnnecessaryReturn Avoid unnecessary return statements 883
UnnecessaryReturn Avoid unnecessary return statements 1159
UnnecessaryReturn Avoid unnecessary return statements 1222
UnnecessaryReturn Avoid unnecessary return statements 1270
UnnecessaryReturn Avoid unnecessary return statements 1353

ubic/basecode/math/linalg/Dqrsl.java

Rule Violation Line
CollapsibleIfStatements These nested if statements could be combined 358–377
UnnecessaryReturn Avoid unnecessary return statements 390

ubic/basecode/math/linalg/QRDecomposition.java

Rule Violation Line
UnusedPrivateField Avoid unused private fields such as 'effects'. 93

ubic/basecode/math/linearmodels/DesignMatrix.java

Rule Violation Line
CollapsibleIfStatements These nested if statements could be combined 552–555

ubic/basecode/math/linearmodels/LeastSquaresFit.java

Rule Violation Line
UnusedFormalParameter Avoid unused method parameters such as 'ypsize'. 1071

ubic/basecode/math/linearmodels/MeanVarianceEstimator.java

Rule Violation Line
TooManyStaticImports Too many static imports may lead to messy code 15–337

ubic/basecode/math/linearmodels/ModeratedTstat.java

Rule Violation Line
UnusedPrivateField Avoid unused private fields such as 'trigammainverse'. 54
UnnecessaryModifier Unnecessary modifier 'final' on method 'okVars': private methods cannot be overridden 99–107
UnnecessaryModifier Unnecessary modifier 'final' on method 'okDfs': private methods cannot be overridden 109–118

ubic/basecode/ontology/model/DatatypeProperty.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getType': the method is declared in an interface type 23

ubic/basecode/ontology/model/ObjectProperty.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRange': the method is declared in an interface type 29

ubic/basecode/ontology/model/OntologyCardinalityRestriction.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on enum 'CardinalityType': the enum is declared in an interface type 27–29
UnnecessaryModifier Unnecessary modifier 'public' on method 'getCardinality': the method is declared in an interface type 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getCardinalityType': the method is declared in an interface type 33

ubic/basecode/ontology/model/OntologyClassRestriction.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type 27

ubic/basecode/ontology/model/OntologyDatatypeRestriction.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type 27

ubic/basecode/ontology/model/OntologyIndividual.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getInstanceOf': the method is declared in an interface type 34

ubic/basecode/ontology/model/OntologyProperty.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'isFunctional': the method is declared in an interface type 30

ubic/basecode/ontology/model/OntologyRestriction.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictionOn': the method is declared in an interface type 29

ubic/basecode/ontology/ncbo/AnnotatorResponse.java

Rule Violation Line
CollapsibleIfStatements These nested if statements could be combined 87–89

ubic/basecode/util/FileTools.java

Rule Violation Line
CollapsibleIfStatements These nested if statements could be combined 567–569

ubic/basecode/util/PrettyPrinter.java

Rule Violation Line
EmptyCatchBlock Avoid empty catch blocks 69–71

ubic/basecode/util/SQLUtils.java

Rule Violation Line
UnusedPrivateField Avoid unused private fields such as 'bac'. 33

ubic/basecode/util/StatusViewer.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'clear': the method is declared in an interface type 33
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 40
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 45
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 50
UnnecessaryModifier Unnecessary modifier 'public' on method 'showProgress': the method is declared in an interface type 52
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type 59
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type 65
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showWarning': the method is declared in an interface type 70

ubic/basecode/util/r/AbstractRClient.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 584–586

