Surefire Report

Summary

[Summary] [Package List] [Test Cases]

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

Package List

[Summary] [Package List] [Test Cases]

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

ubic.basecode.math.linalg

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	QRDecompositionTest	5	0	0	0	100%	0.025

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.139

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParameterKeeperTest	1	0	0	0	100%	0.026
	ParamGrabberTest	1	0	0	0	100%	0

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStringUtil	8	0	0	0	100%	0.015
	SQLUtilsTest	1	0	0	0	100%	0.001
	DateUtilTest	6	0	0	0	100%	0.001
	BatchIteratorTest	3	0	0	0	100%	0.001
	ConfigUtilsTest	13	0	0	0	100%	0.238
	PrettyPrinterTest	1	0	0	0	100%	0.795
	StringUtilTest	5	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.074
	NetUtilsTest	4	0	0	0	100%	3.932

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.451

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixWriterTest	3	0	0	0	100%	0
	TestHistogramWriter	1	0	0	0	100%	0.001

ubic.basecode.ontology.ncbo

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	AnnotatorClientTest	3	0	0	3	0%	0.001

ubic.basecode.math.distribution

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramTest	2	0	0	0	100%	0
	TestWishart	1	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0.001
	HistogramSamplerTest	1	0	0	0	100%	0.027
	UniformDensityComputerTest	1	0	0	0	100%	0

ubic.basecode.math.metaanalysis

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

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	21	0	0	0	100%	6.464
	JRIClientTest	21	0	0	0	100%	0.038

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ModeratedTstatTest	6	0	0	0	100%	0.167
	LeastSquaresFitTest	20	0	0	0	100%	9.322
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.049
	DesignMatrixTest	5	0	0	0	100%	0.01

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JenaUtilsTest	1	0	0	0	100%	0.134
	UberonOntologySearchTest	2	0	0	0	100%	23.367
	OntologyLoaderTest	2	0	0	0	100%	0.15
	OntologySearchTest	9	0	0	0	100%	7.366

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.035

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SparseDoubleMatrixTest	24	0	0	0	100%	0.002
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.015
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.028
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	StringMatrixTest	4	0	0	0	100%	0
	IntegerMatrixTest	16	0	0	0	100%	0.001
	DenseDoubleMatrixTest	39	0	0	0	100%	0.02
	MatrixUtilTest	7	0	0	0	100%	0
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.001

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRank	14	0	0	0	100%	0.001
	RandomChooserTest	7	0	0	0	100%	1.327
	TestMatrixNormalizer	2	0	0	0	100%	0
	TestSpecFunc	7	0	0	0	100%	0
	TestWilcoxon	15	0	0	0	100%	3.069
	TestMatrixStats	15	0	0	0	100%	0.021
	TestMathUtil	5	0	0	0	100%	0
	TestStats	14	0	0	0	100%	0.002
	SingularValueDecompositionTest	1	0	0	0	100%	0.054
	TestMatrixRowStats	6	0	0	0	100%	0.001
	TestDescriptiveWithMissing	38	0	0	0	100%	0.003
	TestROC	3	0	0	0	100%	0.053
	TestKSTest	2	0	0	0	100%	0.001
	CorrelationStatsTest	18	0	0	0	100%	0.096
	PrecisionRecallTest	5	0	0	0	100%	0.001
	StringDistanceTest	16	0	0	0	100%	0.001
	DistanceTest	12	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.111
	KruskalWallisTest	1	0	0	0	100%	0

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDoubleMatrixReader	15	0	0	0	100%	0.143
	HistogramReaderTest	2	0	0	0	100%	0
	TestStringMatrixReader	4	0	0	0	100%	0.006
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.975
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.019
	TestMapReader	3	0	0	0	100%	0.001

