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%	0.041

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	15	0	0	0	100%	0.301

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%	0.023

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	StringUtilTest	5	0	0	0	100%	0.001
	ConfigUtilsTest	13	0	0	0	100%	0.39
	NetUtilsTest	4	0	0	0	100%	3.867
	PrettyPrinterTest	1	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	1.844
	TestStringUtil	8	0	0	0	100%	0.035
	BatchIteratorTest	3	0	0	0	100%	0.001
	DateUtilTest	6	0	0	0	100%	0.001
	SQLUtilsTest	1	0	0	0	100%	0

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.566

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestHistogramWriter	1	0	0	0	100%	0.005
	MatrixWriterTest	3	0	0	0	100%	0.034

ubic.basecode.ontology.ncbo

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	AnnotatorClientTest	3	0	0	3	0%	0.007

ubic.basecode.math.distribution

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestWishart	1	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0.001
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.032

ubic.basecode.math.metaanalysis

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

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.062
	ModeratedTstatTest	6	0	0	0	100%	0.497
	LeastSquaresFitTest	20	0	0	0	100%	14.112
	DesignMatrixTest	5	0	0	0	100%	0.01

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JRIClientTest	21	0	0	0	100%	0.036
	RServeClientTest	21	0	0	0	100%	6.522

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	27.956
	JenaUtilsTest	1	0	0	0	100%	0.245
	OntologyLoaderTest	2	0	0	0	100%	0.176
	OntologySearchTest	11	0	0	0	100%	8.154

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.093

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.011
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.068
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.081
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.003
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.001
	IntegerMatrixTest	16	0	0	0	100%	0.005
	StringMatrixTest	4	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.126
	MatrixUtilTest	7	0	0	0	100%	0.018
	SparseDoubleMatrixTest	24	0	0	0	100%	0.007

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStats	14	0	0	0	100%	0.001
	TestDescriptiveWithMissing	45	0	0	0	100%	0.013
	TestMatrixStats	15	0	0	0	100%	0.155
	TestRank	14	0	0	0	100%	0.006
	TestKSTest	2	0	0	0	100%	0.001
	KruskalWallisTest	1	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0.009
	PrecisionRecallTest	5	0	0	0	100%	0
	DistanceTest	12	0	0	0	100%	0.001
	MultipleTestCorrectionTest	5	0	0	0	100%	0.139
	SingularValueDecompositionTest	1	0	0	0	100%	0.086
	TestMatrixRowStats	6	0	0	0	100%	0.001
	TestROC	3	0	0	0	100%	0.12
	StringDistanceTest	16	0	0	0	100%	0.001
	TestMathUtil	5	0	0	0	100%	0.001
	CorrelationStatsTest	18	0	0	0	100%	0.102
	TestWilcoxon	15	0	0	0	100%	6.757
	TestSpecFunc	7	0	0	0	100%	0.029
	RandomChooserTest	7	0	0	0	100%	1.51

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramReaderTest	2	0	0	0	100%	0.006
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	1.586
	TestStringMatrixReader	4	0	0	0	100%	0.007
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.071
	TestMapReader	3	0	0	0	100%	0.021
	TestDoubleMatrixReader	15	0	0	0	100%	0.36

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAffyNameFilter	2	0	0	0	100%	0.01
	TestRowLevelFilter	23	0	0	0	100%	0.241
	TestRowAbsentFilter	9	0	0	0	100%	0.082
	TestRowNameFilter	4	0	0	0	100%	0.059
	TestItemLevelFilter	1	0	0	0	100%	0.003
	TestRowMissingFilter	11	0	0	0	100%	0.068

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	8.102

ubic.basecode.dataStructure

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	1.008

Test Cases

[Summary] [Package List] [Test Cases]

QRDecompositionTest

	testScaledDesign	0.001
	testSingular2	0.021
	test1	0.003
	test3	0.014
	test2NoPivoting	0.002

CompressedNamedBitMatrixTest

	testGetOutOfBounds	0.006
	testOverlap	0
	testGet	0
	testTotalBitCount	0.001
	testOutOfBounds	0
	testOutOfBounds2	0.001
	testGetRowBitCount	0.001
	testBitMatrix	0.002
	testBitCount	0

