Surefire Report

Summary

[Summary] [Package List] [Test Cases]


Tests Errors Failures Skipped Success Rate Time
740 2 1 3 99.189% 75.804

Note: failures are anticipated and checked for with assertions while errors are unanticipated.


Package List

[Summary] [Package List] [Test Cases]


Package Tests Errors Failures Skipped Success Rate Time
ubic.basecode.io 15 0 0 0 100% 0.049
ubic.basecode.math.linalg 5 0 0 0 100% 0.015
ubic.basecode.util 73 0 0 0 100% 5.505
ubic.basecode.dataStructure.params 2 0 0 0 100% 0.111
ubic.basecode.graphics 4 0 0 0 100% 0.369
ubic.basecode.ontology.search 13 2 0 0 84.615% 39.913
ubic.basecode.io.writer 4 0 0 0 100% 0.007
ubic.basecode.ontology.ncbo 3 0 0 3 0% 0.002
ubic.basecode.math.distribution 9 0 0 0 100% 0.02
ubic.basecode.ontology.providers 5 0 1 0 80% 10.17
ubic.basecode.util.r 42 0 0 0 100% 7.139
ubic.basecode.math.linearmodels 36 0 0 0 100% 5.839
ubic.basecode.math.metaanalysis 19 0 0 0 100% 0.003
ubic.basecode.ontology.jena 2 0 0 0 100% 0.055
ubic.basecode.dataStructure.graph 11 0 0 0 100% 0.246
ubic.basecode.dataStructure.matrix 193 0 0 0 100% 0.277
ubic.basecode.math 192 0 0 0 100% 4.024
ubic.basecode.io.reader 29 0 0 0 100% 0.628
ubic.basecode.datafilter 50 0 0 0 100% 0.119
ubic.basecode.ontology 5 0 0 0 100% 1.173
ubic.basecode.dataStructure.tree 7 0 0 0 100% 0
ubic.basecode.dataStructure 18 0 0 0 100% 0.002
ubic.basecode.io.excel 3 0 0 0 100% 0.138

Note: package statistics are not computed recursively, they only sum up all of its testsuites numbers.

ubic.basecode.io

Class Tests Errors Failures Skipped Success Rate Time
TestByteArrayConverter 15 0 0 0 100% 0.049

ubic.basecode.math.linalg

Class Tests Errors Failures Skipped Success Rate Time
QRDecompositionTest 5 0 0 0 100% 0.015

ubic.basecode.util

Class Tests Errors Failures Skipped Success Rate Time
ConfigUtilsTest 13 0 0 0 100% 0.106
FileToolsTest 32 0 0 0 100% 0.036
PrettyPrinterTest 1 0 0 0 100% 0.001
SQLUtilsTest 1 0 0 0 100% 0
TestStringUtil 8 0 0 0 100% 0.006
BatchIteratorTest 3 0 0 0 100% 0.001
StringUtilTest 5 0 0 0 100% 0
NetUtilsTest 4 0 0 0 100% 5.344
DateUtilTest 6 0 0 0 100% 0.011

ubic.basecode.dataStructure.params

Class Tests Errors Failures Skipped Success Rate Time
ParamGrabberTest 1 0 0 0 100% 0
ParameterKeeperTest 1 0 0 0 100% 0.111

ubic.basecode.graphics

Class Tests Errors Failures Skipped Success Rate Time
MatrixDisplayTest 4 0 0 0 100% 0.369

ubic.basecode.ontology.search

Class Tests Errors Failures Skipped Success Rate Time
OntologySearchTest 13 2 0 0 84.615% 39.913

ubic.basecode.io.writer

Class Tests Errors Failures Skipped Success Rate Time
TestHistogramWriter 1 0 0 0 100% 0.002
MatrixWriterTest 3 0 0 0 100% 0.005

ubic.basecode.ontology.ncbo

Class Tests Errors Failures Skipped Success Rate Time
AnnotatorClientTest 3 0 0 3 0% 0.002

ubic.basecode.math.distribution

Class Tests Errors Failures Skipped Success Rate Time
UniformDensityComputerTest 1 0 0 0 100% 0
TestWishart 1 0 0 0 100% 0.002
HistogramSamplerTest 1 0 0 0 100% 0.016
NormalProbabilityComputerTest 4 0 0 0 100% 0.001
HistogramTest 2 0 0 0 100% 0.001