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestItemLevelFilter	1	0	0	0	100%	0
	TestRowMissingFilter	11	0	0	0	100%	0.025
	TestRowAbsentFilter	9	0	0	0	100%	0.015
	TestRowLevelFilter	23	0	0	0	100%	0.065
	TestRowAffyNameFilter	2	0	0	0	100%	0.001
	TestRowNameFilter	4	0	0	0	100%	0.003

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	1.144

ubic.basecode.dataStructure

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

ubic.basecode.dataStructure.tree

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.51

Test Cases

[Summary] [Package List] [Test Cases]

SparseDoubleMatrixTest

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

TestRank

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

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.001
	testReadInputStreamRowCount	0.002
	testReadInputStreamGotColName	0.002
	testReadInputStreamGotRowName	0.002
	testSmallNumbers	0.089
	testReadInputStreamMissingSpaces	0.023
	testReadBad	0.003
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.003
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0.004
	testReadChooseRows	0.002
	testReadInputStreamColumnCount	0.004

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

TestWishart

testNextDoubleMatrix

0

MatrixWriterTest

	testWriteMatrixB	0
	testWriteMatrix	0
	testWrite3DMatrix	0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

ParameterKeeperTest

test

0.026

RandomChooserTest

	testChooseRandomDeck	0.028
	testRepeatSubset	0.668
	testChooserandomInts	0.013
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.057
	testRepeat	0.56

AnnotatorClientTest

	test + - [ Detail ]	0
	This test require -Dncbi.api.key to be set.
	testB + - [ Detail ]	0
	This test require -Dncbi.api.key to be set.
	testC + - [ Detail ]	0
	This test require -Dncbi.api.key to be set.

TestStringMatrixReader

	testReadInputStreamRowCount	0.001
	testReadInputStreamGotColName	0.002
	testReadInputStreamGotRowName	0.001
	testReadInputStreamColumnCount	0.001

MatrixDisplayTest

	testWriteOutAsPNG2	0.408
	testWriteOutAsPNG	0.013
	testSaveImage	0.009
	testSaveImageStandardize	0.021

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.012
	testCsvSplitB	0
	testCsvSplitC	0
	testCsvSplitD	0.001
	testCsvSplitE	0
	testCsvSplitF	0.001
	testTwoStringHashKeyB	0

DoubleAddingMapTest

test

0

SparseRaggedDoubleMatrixTest

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

SQLUtilsTest

testBlobToString

0

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

TestItemLevelFilter

testFilter

0

JenaUtilsTest

testInferenceCapabilities

0.133

UberonOntologySearchTest

	testScore	0.027
	testOmitDefinition	0.017

TestMeanDifferenceMetaAnalysis

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

DateUtilTest

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

TestSpecFunc

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

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.001
	testFilterWithMissing	0.001
	testFilterWithMissingLessStringent	0.003
	testFilterFractionInvalid2	0.002
	testFilterFractionInvalid	0.003
	testFilterStringMatrix	0.003
	testFilterFraction	0.002
	testFilter	0.003
	testMaxFractionRemovedInvalid	0.002
	testFilterNoFiltering	0.004

CountingMapTest

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

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.034

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	3.054
	testWilxcoxonPGaussB	0.001
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.004
	testWilxcoxonPWithTies	0.001
	testEVolume	0

BatchIteratorTest

	testBatches	0.001
	testBatchIterator	0
	testConcurrentModificationException	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.022
	testReadInputStream	0.007
	testReadStreamAdjListBig	0.945

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0
	testCorrelationMatrix	0.003
	testMax	0
	testMin	0
	testNan	0.001
	testColSumsWithMissing	0
	testLogTransform	0.001
	testDoubleStandardize	0.006
	testCov2Cor	0.004
	testConvertToLog2Cpm	0
	testConvertLog	0.001
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.003

TestRowAbsentFilter

	testFilterKeepMarginal	0.001
	testFilterPresentCountInvalid	0
	testFilterWithMissing	0
	testFilterNullFlags	0
	testFilterWithMissingLessStringent	0.001
	testFilterFractionInvalid	0.002
	testFilterStringMatrix	0.003
	testFilterFraction	0.003
	testFilter	0.004