ubic/basecode/util/r/HTest.java

Rule Violation Line
EmptyIfStmt Avoid empty if statements 41–43

ubic/basecode/util/r/RClient.java

Rule Violation Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 44
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 51
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 58
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 60
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type 66
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type 73
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 81
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 89
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 98
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignStringList': the method is declared in an interface type 106
UnnecessaryModifier Unnecessary modifier 'public' on method 'booleanDoubleArrayEval': the method is declared in an interface type 116
UnnecessaryModifier Unnecessary modifier 'public' on method 'dataFrame': the method is declared in an interface type 125
UnnecessaryModifier Unnecessary modifier 'public' on method 'dataFrameEval': the method is declared in an interface type 133
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayDoubleArrayEval': the method is declared in an interface type 143
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayEval': the method is declared in an interface type 151
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayTwoDoubleArrayEval': the method is declared in an interface type 163–164
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleTwoDoubleArrayEval': the method is declared in an interface type 176
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'eval': the method is declared in an interface type 184
UnnecessaryModifier Unnecessary modifier 'public' on method 'getLastError': the method is declared in an interface type 191
UnnecessaryModifier Unnecessary modifier 'public' on method 'intArrayEval': the method is declared in an interface type 193
UnnecessaryModifier Unnecessary modifier 'public' on method 'isConnected': the method is declared in an interface type 195
UnnecessaryModifier Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type 204
UnnecessaryModifier Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type 213
UnnecessaryModifier Unnecessary modifier 'public' on method 'listEval': the method is declared in an interface type 221
UnnecessaryModifier Unnecessary modifier 'public' on method 'loadLibrary': the method is declared in an interface type 223
UnnecessaryModifier Unnecessary modifier 'public' on method 'oneWayAnova': the method is declared in an interface type 232
UnnecessaryModifier Unnecessary modifier 'public' on method 'oneWayAnovaEval': the method is declared in an interface type 234
UnnecessaryModifier Unnecessary modifier 'public' on method 'remove': the method is declared in an interface type 241
UnnecessaryModifier Unnecessary modifier 'public' on method 'retrieveMatrix': the method is declared in an interface type 250
UnnecessaryModifier Unnecessary modifier 'public' on method 'rowApplyLinearModel': the method is declared in an interface type 261–262
UnnecessaryModifier Unnecessary modifier 'public' on method 'stringEval': the method is declared in an interface type 270
UnnecessaryModifier Unnecessary modifier 'public' on method 'stringListEval': the method is declared in an interface type 272
UnnecessaryModifier Unnecessary modifier 'public' on method 'twoWayAnova': the method is declared in an interface type 283–284
UnnecessaryModifier Unnecessary modifier 'public' on method 'twoWayAnovaEval': the method is declared in an interface type 300
UnnecessaryModifier Unnecessary modifier 'public' on method 'voidEval': the method is declared in an interface type 302

ubic/basecode/util/r/RConnectionFactory.java

Rule Violation Line
EmptyCatchBlock Avoid empty catch blocks 54–56

Priority 4

ubic/basecode/dataStructure/CountingMap.java

Rule Violation Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.util.Map.Entry' due to existing import 'java.util.Map' 133

ubic/basecode/graphics/ColorMatrix.java

Rule Violation Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'cern.colt.list.DoubleArrayList' due to existing import 'cern.colt.list.DoubleArrayList' 331

ubic/basecode/graphics/MatrixDisplay.java

Rule Violation Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 229
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 275
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 284

ubic/basecode/math/Distance.java

Rule Violation Line
UselessParentheses Useless parentheses. 105

ubic/basecode/math/Smooth.java

Rule Violation Line
UnusedImports Avoid unused imports such as 'ubic.basecode.math.linearmodels.MeanVarianceEstimator' 32

ubic/basecode/math/StringDistance.java

Rule Violation Line
UselessParentheses Useless parentheses. 153

ubic/basecode/math/Wilcoxon.java

Rule Violation Line
UselessParentheses Useless parentheses. 103
UselessParentheses Useless parentheses. 104–105
UselessParentheses Useless parentheses. 105

ubic/basecode/math/linalg/Blas.java

Rule Violation Line
ExtendsObject No need to explicitly extend Object. 127
UselessParentheses Useless parentheses. 717
UselessParentheses Useless parentheses. 717
UselessParentheses Useless parentheses. 788
UselessParentheses Useless parentheses. 788
UselessParentheses Useless parentheses. 914
UselessParentheses Useless parentheses. 914
UselessParentheses Useless parentheses. 1140
UselessParentheses Useless parentheses. 1140
UselessParentheses Useless parentheses. 1300
UselessParentheses Useless parentheses. 1300

ubic/basecode/math/linalg/Dqrsl.java

Rule Violation Line
ExtendsObject No need to explicitly extend Object. 95
UselessParentheses Useless parentheses. 243
UselessParentheses Useless parentheses. 244
UselessParentheses Useless parentheses. 610
UselessParentheses Useless parentheses. 611
UselessParentheses Useless parentheses. 611
UselessParentheses Useless parentheses. 612
UselessParentheses Useless parentheses. 613
UselessParentheses Useless parentheses. 614
UselessParentheses Useless parentheses. 614
UselessParentheses Useless parentheses. 694