ubic.basecode.ontology.providers

Class Tests Errors Failures Skipped Success Rate Time
ObiServiceTest 2 0 1 0 50% 8.176
AbstractOntologyServiceTest 3 0 0 0 100% 1.994

ubic.basecode.util.r

Class Tests Errors Failures Skipped Success Rate Time
JRIClientTest 21 0 0 0 100% 0.002
RServeClientTest 21 0 0 0 100% 7.137

ubic.basecode.math.linearmodels

Class Tests Errors Failures Skipped Success Rate Time
MeanVarianceEstimatorTest 5 0 0 0 100% 0.045
LeastSquaresFitTest 20 0 0 0 100% 5.658
ModeratedTstatTest 6 0 0 0 100% 0.131
DesignMatrixTest 5 0 0 0 100% 0.005

ubic.basecode.math.metaanalysis

Class Tests Errors Failures Skipped Success Rate Time
TestCorrelationEffectMetaAnalysis 9 0 0 0 100% 0.002
MetaAnalysisTest 2 0 0 0 100% 0.001
TestMeanDifferenceMetaAnalysis 8 0 0 0 100% 0

ubic.basecode.ontology.jena

Class Tests Errors Failures Skipped Success Rate Time
OntologyLoaderTest 2 0 0 0 100% 0.055

ubic.basecode.dataStructure.graph

Class Tests Errors Failures Skipped Success Rate Time
TestDirectedGraph 11 0 0 0 100% 0.246

ubic.basecode.dataStructure.matrix

Class Tests Errors Failures Skipped Success Rate Time
CompressedSparseDoubleMatrixTest 38 0 0 0 100% 0.108
DenseDoubleMatrixTest 39 0 0 0 100% 0.061
CompressedNamedBitMatrixTest 9 0 0 0 100% 0.003
FastRowAccessDoubleMatrixTest 39 0 0 0 100% 0.042
DenseDouble3dMatrixTest 4 0 0 0 100% 0.003
StringMatrixTest 4 0 0 0 100% 0.004
MatrixUtilTest 7 0 0 0 100% 0.023
SparseRaggedDoubleMatrixTest 10 0 0 0 100% 0.016
RCDoubleMatrix1DTest 3 0 0 0 100% 0
SparseDoubleMatrixTest 24 0 0 0 100% 0.011
IntegerMatrixTest 16 0 0 0 100% 0.006

ubic.basecode.math

Class Tests Errors Failures Skipped Success Rate Time
TestSpecFunc 7 0 0 0 100% 0.001
TestDescriptiveWithMissing 44 0 0 0 100% 0.002
TestRank 14 0 0 0 100% 0.003
RandomChooserTest 7 0 0 0 100% 0.497
TestMatrixStats 15 0 0 0 100% 0.02
StringDistanceTest 16 0 0 0 100% 0.003
TestKSTest 2 0 0 0 100% 0
TestROC 3 0 0 0 100% 0.03
TestWilcoxon 15 0 0 0 100% 3.256
TestMatrixNormalizer 2 0 0 0 100% 0.001
TestStats 14 0 0 0 100% 0
TestMathUtil 5 0 0 0 100% 0
KruskalWallisTest 1 0 0 0 100% 0.001
TestMatrixRowStats 6 0 0 0 100% 0.001
SingularValueDecompositionTest 1 0 0 0 100% 0.102
CorrelationStatsTest 18 0 0 0 100% 0.059
PrecisionRecallTest 5 0 0 0 100% 0
MultipleTestCorrectionTest 5 0 0 0 100% 0.048
DistanceTest 12 0 0 0 100% 0

ubic.basecode.io.reader

Class Tests Errors Failures Skipped Success Rate Time
TestSparseRaggedDouble2DNamedMatrixReader 3 0 0 0 100% 0.577
TestDoubleMatrixReader 15 0 0 0 100% 0.042
TestSparseDoubleMatrixReader 2 0 0 0 100% 0.005
TestMapReader 3 0 0 0 100% 0
TestStringMatrixReader 4 0 0 0 100% 0.001
HistogramReaderTest 2 0 0 0 100% 0.003

ubic.basecode.datafilter

Class Tests Errors Failures Skipped Success Rate Time
TestRowNameFilter 4 0 0 0 100% 0.012
TestRowAffyNameFilter 2 0 0 0 100% 0.005
TestRowAbsentFilter 9 0 0 0 100% 0.016
TestRowMissingFilter 11 0 0 0 100% 0.012
TestRowLevelFilter 23 0 0 0 100% 0.074
TestItemLevelFilter 1 0 0 0 100% 0