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

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

TestRowLevelFilter

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

ParamGrabberTest

test

0

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.142
	testHasChanged	0.003

BinaryTreeTest

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

SingularValueDecompositionTest

testSingularValueDecomposition

0.054

CompressedNamedBitMatrixTest

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

FastRowAccessDoubleMatrixTest

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

TestMatrixRowStats

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

OntologySearchTest

	testPersistence	1.883
	testOmitDefinitions2	0.192
	testOmitDefinitions3	0.052
	testOmitDefinitions4	1.937
	testOmitBadPredicates2	0.072
	testOmitBadPredicates	2.143
	testIndexing	0.657
	testOmitDefinitions	0.049
	testStemming	0.334

ConfigUtilsTest

	testLoadConfigURL	0.112
	testGetConfigBuilderFile	0.094
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.003
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.004
	testLoadConfigStringNewName	0.012
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.001

CompressedSparseDoubleMatrixTest

	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0
	testGet	0
	testSet	0
	testRows2	0
	testCopy	0
	testGet2	0
	testRows	0.001
	testSet2	0
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	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	0.001
	testViewColumn	0.001
	testGetColObj2	0
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0
	testGetRowArrayList2	0
	testViewRow2	0.001

TestDescriptiveWithMissing

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

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

TestROC

	testBig	0.049
	testAroc	0.001
	testArocPvalue	0.003

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

PrettyPrinterTest

testPrintBeans

0.742

TestKSTest

	testKSTestTwoSample	0.001
	testKSTestOneSample	0

IntegerMatrixTest

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

RServeClientTest

	testExec	0.335
	testListEvalA	0.307
	testListEvalB	0.308
	testExecError	0.308
	testDataFrameA	0.306
	testAssignAndRetrieveMatrix	0.306
	testAnovaA	0.306
	testAnovaB	0.306
	testAnovaC	0.306
	testAnovaD	0.312
	testAnovaE	0.306
	testAnovaF	0.305
	testLimmaA	0.306
	testExecDoubleArray	0.306
	testAssignAndRetrieveMatrixB	0.306
	testAssignAndRetrieveMatrixD	0.308
	testLinearModelA	0.305
	testLinearModelB	0.305
	testLinearModelC	0.305
	testLinearModelD	0.305
	testStringListEvalB	0.304

QRDecompositionTest

	testScaledDesign	0.004
	testSingular2	0.006
	test1	0.008
	test3	0.007
	test2NoPivoting	0

TestHistogramWriter

testWriter

0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.014
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.071
	testCorrelationForPvalue	0
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0
	testSpearmanPvalueEm	0.01
	testSpearmanPvalueG2	0

ModeratedTstatTest

	testLimmaMissing	0.018
	testFdist	0.001
	testLimma	0.021
	testSqueezeVarB	0.126
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

ExcelUtilTest

	testGetSheetFromFile	0.493
	testGetSet	0.003
	testSetFormula	0.013

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.053
	testThreeWaySingular	0.182
	testEstrogen	3.939
	testVectorWeightedRegress	0
	testNHBE	4.993
	testLSFTwoLevels2	0.037
	testLSFTwoLevels3	0.027
	testSingular2	0.005
	testVectorWeightedRegressWithMissing	0.003
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.009
	testTwoWayAnovaWithInteractions	0.004
	testLSFTwoLevels	0.004
	testOneWayAnova	0.02
	testTwoWayTwoLevelsOneContinousInteractionC	0.007
	testLSFThreeLevelsOnecontinous2	0.004
	testMatrixWeightedRegress	0.001
	testSingular	0.02
	testLSFTwoLevelsOneContinuous	0.007
	testLSFOneContinuousWithMissing3	0.005

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

StringUtilTest

	testMakeRnames	0
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0

StringDistanceTest

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

MeanVarianceEstimatorTest

	testVoom	0.031
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.015
	testInterpolate	0.001
	testMeanVarianceNoDesignWithMissing	0.001