ubic/basecode/math/linearmodels/DesignMatrix.java

Rule Violation Line
UnusedImports Avoid unused imports such as 'java.util.Collections' 20

ubic/basecode/math/linearmodels/MeanVarianceEstimator.java

Rule Violation Line
UselessParentheses Useless parentheses. 293

ubic/basecode/ontology/jena/ObjectPropertyImpl.java

Rule Violation Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'com.hp.hpl.jena.ontology.ObjectProperty' due to existing import 'com.hp.hpl.jena.ontology.ObjectProperty' 37

ubic/basecode/ontology/jena/PropertyFactory.java

Rule Violation Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 51
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 58
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 60
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Boolean' due to existing implicit import 'java.lang.*' 62
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Double' due to existing implicit import 'java.lang.*' 64
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Double' due to existing implicit import 'java.lang.*' 66
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Integer' due to existing implicit import 'java.lang.*' 68

ubic/basecode/util/DateUtil.java

Rule Violation Line
UselessParentheses Useless parentheses. 77

ubic/basecode/util/FileTools.java

Rule Violation Line
UselessParentheses Useless parentheses. 79–80
UselessParentheses Useless parentheses. 88–89
UselessParentheses Useless parentheses. 100

ubic/basecode/util/StringUtil.java

Rule Violation Line
UselessParentheses Useless parentheses. 186
UselessParentheses Useless parentheses. 186
UselessParentheses Useless parentheses. 260
UselessParentheses Useless parentheses. 262

ubic/basecode/util/r/AbstractRClient.java

Rule Violation Line
UselessParentheses Useless parentheses. 177

ubic/basecode/util/r/LinearModelSummaryImpl.java

Rule Violation Line
UselessParentheses Useless parentheses. 115

Files

ubic/basecode/dataStructure/CountingMap.java

Rule Violation Priority Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.util.Map.Entry' due to existing import 'java.util.Map' 4 133

ubic/basecode/dataStructure/graph/Graph.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'addNode': the method is declared in an interface type 3 27
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsKey': the method is declared in an interface type 3 29
UnnecessaryModifier Unnecessary modifier 'public' on method 'get': the method is declared in an interface type 3 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getNodeContents': the method is declared in an interface type 3 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'unmarkAll': the method is declared in an interface type 3 35

ubic/basecode/dataStructure/graph/GraphNode.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getGraph': the method is declared in an interface type 3 30
UnnecessaryModifier Unnecessary modifier 'public' on method 'getItem': the method is declared in an interface type 3 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'getKey': the method is declared in an interface type 3 40
UnnecessaryModifier Unnecessary modifier 'public' on method 'setItem': the method is declared in an interface type 3 47
UnnecessaryModifier Unnecessary modifier 'public' on method 'setValue': the method is declared in an interface type 3 55

ubic/basecode/dataStructure/matrix/Matrix2D.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'abstract' on interface 'Matrix2D': interface types are implicitly abstract 3 31–218
UnnecessaryModifier Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type 3 38
UnnecessaryModifier Unnecessary modifier 'public' on method 'asDoubles': the method is declared in an interface type 3 49
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 3 56
UnnecessaryModifier Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type 3 63
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type 3 69
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type 3 75
UnnecessaryModifier Unnecessary modifier 'public' on method 'getByKeys': the method is declared in an interface type 3 81
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type 3 89
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type 3 97
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type 3 102
UnnecessaryModifier Unnecessary modifier 'public' on method 'getEntry': the method is declared in an interface type 3 109
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type 3 117
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type 3 125
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNameMapIterator': the method is declared in an interface type 3 130
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type 3 135
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type 3 142
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type 3 148
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type 3 153
UnnecessaryModifier Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type 3 162
UnnecessaryModifier Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type 3 169
UnnecessaryModifier Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type 3 176
UnnecessaryModifier Unnecessary modifier 'public' on method 'set': the method is declared in an interface type 3 183
UnnecessaryModifier Unnecessary modifier 'public' on method 'setByKeys': the method is declared in an interface type 3 190
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnName': the method is declared in an interface type 3 198
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type 3 203
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowName': the method is declared in an interface type 3 211
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type 3 216