ubic.basecode.ontology

Class Tests Errors Failures Skipped Success Rate Time
OntologyTermTest 5 0 0 0 100% 1.173

ubic.basecode.dataStructure.tree

Class Tests Errors Failures Skipped Success Rate Time
BinaryTreeTest 7 0 0 0 100% 0

ubic.basecode.dataStructure

Class Tests Errors Failures Skipped Success Rate Time
StringToStringSetMapTest 6 0 0 0 100% 0.001
DoubleAddingMapTest 1 0 0 0 100% 0
CountingMapTest 6 0 0 0 100% 0.001
BitUtilTest 5 0 0 0 100% 0

ubic.basecode.io.excel

Class Tests Errors Failures Skipped Success Rate Time
ExcelUtilTest 3 0 0 0 100% 0.138

Test Cases

[Summary] [Package List] [Test Cases]

JRIClientTest

testExec 0
testListEvalA 0
testListEvalB 0
testExecError 0
testDataFrameA 0
testAssignAndRetrieveMatrix 0
testAnovaA 0
testAnovaB 0
testAnovaC 0
testAnovaD 0
testAnovaE 0
testAnovaF 0
testLimmaA 0
testExecDoubleArray 0.001
testAssignAndRetrieveMatrixB 0
testAssignAndRetrieveMatrixD 0
testLinearModelA 0
testLinearModelB 0
testLinearModelC 0
testLinearModelD 0
testStringListEvalB 0

RServeClientTest

testExec 0.93
testListEvalA 0.306
testListEvalB 0.313
testExecError 0.316
testDataFrameA 0.306
testAssignAndRetrieveMatrix 0.303
testAnovaA 0.309
testAnovaB 0.31
testAnovaC 0.31
testAnovaD 0.31
testAnovaE 0.306
testAnovaF 0.309
testLimmaA 0.309
testExecDoubleArray 0.304
testAssignAndRetrieveMatrixB 0.305
testAssignAndRetrieveMatrixD 0.307
testLinearModelA 0.308
testLinearModelB 0.307
testLinearModelC 0.308
testLinearModelD 0.306
testStringListEvalB 0.308

ConfigUtilsTest

testLoadConfigURL 0.046
testGetConfigBuilderFile 0.045
testGetConfigBuilderString 0.001
testGetConfigBuilderURLNew 0.001
testGetConfigBuilderStringNew 0.001
testLoadConfigString 0.001
testLoadConfigURLNew 0.001
testLoadConfigStringNewName 0.005
testGetConfigBuilderURL 0.001
testLoadConfigStringNew 0.001
testLoadConfigFile 0.001
testGetConfigBuilderFileNew 0.001
testLoadConfigFileNew 0

FileToolsTest

testHasImageExtension 0.002
testTestDir 0
testGetWithoutExtension 0.001
testGetLines 0.001
testTouch 0
testListDirectoryFiles 0.002
testAddImageExtension 0.001
testChangeExtension 0
testDeleteFilesAndDir 0.002
testCleanFileName 0.001
testgetStringListFromFile 0.001
testGetWithoutExtensionB 0.001
testGetWithoutExtensionC 0
testResourcetoPath 0.001
testCleanFileNameErr 0.001
testIsGZipped 0.001
testUnGzipFile 0.002
testCopyFileFailOnDirectoryOutput 0
testTestFileString 0.001
testGetCompressedFile 0.001
testCopyFile 0.001
testGetExtension 0
testCheckPathIsReadableFile 0.001
testIsZipped 0
testAddDataExtension 0.001
testGetCompressedFileZip 0.002
testTestFileFile 0
testCheckPathIsReadableFileNot 0.001
testCopyFileFailOnDirectoryInput 0.001
testGetInputStreamFromPlainOrCompressedFile 0
testHasXMLExtension 0.001
testUnzipFile 0.008

PrettyPrinterTest

testPrintBeans 0

SQLUtilsTest

testBlobToString 0

TestStringUtil

testTwoStringHashKey 0
testCsvSplitA 0.004
testCsvSplitB 0
testCsvSplitC 0
testCsvSplitD 0.001
testCsvSplitE 0
testCsvSplitF 0
testTwoStringHashKeyB 0

BatchIteratorTest

testBatches 0
testBatchIterator 0
testConcurrentModificationException 0

StringUtilTest

testMakeRnames 0
testCommonPrefixNone 0
testCommonSuffixNone 0
testCommonPrefix 0
testCommonSuffix 0