FileToolsTest

	testHasImageExtension	0
	testTestDir	0
	testGetWithoutExtension	0.001
	testGetLines	0.004
	testTouch	0.001
	testListDirectoryFiles	0.008
	testAddImageExtension	0.001
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.004
	testCleanFileName	0.002
	testgetStringListFromFile	0.002
	testGetWithoutExtensionB	0.001
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0.002
	testCleanFileNameErr	0.002
	testIsGZipped	0.003
	testUnGzipFile	0.003
	testCopyFileFailOnDirectoryOutput	0.001
	testTestFileString	0.001
	testGetCompressedFile	0.002
	testCopyFile	0.002
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.001
	testAddDataExtension	0.001
	testGetCompressedFileZip	0.003
	testTestFileFile	0.002
	testCheckPathIsReadableFileNot	0.001
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.001
	testHasXMLExtension	0.001
	testUnzipFile	0.016

TestSparseDoubleMatrixReader

	testReadStream	0.008
	testReadJW	0.011

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

NetUtilsTest

	testFtpFileSize	0.85
	testCheckForFile	0.778
	testFtpFileSizeDoesntExist	1.239
	testDownloadFile	1.065

StringToStringSetMapTest

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

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

DenseDoubleMatrixTest

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

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

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.013
	testBenjaminiHochbergCut	0.02
	testBenjaminiHochberg	0.031
	testBenjaminiHochbergM	0.029
	testBonferroniCut	0.018

JRIClientTest

	testExec	0.02
	testListEvalA	0.001
	testListEvalB	0.001
	testExecError	0
	testDataFrameA	0
	testAssignAndRetrieveMatrix	0
	testAnovaA	0.001
	testAnovaB	0.001
	testAnovaC	0.001
	testAnovaD	0.001
	testAnovaE	0.001
	testAnovaF	0
	testLimmaA	0.001
	testExecDoubleArray	0.001
	testAssignAndRetrieveMatrixB	0.001
	testAssignAndRetrieveMatrixD	0.002
	testLinearModelA	0.001
	testLinearModelB	0.001
	testLinearModelC	0.001
	testLinearModelD	0
	testStringListEvalB	0.001

OntologyTermTest

	testGetParentsHasProperPart	0.057
	testGetChildren	0.496
	testGetChildrenHasProperPart	0.031
	testGetParents	0.254
	testRejectNonEnglish	0.295

TestCorrelationEffectMetaAnalysis

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

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0

KruskalWallisTest

testKW

0

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.021
	testByteArrayToBooleans	0.009
	testStringToDoubleArrayConversionSpeed	0.008
	testByteArrayToDoubleConversionSpeed	0.008
	testByteArrayToTabbedString	0.007
	testDoubleArrayToBytes	0.005
	testIntsToBytes	0.006
	testBooleansToLongArray	0.012
	testByteArrayToSquareDoubleMatrix	0.007
	testByteArrayToDoubles	0.005
	testStringArrayToBytes	0.003
	testDoubleArrayToDelimitedStringConversionSpeed	0.017
	testStringArrayToTabbedBytes	0.007
	testObjectToBytes	0.006
	testBooleansToByteArray	0.006
	testByteArrayToLongs	0.007
	testByteArrayToDoubleMatrix	0.005

HistogramSamplerTest

testNextSample

0.027

UniformDensityComputerTest

testDensity

0

MatrixUtilTest

	testSelectColumnsAndRowsBad	0
	testSelectColumns	0
	testDropColumn	0
	testSelectColumnsAndRows	0
	testRemoveMissing1	0
	testRemoveMissing2	0
	testSelectRows	0

DesignMatrixTest

	testInteractionC	0
	test2	0.001
	testA	0
	testB	0.003
	testInteractionAndRelevel	0.005

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

TestRowNameFilter

	testFilterString	0.002
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0

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.