ubic/basecode/dataStructure/matrix/Matrix3D.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type 3 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'addRowName': the method is declared in an interface type 3 43
UnnecessaryModifier Unnecessary modifier 'public' on method 'addSliceName': the method is declared in an interface type 3 51
UnnecessaryModifier Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type 3 58
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type 3 66
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type 3 74
UnnecessaryModifier Unnecessary modifier 'public' on method 'containsSliceName': the method is declared in an interface type 3 82
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type 3 90
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type 3 98
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNameIterator': the method is declared in an interface type 3 100
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type 3 105
UnnecessaryModifier Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type 3 107
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type 3 115
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type 3 123
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNameIterator': the method is declared in an interface type 3 128
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type 3 133
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceIndexByName': the method is declared in an interface type 3 141
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceName': the method is declared in an interface type 3 149
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceNameIterator': the method is declared in an interface type 3 151
UnnecessaryModifier Unnecessary modifier 'public' on method 'getSliceNames': the method is declared in an interface type 3 153
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type 3 160
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type 3 166
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type 3 171
UnnecessaryModifier Unnecessary modifier 'public' on method 'hasSliceNames': the method is declared in an interface type 3 173
UnnecessaryModifier Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type 3 183
UnnecessaryModifier Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type 3 190
UnnecessaryModifier Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type 3 197
UnnecessaryModifier Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type 3 202
UnnecessaryModifier Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type 3 207
UnnecessaryModifier Unnecessary modifier 'public' on method 'setSliceNames': the method is declared in an interface type 3 209
UnnecessaryModifier Unnecessary modifier 'public' on method 'slices': the method is declared in an interface type 3 211

ubic/basecode/dataStructure/matrix/ObjectMatrix.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'get': the method is declared in an interface type 3 29
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColumn': the method is declared in an interface type 3 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRow': the method is declared in an interface type 3 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'subset': the method is declared in an interface type 3 42
UnnecessaryModifier Unnecessary modifier 'public' on method 'subsetColumns': the method is declared in an interface type 3 48

ubic/basecode/dataStructure/matrix/PrimitiveMatrix.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getColObj': the method is declared in an interface type 3 33
UnnecessaryModifier Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type 3 40
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRowObj': the method is declared in an interface type 3 46

ubic/basecode/dataStructure/matrix/RCDoubleMatrix1D.java

Rule Violation Priority Line
UnusedFormalParameter Avoid unused constructor parameters such as 'length'. 3 53

ubic/basecode/datafilter/Filter.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'filter': the method is declared in an interface type 3 39

ubic/basecode/graphics/ColorMatrix.java

Rule Violation Priority Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'cern.colt.list.DoubleArrayList' due to existing import 'cern.colt.list.DoubleArrayList' 4 331

ubic/basecode/graphics/MatrixDisplay.java

Rule Violation Priority Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 4 229
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 4 275
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.io.IOException' due to existing import 'java.io.IOException' 4 284

ubic/basecode/io/excel/CreateSpreadSheet.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 45–47

ubic/basecode/io/reader/AbstractMatrixReader.java

Rule Violation Priority Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 2 66
EmptyIfStmt Avoid empty if statements 3 103–106
EmptyIfStmt Avoid empty if statements 3 109–111

ubic/basecode/io/reader/DoubleMatrixReader.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 85–87
EmptyIfStmt Avoid empty if statements 3 311–313

ubic/basecode/io/reader/SparseDoubleMatrixReader.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 78–80
EmptyIfStmt Avoid empty if statements 3 91–93
UnnecessaryConversionTemporary Avoid unnecessary temporaries when converting primitives to Strings 3 183
UnnecessaryConversionTemporary Avoid unnecessary temporaries when converting primitives to Strings 3 184

ubic/basecode/io/reader/StringMatrixReader.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 101–103

ubic/basecode/math/DescriptiveWithMissing.java

Rule Violation Priority Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 2 228

ubic/basecode/math/Distance.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 105

ubic/basecode/math/MatrixStats.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 186–188
EmptyIfStmt Avoid empty if statements 3 196–198
EmptyIfStmt Avoid empty if statements 3 206–208
EmptyIfStmt Avoid empty if statements 3 216–218

ubic/basecode/math/Smooth.java

Rule Violation Priority Line
UnusedImports Avoid unused imports such as 'ubic.basecode.math.linearmodels.MeanVarianceEstimator' 4 32

ubic/basecode/math/StringDistance.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 153

ubic/basecode/math/Wilcoxon.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 103
UselessParentheses Useless parentheses. 4 104–105
UselessParentheses Useless parentheses. 4 105
CollapsibleIfStatements These nested if statements could be combined 3 135–138