NetUtilsTest

testFtpFileSize 1.469
testCheckForFile 0.906
testFtpFileSizeDoesntExist 1.729
testDownloadFile 1.24

DateUtilTest

testgetRelative5yearsFromnow 0.004
testRange 0.002
testgetRelative5yearsago 0
testgetRelativeTomorrow 0.001
testgetRelativeDateDayago 0
testRangeBad 0.001

TestDirectedGraph

testDeleteLeaf1 0.002
testDeleteLeafFail 0.001
testGetChildren 0
testToString 0
testAddChild 0
testTopoSort 0
testAddParent 0.001
testDeleteLeafNotLeaf 0
testAddChildFail 0
testAddParentFail 0
testTreeView 0.24

CompressedSparseDoubleMatrixTest

testSubsetRows 0.01
testToArray 0.003
testSortByColumnAbsoluteValue 0.021
testGet 0.002
testSet 0.003
testRows2 0.002
testCopy 0.003
testGet2 0.002
testRows 0.002
testSet2 0.002
testSize 0.002
testToString 0.002
testGetRowByNameFail 0.001
testGetRowByNameNull 0.002
testSetIntIntObject 0.002
testGetRow2 0.002
testSubsetColumns 0.004
testViewRow 0.003
testColumns 0.001
testGetColRange 0.002
testGetByKeys 0.001
testGetColObj 0.002
testGetColumn 0.001
testIsMissing 0.004
testViewColumn 0.002
testGetColObj2 0.002
testGetObject 0.002
testGetRow 0.002
testGetRowObj 0.001
testGetRowRange 0.002
testGetRowByName 0.002
testIsMissing2 0.001
testGetColByNameFail 0.002
testGetColByNameNull 0.003
testGetRowObj2 0.002
testGetColByName 0.002
testGetRowArrayList2 0.002
testViewRow2 0.002

DenseDoubleMatrixTest

testConstructFromArray 0.002
testSubsetRows 0.002
testToArray 0.001
testSortByColumnAbsoluteValue 0.007
testGet 0.002
testSet 0.001
testRows2 0.001
testCopy 0.002
testGet2 0.002
testRows 0.001
testSet2 0.001
testSize 0.002
testToString 0.002
testGetRowByNameFail 0.001
testGetRowByNameNull 0.002
testSetIntIntObject 0.002
testGetRow2 0.001
testSubsetColumns 0.001
testViewRow 0.001
testColumns 0.002
testGetColRange 0.001
testGetByKeys 0.001
testGetColObj 0.001
testGetColumn 0.002
testIsMissing 0.002
testViewColumn 0.002
testGetColObj2 0.001
testGetObject 0.001
testGetRow 0.001
testGetRowObj 0.001
testGetRowRange 0.001
testGetRowByName 0.001
testIsMissing2 0.001
testGetColByNameFail 0.002
testGetColByNameNull 0.001
testGetRowObj2 0.001
testGetColByName 0.001
testGetRowArrayList2 0.001
testViewRow2 0.002

CompressedNamedBitMatrixTest

testGetOutOfBounds 0.001
testOverlap 0
testGet 0
testTotalBitCount 0
testOutOfBounds 0
testOutOfBounds2 0
testGetRowBitCount 0
testBitMatrix 0
testBitCount 0.001

FastRowAccessDoubleMatrixTest

testConstructFromArray 0.001
testSubsetRows 0.001
testToArray 0.001
testSortByColumnAbsoluteValue 0.004
testGet 0.001
testSet 0.001
testRows2 0.001
testCopy 0.002
testGet2 0.001
testRows 0.001
testSet2 0.001
testSize 0
testToString 0.001
testGetRowByNameFail 0.001
testGetRowByNameNull 0
testSetIntIntObject 0.002
testGetRow2 0.001
testSubsetColumns 0.001
testViewRow 0.001
testColumns 0.001
testGetColRange 0.001
testGetByKeys 0.001
testGetColObj 0.001
testGetColumn 0.001
testIsMissing 0.002
testViewColumn 0
testGetColObj2 0.001
testGetObject 0.001
testGetRow 0.001
testGetRowObj 0.001
testGetRowRange 0.001
testGetRowByName 0.001
testIsMissing2 0.001
testGetColByNameFail 0.001
testGetColByNameNull 0.001
testGetRowObj2 0.001
testGetColByName 0.001
testGetRowArrayList2 0.001
testViewRow2 0

DenseDouble3dMatrixTest

testget 0.002
testtostring 0.001
testgetcolobj 0
testgetrowobj 0

StringMatrixTest

testToString 0.001
testSubsetColumns 0.001
testGetColObj 0.001
testSubset 0.001

MatrixUtilTest

testSelectColumnsAndRowsBad 0.003
testSelectColumns 0.002
testDropColumn 0.002
testSelectColumnsAndRows 0.01
testRemoveMissing1 0.002
testRemoveMissing2 0.002
testSelectRows 0.002

SparseRaggedDoubleMatrixTest

testSubsetRows 0.011
testSubsetRowsFail 0
testRows 0.001
testGetRowMatrix1D 0.001
testGetRowArrayList 0
testColumns 0.001
testGetColRange 0
testAddrow 0.001
testGetRow 0
testGetRowRange 0

RCDoubleMatrix1DTest

testZSum 0
testAssignAr 0
testAssign 0

SparseDoubleMatrixTest

testSubsetCols 0.003
testSubsetRows 0.001
testToArray 0.001
testGet 0
testSet 0
testCopy 0.001
testRows 0
testSize 0
testToString 0.001
testGetRowArrayList 0
testViewRow 0
testColumns 0.001
testGetColRange 0
testGetByKeys 0
testGetColObj 0.001
testGetColumn 0.001
testIsMissing 0
testViewColumn 0
testGetObject 0
testGetRow 0
testGetRowObj 0.001
testGetRowRange 0
testGetRowByName 0
testGetColByName 0

IntegerMatrixTest

testGetEntry 0.003
testGet 0
testSet 0
testRows 0
testSize 0
testColumns 0.001
testSetByKeys 0
testToInteger 0
testGetByKeys 0
testGetColObj 0
testGetColumn 0.001
testIsMissing 0
testGetObject 0
testGetRow 0
testGetRowObj 0
testSetObj 0.001

ParamGrabberTest

test 0

ParameterKeeperTest

test 0.111

BinaryTreeTest

testGetRight 0
testInsertRight 0
testGetLeft 0
testGetRoot 0
testInsertLeft 0
testIsLeaf 0
testIsEmpty 0

StringToStringSetMapTest

testExpandedValues 0
testMatrix2 0.001
testExpandedSize 0
testWhereIs 0
testMatrix 0
testSeenValues 0

DoubleAddingMapTest

test 0

CountingMapTest

testSummation 0
testCount 0
testSeen 0
testIncrement 0
testSortedKeyList 0.001
testSortedKeyListBoolean 0

BitUtilTest

testGet 0
testSet 0
testClear 0
testCount 0
testToBool 0

TestRowNameFilter

testFilterString 0.002
testFilterExclude 0.004
testFilter 0.003
testFilterStringExclude 0.003

TestRowAffyNameFilter

testStringFilter 0.002
testFilter 0.003

TestRowAbsentFilter

testFilterKeepMarginal 0.003
testFilterPresentCountInvalid 0.001
testFilterWithMissing 0.002
testFilterNullFlags 0.001
testFilterWithMissingLessStringent 0.002
testFilterFractionInvalid 0.001
testFilterStringMatrix 0.002
testFilterFraction 0.002
testFilter 0.002

TestRowMissingFilter

testFilterPresentCountInvalid 0.001
testFilterWithMissingLowMaxFraction 0.001
testFilterWithMissing 0.001
testFilterWithMissingLessStringent 0.002
testFilterFractionInvalid2 0.001
testFilterFractionInvalid 0.001
testFilterStringMatrix 0.001
testFilterFraction 0.001
testFilter 0.001
testMaxFractionRemovedInvalid 0.001
testFilterNoFiltering 0.001

TestRowLevelFilter

testFilterMinHigh 0.004
testFilterFractionMaxRemoveHighAndLowBothFraction 0.003
testFilterMaxTooHigh 0.004
testFilterMedian 0.005
testFilterNoFilter 0.002
testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow 0.003
testFilterFractionMaxRemoveNegHigh 0.003
testFilterMax 0.002
testFilterMin 0.003
testFilterMaxFractionNoneRemoveNeg 0.003
testFilterMedianHigh 0.003
testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove 0.002
testFilterFractionMaxRemoveNeg 0.002
testFilterMaxFractionAll 0.003
testFilterFractionMaxRemoveHighAndLowBothLevels 0.002
testFilterMaxFraction 0.002
testFilterBadFraction 0.002
testFilterMaxFractionHigh 0.002
testFilterMaxFractionNone 0.003
testFilterFractionMaxRemoveHighAndLow 0.002
testFilterMeanHigh 0.013
testFilterMean 0.002
testFilterMaxHigh 0.002