ubic/basecode/math/distribution/DensityGenerator.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'density': the method is declared in an interface type 3 33

ubic/basecode/math/distribution/ProbabilityComputer.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type 3 35
UnnecessaryModifier Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type 3 44

ubic/basecode/math/linalg/Blas.java

Rule Violation Priority Line
ExtendsObject No need to explicitly extend Object. 4 127
UnnecessaryReturn Avoid unnecessary return statements 3 178
UnnecessaryReturn Avoid unnecessary return statements 3 419
UnnecessaryReturn Avoid unnecessary return statements 3 468
UnnecessaryReturn Avoid unnecessary return statements 3 522
UnnecessaryReturn Avoid unnecessary return statements 3 576
UnnecessaryReturn Avoid unnecessary return statements 3 685
UselessParentheses Useless parentheses. 4 717
UselessParentheses Useless parentheses. 4 717
UnnecessaryReturn Avoid unnecessary return statements 3 759
UselessParentheses Useless parentheses. 4 788
UselessParentheses Useless parentheses. 4 788
UnnecessaryReturn Avoid unnecessary return statements 3 833
UnnecessaryReturn Avoid unnecessary return statements 3 883
UselessParentheses Useless parentheses. 4 914
UselessParentheses Useless parentheses. 4 914
UselessParentheses Useless parentheses. 4 1140
UselessParentheses Useless parentheses. 4 1140
UnnecessaryReturn Avoid unnecessary return statements 3 1159
UnnecessaryReturn Avoid unnecessary return statements 3 1222
UnnecessaryReturn Avoid unnecessary return statements 3 1270
UselessParentheses Useless parentheses. 4 1300
UselessParentheses Useless parentheses. 4 1300
UnnecessaryReturn Avoid unnecessary return statements 3 1353

ubic/basecode/math/linalg/Dqrsl.java

Rule Violation Priority Line
ExtendsObject No need to explicitly extend Object. 4 95
UselessParentheses Useless parentheses. 4 243
UselessParentheses Useless parentheses. 4 244
CollapsibleIfStatements These nested if statements could be combined 3 358–377
UnnecessaryReturn Avoid unnecessary return statements 3 390
UselessParentheses Useless parentheses. 4 610
UselessParentheses Useless parentheses. 4 611
UselessParentheses Useless parentheses. 4 611
UselessParentheses Useless parentheses. 4 612
UselessParentheses Useless parentheses. 4 613
UselessParentheses Useless parentheses. 4 614
UselessParentheses Useless parentheses. 4 614
UselessParentheses Useless parentheses. 4 694

ubic/basecode/math/linalg/QRDecomposition.java

Rule Violation Priority Line
UnusedPrivateField Avoid unused private fields such as 'effects'. 3 93

ubic/basecode/math/linearmodels/DesignMatrix.java

Rule Violation Priority Line
UnusedImports Avoid unused imports such as 'java.util.Collections' 4 20
CollapsibleIfStatements These nested if statements could be combined 3 552–555

ubic/basecode/math/linearmodels/LeastSquaresFit.java

Rule Violation Priority Line
UnusedFormalParameter Avoid unused method parameters such as 'ypsize'. 3 1071

ubic/basecode/math/linearmodels/MeanVarianceEstimator.java

Rule Violation Priority Line
TooManyStaticImports Too many static imports may lead to messy code 3 15–337
UselessParentheses Useless parentheses. 4 293

ubic/basecode/math/linearmodels/ModeratedTstat.java

Rule Violation Priority Line
UnusedPrivateField Avoid unused private fields such as 'trigammainverse'. 3 54
UnnecessaryModifier Unnecessary modifier 'final' on method 'okVars': private methods cannot be overridden 3 99–107
UnnecessaryModifier Unnecessary modifier 'final' on method 'okDfs': private methods cannot be overridden 3 109–118

ubic/basecode/ontology/jena/ObjectPropertyImpl.java

Rule Violation Priority Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'com.hp.hpl.jena.ontology.ObjectProperty' due to existing import 'com.hp.hpl.jena.ontology.ObjectProperty' 4 37