TestItemLevelFilter

testFilter 0

MatrixDisplayTest

testWriteOutAsPNG2 0.348
testWriteOutAsPNG 0.006
testSaveImage 0.004
testSaveImageStandardize 0.011

ExcelUtilTest

testGetSheetFromFile 0.136
testGetSet 0
testSetFormula 0.002

TestSparseRaggedDouble2DNamedMatrixReader

testReadStreamAdjList 0.001
testReadInputStream 0.001
testReadStreamAdjListBig 0.575

TestDoubleMatrixReader

testReadChooseRowsBadfileName 0.001
testReadInputStreamMissingBad 0
testReadInputStreamGotColNameSkipColumn 0.001
testReadInputStreamRowCount 0
testReadInputStreamGotColName 0.001
testReadInputStreamGotRowName 0
testSmallNumbers 0.025
testReadInputStreamMissingSpaces 0.008
testReadBad 0.001
testBadFileName 0
testReadChooseRowsSkipcols 0
testReadBlankCorner 0.002
testReadInputStreamMissing 0.001
testReadChooseRows 0
testReadInputStreamColumnCount 0.001

TestSparseDoubleMatrixReader

testReadStream 0
testReadJW 0.005

TestMapReader

testRead 0
testReadNoHeader 0
testReadNoHeaderFile 0

TestStringMatrixReader

testReadInputStreamRowCount 0
testReadInputStreamGotColName 0.001
testReadInputStreamGotRowName 0
testReadInputStreamColumnCount 0

HistogramReaderTest

testHistogramReaderIs 0.003
testHistogramReaderString 0

TestHistogramWriter

testWriter 0.002

MatrixWriterTest

testWriteMatrixB 0.003
testWriteMatrix 0.001
testWrite3DMatrix 0.001

TestByteArrayConverter

testDoubleArrayToByteArrayConversionSpeed 0.004
testByteArrayToBooleans 0.003
testStringToDoubleArrayConversionSpeed 0.004
testByteArrayToDoubleConversionSpeed 0.004
testByteArrayToTabbedString 0.003
testDoubleArrayToBytes 0.003
testIntsToBytes 0.003
testBooleansToLongArray 0.002
testByteArrayToDoubles 0.002
testStringToBytes 0.004
testDoubleArrayToDelimitedStringConversionSpeed 0.004
testObjectToBytes 0.003
testBooleansToByteArray 0.005
testByteArrayToLongs 0.002
testByteArrayToDoubleMatrix 0.003

UniformDensityComputerTest

testDensity 0

TestWishart

testNextDoubleMatrix 0.002

HistogramSamplerTest

testNextSample 0.016

NormalProbabilityComputerTest

testProbabilityDoubleBoolean 0.001
testProbabilityDoubleBooleanLower 0
testInvalidVariance 0
testProbabilityDouble 0

HistogramTest

testGetBiggestBinSize 0.001
testGetApproximateQuantile 0

QRDecompositionTest

testScaledDesign 0.006
testSingular2 0.002
test1 0.004
test3 0.002
test2NoPivoting 0.001

MeanVarianceEstimatorTest

testVoom 0.033
testMeanVarianceNoDesignWithColsRowAllMissing 0
testDuplicateRows 0.011
testInterpolate 0
testMeanVarianceNoDesignWithMissing 0.001

LeastSquaresFitTest

testTwoWayAnovaUnfittable 0.019
testThreeWaySingular 0.092
testEstrogen 2.426
testVectorWeightedRegress 0
testNHBE 3.031
testLSFTwoLevels2 0.019
testLSFTwoLevels3 0.014
testSingular2 0.003
testVectorWeightedRegressWithMissing 0.001
testVectorRegress 0
testLSFThreeLevelsOneContinuousWithMissing3 0.002
testTwoWayAnovaWithInteractions 0.002
testLSFTwoLevels 0.002
testOneWayAnova 0.01
testTwoWayTwoLevelsOneContinousInteractionC 0.003
testLSFThreeLevelsOnecontinous2 0.001
testMatrixWeightedRegress 0
testSingular 0.007
testLSFTwoLevelsOneContinuous 0.021
testLSFOneContinuousWithMissing3 0.005

ModeratedTstatTest

testLimmaMissing 0.021
testFdist 0
testLimma 0.015
testSqueezeVarB 0.094
testSqueezeVar 0.001
testSqueezeVarWMissing 0

DesignMatrixTest

testInteractionC 0.001
test2 0.001
testA 0
testB 0.001
testInteractionAndRelevel 0.002

TestCorrelationEffectMetaAnalysis

testRunUFEffect 0.001
testRunZFEffect 0.001
testRunZRQval 0
testRunUFZscore 0
testRunZFZscore 0
testRunUFVar 0
testRunURBSV 0
testRunZFVar 0
testRunZRBSV 0

MetaAnalysisTest

testFisherCombinePvaluesB 0.001
testFisherCombinePvalues 0

TestMeanDifferenceMetaAnalysis

testRunRandomE 0
testRunRandomZ 0
testRunFixedE 0
testRunFixedQ 0
testRunFixedZ 0
testRunRandomBSV 0
testRunRandomVar 0
testRunFixedVar 0

TestSpecFunc

testdBinom 0
testCumHyperGeometricB 0
testTrigammaInverse 0
testCumHyperGeometric 0
testTrigammaInverseB 0
testHypergeometric 0
testCumHyperGeometricUT 0

TestDescriptiveWithMissing

testRankInterpolated 0
testKurtosis 0
testCorrelationA 0
testCorrelationB 0
testQuantileInverse 0
testStandardize 0
testIncrementalWeightedUpdate 0
testSumOfPowerDeviationsA 0
testOptimizedCorrelation 0
testMad 0
testMax 0
testMin 0
testSum 0
testMeanDoubleArB 0
testSumOfInversions 0
testLag1 0.001
testMean 0
testSkew 0
testDurbinWatson 0
testMeanAboveQuantile 0
testSumOfSquares 0
testProduct 0
testGeometricMean 0
testMeanDoubleAr 0
testSampleSkew 0
testQuantile 0
testVariance 0
testQuantiles 0
testSampleKurtosis 0
testDurbinWatsonTwo 0
testKurtosisList 0.001
testSumOfSquaredDeviations 0
testSampleStandardDeviation 0
testMeanEff 0
testSumOfPowers 0
testSampleVariance 0
testWeightedMean 0
testCovariance 0
testIncrementalUpdate 0
testMedian 0
testTrimmedMean 0
testIncrementalUpdateSums 0
testDurbinWatsonShort 0
testAutoCorrelation 0

TestRank

testRankTransformMapDesc 0
testRankTransformDoubleArrayListDesc 0
testRankTransformMap 0
testOrder 0.001
testRankWithTies 0
testWithNaNs 0
testRankTransformDoubleArrayList 0
testRankWithTiesB 0
testRankWithTiesC 0
testRankWithTiesD 0
testRankWithTiesE 0
testWithNaNs2 0
testWithNaNs3 0
testOrderB 0

RandomChooserTest

testChooseRandomDeck 0.021
testRepeatSubset 0.238
testChooserandomInts 0.008
testChooserandomWrep 0.001
testRandomSubset 0
testChooserandomInt 0.03
testRepeat 0.199

TestMatrixStats

testRbfNormalize 0.001
testSelfSquare 0
testStandardize 0.002
testCorrelationMatrix 0.002
testMax 0
testMin 0.001
testNan 0
testColSumsWithMissing 0
testLogTransform 0.001
testDoubleStandardize 0.005
testCov2Cor 0.002
testConvertToLog2Cpm 0.001
testConvertLog 0.001
testCountsPerMillionWithMissing 0
testCorrelationMatrixThreshold 0.004

StringDistanceTest

testWeightedHammingA 0
testWeightedHammingB 0
testWeightedHammingC 0
testHammingDistance 0
testBadMatch 0.002
testEditDistanceA 0
testEditDistanceB 0
testEditDistanceC 0
testEditDistanceD 0
testEditDistanceE 0
testEditDistanceF 0
testEditDistanceG 0
testEditDistanceH 0
testWeightedSuffixHammingA 0
testWeightedSuffixHammingB 0
testWeightedSuffixHammingC 0.001

TestKSTest

testKSTestTwoSample 0
testKSTestOneSample 0

TestROC

testBig 0.028
testAroc 0
testArocPvalue 0.002

TestWilcoxon

testWilxcoxonPExactB 0
testWilxcoxonPExactC 0
testWilxcoxonPExactD 3.246
testWilxcoxonPGaussB 0
testBGaussian 0
testFVolume 0.001
testWilxcoxonPVolume 0.003
testBig 0
testWilxcoxonPGauss 0
testWilcoxonPExactA 0
testCGaussian 0
testDVolume 0.001
testAExact 0.003
testWilxcoxonPWithTies 0
testEVolume 0