ubic/basecode/ontology/jena/PropertyFactory.java

Rule Violation Priority Line
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 4 51
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 4 58
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.String' due to existing implicit import 'java.lang.*' 4 60
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Boolean' due to existing implicit import 'java.lang.*' 4 62
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Double' due to existing implicit import 'java.lang.*' 4 64
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Double' due to existing implicit import 'java.lang.*' 4 66
UnnecessaryFullyQualifiedName Unnecessary use of fully qualified name 'java.lang.Integer' due to existing implicit import 'java.lang.*' 4 68

ubic/basecode/ontology/model/DatatypeProperty.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getType': the method is declared in an interface type 3 23

ubic/basecode/ontology/model/ObjectProperty.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRange': the method is declared in an interface type 3 29

ubic/basecode/ontology/model/OntologyCardinalityRestriction.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on enum 'CardinalityType': the enum is declared in an interface type 3 27–29
UnnecessaryModifier Unnecessary modifier 'public' on method 'getCardinality': the method is declared in an interface type 3 31
UnnecessaryModifier Unnecessary modifier 'public' on method 'getCardinalityType': the method is declared in an interface type 3 33

ubic/basecode/ontology/model/OntologyClassRestriction.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type 3 27

ubic/basecode/ontology/model/OntologyDatatypeRestriction.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type 3 27

ubic/basecode/ontology/model/OntologyIndividual.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getInstanceOf': the method is declared in an interface type 3 34

ubic/basecode/ontology/model/OntologyProperty.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'isFunctional': the method is declared in an interface type 3 30

ubic/basecode/ontology/model/OntologyRestriction.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'getRestrictionOn': the method is declared in an interface type 3 29

ubic/basecode/ontology/ncbo/AnnotatorResponse.java

Rule Violation Priority Line
CollapsibleIfStatements These nested if statements could be combined 3 87–89

ubic/basecode/util/DateUtil.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 77

ubic/basecode/util/FileTools.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 79–80
UselessParentheses Useless parentheses. 4 88–89
UselessParentheses Useless parentheses. 4 100
CollapsibleIfStatements These nested if statements could be combined 3 567–569

ubic/basecode/util/PrettyPrinter.java

Rule Violation Priority Line
EmptyCatchBlock Avoid empty catch blocks 3 69–71

ubic/basecode/util/SQLUtils.java

Rule Violation Priority Line
UnusedPrivateField Avoid unused private fields such as 'bac'. 3 33

ubic/basecode/util/StatusViewer.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'clear': the method is declared in an interface type 3 33
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 3 40
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 3 45
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type 3 50
UnnecessaryModifier Unnecessary modifier 'public' on method 'showProgress': the method is declared in an interface type 3 52
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type 3 59
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type 3 65
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'showWarning': the method is declared in an interface type 3 70

ubic/basecode/util/StringUtil.java

Rule Violation Priority Line
AvoidBranchingStatementAsLastInLoop Avoid using a branching statement as the last in a loop. 2 149
UselessParentheses Useless parentheses. 4 186
UselessParentheses Useless parentheses. 4 186
UselessParentheses Useless parentheses. 4 260
UselessParentheses Useless parentheses. 4 262

ubic/basecode/util/r/AbstractRClient.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 177
EmptyIfStmt Avoid empty if statements 3 584–586