TestMatrixNormalizer

testQuantileNormalize 0
testQuantileNormalizeWithMissing 0.001

TestStats

testNormalizeDoubleArrayListdouble 0
testCdf 0
testRange 0
testMeanAboveQuantile 0
testCv 0
testCumulateRight 0
testQuantile 0
testIsValidFraction 0
testIsValidFraction2 0
testNumberOfDistinctValues 0
testCumulate 0
testQuantile75 0
testNormalizeDoubleArrayList 0
testNumberOfDistinctValuesNonNA 0

TestMathUtil

testMax 0
testSumArray 0
testFillRangeDown 0
testFillRange 0
testFillRangeNo 0

KruskalWallisTest

testKW 0

TestMatrixRowStats

testSumOfSquaresDoubleMatrixNamed 0
testMeans 0
testSums 0
testMeans2 0
testStandardDeviations 0
testSumOfSquaresDoubleMatrixNamedDoubleArrayList 0

SingularValueDecompositionTest

testSingularValueDecomposition 0.102

CorrelationStatsTest

testSpearmanPvalueA 0
testSpearmanPvalueB 0
testSpearmanPvalueD 0
testSpearmanPvalueE 0.035
testSpearmanPvalueF 0
testSpearmanPvalueG 0.018
testCorrelationForPvalue 0
testCorrelTooSmall 0
testInverseFisherTransform 0
testSpearmanPvalueTDist 0
testCorrel 0
testCorrelAsByte 0
testPvalue 0
testSpearmanPvalueA2 0
testSpearmanPvalueD2 0
testSpearmanPvalueEh 0.001
testSpearmanPvalueEm 0.005
testSpearmanPvalueG2 0

PrecisionRecallTest

testAveragePrecisionB 0
testAveragePrecisionWithTie 0
testAveragePrecisionNotInOrder 0
testAveragePrecision 0
testAveragePrecisionBNotInOrder 0

MultipleTestCorrectionTest

testBenjaminiYekuteliCut 0.008
testBenjaminiHochbergCut 0.008
testBenjaminiHochberg 0.011
testBenjaminiHochbergM 0.011
testBonferroniCut 0.01

DistanceTest

testSpearmanRankCorrelation 0
testCorrelationOfStandardizedDoubleArrayDoubleArray 0
testSpearmanRankCorrelation2 0
testSpearmanRankCorrelation3 0
testManhattanDistance 0
testSpearmanRankCorrelationNaN 0
testEuclDistance 0
testSpearmanOneList1 0
testSpearmanOneList2 0
testSpearmanOneList3 0
testSpearmanOneList4 0
testCorrelationOfStandardizedDoubleArrayListDoubleArrayList 0

AnnotatorClientTest

test 0
This test require -Dncbi.api.key to be set.
testB 0
This test require -Dncbi.api.key to be set.
testC 0
This test require -Dncbi.api.key to be set.

OntologySearchTest

testPersistence 0.49
org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.645
testOmitDefinitions2 0.023
testOmitDefinitions3 0.017
testOmitDefinitions4 0.719
testScore 0.015
testOmitBadPredicates2 0.02
testOmitBadPredicates 0.018
testOmitDefinition 0.005
testIndexing 0.15
org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.002
matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.003
testOmitDefinitions 0.019

OntologyLoaderTest

testCacheOntologyToDisk 0.049
testHasChanged 0.004

OntologyTermTest

testGetParentsHasProperPart 0.034
testGetChildren 0.578
testGetChildrenHasProperPart 0.012
testGetParents 0.219
testRejectNonEnglish 0.325

ObiServiceTest

testLoadAndSearch 7.908
testWithoutCache 0.229

AbstractOntologyServiceTest

testInitializeInBackgroundThread 0.001
testCacheOntologyToDisk 1.951
testGenericOntologyServiceMem 0.036

Failure Details

[Summary] [Package List] [Test Cases]


test
skipped: This test require -Dncbi.api.key to be set.
testB
skipped: This test require -Dncbi.api.key to be set.
testC
skipped: This test require -Dncbi.api.key to be set.
testPersistence
com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
testIndexing
com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
testLoadAndSearch
java.lang.AssertionError