ubic/basecode/util/r/HTest.java

Rule Violation Priority Line
EmptyIfStmt Avoid empty if statements 3 41–43

ubic/basecode/util/r/LinearModelSummaryImpl.java

Rule Violation Priority Line
UselessParentheses Useless parentheses. 4 115

ubic/basecode/util/r/RClient.java

Rule Violation Priority Line
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 3 44
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 3 51
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 3 58
UnnecessaryModifier Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type 3 60
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type 3 66
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type 3 73
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 3 81
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 3 89
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type 3 98
UnnecessaryModifier Unnecessary modifier 'public' on method 'assignStringList': the method is declared in an interface type 3 106
UnnecessaryModifier Unnecessary modifier 'public' on method 'booleanDoubleArrayEval': the method is declared in an interface type 3 116
UnnecessaryModifier Unnecessary modifier 'public' on method 'dataFrame': the method is declared in an interface type 3 125
UnnecessaryModifier Unnecessary modifier 'public' on method 'dataFrameEval': the method is declared in an interface type 3 133
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayDoubleArrayEval': the method is declared in an interface type 3 143
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayEval': the method is declared in an interface type 3 151
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleArrayTwoDoubleArrayEval': the method is declared in an interface type 3 163–164
UnnecessaryModifier Unnecessary modifier 'public' on method 'doubleTwoDoubleArrayEval': the method is declared in an interface type 3 176
UnnecessaryModifier Unnecessary modifiers 'public abstract' on method 'eval': the method is declared in an interface type 3 184
UnnecessaryModifier Unnecessary modifier 'public' on method 'getLastError': the method is declared in an interface type 3 191
UnnecessaryModifier Unnecessary modifier 'public' on method 'intArrayEval': the method is declared in an interface type 3 193
UnnecessaryModifier Unnecessary modifier 'public' on method 'isConnected': the method is declared in an interface type 3 195
UnnecessaryModifier Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type 3 204
UnnecessaryModifier Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type 3 213
UnnecessaryModifier Unnecessary modifier 'public' on method 'listEval': the method is declared in an interface type 3 221
UnnecessaryModifier Unnecessary modifier 'public' on method 'loadLibrary': the method is declared in an interface type 3 223
UnnecessaryModifier Unnecessary modifier 'public' on method 'oneWayAnova': the method is declared in an interface type 3 232
UnnecessaryModifier Unnecessary modifier 'public' on method 'oneWayAnovaEval': the method is declared in an interface type 3 234
UnnecessaryModifier Unnecessary modifier 'public' on method 'remove': the method is declared in an interface type 3 241
UnnecessaryModifier Unnecessary modifier 'public' on method 'retrieveMatrix': the method is declared in an interface type 3 250
UnnecessaryModifier Unnecessary modifier 'public' on method 'rowApplyLinearModel': the method is declared in an interface type 3 261–262
UnnecessaryModifier Unnecessary modifier 'public' on method 'stringEval': the method is declared in an interface type 3 270
UnnecessaryModifier Unnecessary modifier 'public' on method 'stringListEval': the method is declared in an interface type 3 272
UnnecessaryModifier Unnecessary modifier 'public' on method 'twoWayAnova': the method is declared in an interface type 3 283–284
UnnecessaryModifier Unnecessary modifier 'public' on method 'twoWayAnovaEval': the method is declared in an interface type 3 300
UnnecessaryModifier Unnecessary modifier 'public' on method 'voidEval': the method is declared in an interface type 3 302

ubic/basecode/util/r/RConnectionFactory.java

Rule Violation Priority Line
EmptyCatchBlock Avoid empty catch blocks 3 54–56

Processing Errors

Filename Problem
ubic/basecode/math/SpecFunc.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/math/SpecFunc.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/math/SpecFunc.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 169, Column 64: Cannot use lambda expressions when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadLambdaUsage(JavaParser.java:113)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LambdaExpression(JavaParser.java:4548)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryPrefix(JavaParser.java:4480)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4304)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5046)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableInitializer(JavaParser.java:1998)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableDeclarator(JavaParser.java:1898)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LocalVariableDeclaration(JavaParser.java:5561)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5469)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/math/linearmodels/GenericAnovaResultImpl.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/math/linearmodels/GenericAnovaResultImpl.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/math/linearmodels/GenericAnovaResultImpl.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 121, Column 22: Cannot use lambda expressions when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadLambdaUsage(JavaParser.java:113)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LambdaExpression(JavaParser.java:4548)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryPrefix(JavaParser.java:4480)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4304)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ReturnStatement(JavaParser.java:6407)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Statement(JavaParser.java:5300)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5472)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/jena/AbstractOntologyService.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/AbstractOntologyService.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/AbstractOntologyService.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 90, Column 104: Cannot use method references when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadMethodReferenceUsage(JavaParser.java:118)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodReference(JavaParser.java:4388)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MemberSelector(JavaParser.java:4354)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4805)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableInitializer(JavaParser.java:1998)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableDeclarator(JavaParser.java:1898)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.FieldDeclaration(JavaParser.java:1850)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1800)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/jena/JenaUtils.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/JenaUtils.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/JenaUtils.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 57, Column 21: Cannot use lambda expressions when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadLambdaUsage(JavaParser.java:113)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LambdaExpression(JavaParser.java:4548)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryPrefix(JavaParser.java:4480)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4304)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.StatementExpression(JavaParser.java:5656)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Statement(JavaParser.java:5274)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5472)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/jena/OntologyIndexer.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/OntologyIndexer.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/OntologyIndexer.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 201, Column 47: Cannot use lambda expressions when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadLambdaUsage(JavaParser.java:113)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LambdaExpression(JavaParser.java:4548)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryPrefix(JavaParser.java:4480)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4304)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableInitializer(JavaParser.java:1998)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.VariableDeclarator(JavaParser.java:1898)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LocalVariableDeclaration(JavaParser.java:5561)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5469)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TryStatement(JavaParser.java:6516)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Statement(JavaParser.java:5309)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5472)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/jena/OntologyTermImpl.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/OntologyTermImpl.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/jena/OntologyTermImpl.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 64, Column 85: Cannot use method references when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadMethodReferenceUsage(JavaParser.java:118)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodReference(JavaParser.java:4388)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MemberSelector(JavaParser.java:4354)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4805)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ReturnStatement(JavaParser.java:6407)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Statement(JavaParser.java:5300)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5472)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/model/OntologyTerm.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/model/OntologyTerm.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/model/OntologyTerm.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 55, Column 5: Cannot use default implementations in interfaces when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadDefaultImplementationUsage(JavaParser.java:123)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Modifiers(JavaParser.java:739)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1790)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/ontology/providers/OntologyService.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/providers/OntologyService.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/ontology/providers/OntologyService.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 201, Column 5: Cannot use default implementations in interfaces when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadDefaultImplementationUsage(JavaParser.java:123)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Modifiers(JavaParser.java:739)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1790)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more
ubic/basecode/util/r/GenericAnovaResultImpl.java PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/util/r/GenericAnovaResultImpl.java 
net.sourceforge.pmd.PMDException: Error while parsing /space/jenkins/.jenkins/workspace/basecode/src/ubic/basecode/util/r/GenericAnovaResultImpl.java
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:110)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:89)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCode(SourceCodeProcessor.java:51)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:78)
	at net.sourceforge.pmd.processor.PmdRunnable.call(PmdRunnable.java:24)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: net.sourceforge.pmd.lang.java.ast.ParseException: Line 201, Column 22: Cannot use lambda expressions when running in JDK inferior to 1.8 mode!
	at net.sourceforge.pmd.lang.java.ast.JavaParser.throwParseException(JavaParser.java:30)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.checkForBadLambdaUsage(JavaParser.java:113)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.LambdaExpression(JavaParser.java:4548)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryPrefix(JavaParser.java:4480)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4304)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ArgumentList(JavaParser.java:5034)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Arguments(JavaParser.java:5000)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimarySuffix(JavaParser.java:4826)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PrimaryExpression(JavaParser.java:4312)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.PostfixExpression(JavaParser.java:4126)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpressionNotPlusMinus(JavaParser.java:4024)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.UnaryExpression(JavaParser.java:3901)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MultiplicativeExpression(JavaParser.java:3816)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AdditiveExpression(JavaParser.java:3763)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ShiftExpression(JavaParser.java:3706)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.RelationalExpression(JavaParser.java:3645)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InstanceOfExpression(JavaParser.java:3574)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.EqualityExpression(JavaParser.java:3521)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.AndExpression(JavaParser.java:3481)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ExclusiveOrExpression(JavaParser.java:3441)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.InclusiveOrExpression(JavaParser.java:3401)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalAndExpression(JavaParser.java:3361)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalOrExpression(JavaParser.java:3321)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ConditionalExpression(JavaParser.java:3283)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Expression(JavaParser.java:3140)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ReturnStatement(JavaParser.java:6407)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Statement(JavaParser.java:5300)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.BlockStatement(JavaParser.java:5472)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.Block(JavaParser.java:5389)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.MethodDeclaration(JavaParser.java:2121)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBodyDeclaration(JavaParser.java:1802)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceBody(JavaParser.java:1755)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.ClassOrInterfaceDeclaration(JavaParser.java:880)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.TypeDeclaration(JavaParser.java:782)
	at net.sourceforge.pmd.lang.java.ast.JavaParser.CompilationUnit(JavaParser.java:502)
	at net.sourceforge.pmd.lang.java.AbstractJavaParser.parse(AbstractJavaParser.java:62)
	at net.sourceforge.pmd.SourceCodeProcessor.parse(SourceCodeProcessor.java:121)
	at net.sourceforge.pmd.SourceCodeProcessor.processSource(SourceCodeProcessor.java:185)
	at net.sourceforge.pmd.SourceCodeProcessor.processSourceCodeWithoutCache(SourceCodeProcessor.java:107)
	... 10 more