HistogramReaderTest

	testHistogramReaderIs	0.003
	testHistogramReaderString	0.002

CompressedSparseDoubleMatrixTest

	testSubsetRows	0
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.009
	testGet	0.002
	testSet	0.001
	testRows2	0.005
	testCopy	0.004
	testGet2	0.002
	testRows	0.001
	testSet2	0.002
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.002
	testSetIntIntObject	0.001
	testGetRow2	0.002
	testSubsetColumns	0.003
	testViewRow	0.001
	testColumns	0.001
	testGetColRange	0.002
	testGetByKeys	0.001
	testGetColObj	0.002
	testGetColumn	0.001
	testIsMissing	0.002
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.002
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.002
	testIsMissing2	0.001
	testGetColByNameFail	0.002
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.001
	testViewRow2	0.001

TestDirectedGraph

	testDeleteLeaf1	0.005
	testDeleteLeafFail	0
	testGetChildren	0.001
	testToString	0.001
	testAddChild	0
	testTopoSort	0
	testAddParent	0.001
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.082

TestStats

	testNormalizeDoubleArrayListdouble	0
	testCdf	0
	testRange	0
	testMeanAboveQuantile	0
	testCv	0
	testCumulateRight	0
	testQuantile	0
	testIsValidFraction	0
	testIsValidFraction2	0
	testNumberOfDistinctValues	0
	testCumulate	0
	testQuantile75	0.001
	testNormalizeDoubleArrayList	0
	testNumberOfDistinctValuesNonNA	0

TestWishart

testNextDoubleMatrix

0

TestDescriptiveWithMissing

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

UberonOntologySearchTest

	testScore	0.041
	testOmitDefinition	0.02

TestRowAffyNameFilter

	testStringFilter	0.003
	testFilter	0.006

TestMatrixStats

	testRbfNormalize	0.01
	testSelfSquare	0.001
	testStandardize	0.017
	testCorrelationMatrix	0.01
	testMax	0.002
	testMin	0.001
	testNan	0.001
	testColSumsWithMissing	0.002
	testLogTransform	0.004
	testDoubleStandardize	0.048
	testCov2Cor	0.019
	testConvertToLog2Cpm	0.011
	testConvertLog	0.005
	testCountsPerMillionWithMissing	0.004
	testCorrelationMatrixThreshold	0.014

TestMeanDifferenceMetaAnalysis

	testRunRandomE	0
	testRunRandomZ	0
	testRunFixedE	0
	testRunFixedQ	0
	testRunFixedZ	0
	testRunRandomBSV	0.001
	testRunRandomVar	0
	testRunFixedVar	0

TestRank

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

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

KruskalWallisTest

testKW

0

ParamGrabberTest

test

0

JenaUtilsTest

testInferenceCapabilities

0.245

StringUtilTest

	testMakeRnames	0
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0

ConfigUtilsTest

	testLoadConfigURL	0.186
	testGetConfigBuilderFile	0.15
	testGetConfigBuilderString	0.003
	testGetConfigBuilderURLNew	0.002
	testGetConfigBuilderStringNew	0.002
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.003
	testLoadConfigStringNewName	0.032
	testGetConfigBuilderURL	0.002
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.002
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.002

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

TestMatrixNormalizer

	testQuantileNormalize	0.004
	testQuantileNormalizeWithMissing	0.004

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	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

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0.001
	testToArray	0.003
	testSortByColumnAbsoluteValue	0.009
	testGet	0.003
	testSet	0.003
	testRows2	0.002
	testCopy	0.003
	testGet2	0.002
	testRows	0.002
	testSet2	0.003
	testSize	0.003
	testToString	0.003
	testGetRowByNameFail	0.003
	testGetRowByNameNull	0.002
	testSetIntIntObject	0.003
	testGetRow2	0.003
	testSubsetColumns	0.003
	testViewRow	0.003
	testColumns	0.003
	testGetColRange	0.002
	testGetByKeys	0.003
	testGetColObj	0.002
	testGetColumn	0.003
	testIsMissing	0.005
	testViewColumn	0
	testGetColObj2	0.001
	testGetObject	0
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0.001
	testIsMissing2	0
	testGetColByNameFail	0.001
	testGetColByNameNull	0
	testGetRowObj2	0.001
	testGetColByName	0
	testGetRowArrayList2	0.001
	testViewRow2	0.001

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.021
	testBenjaminiHochbergCut	0.029
	testBenjaminiHochberg	0.033
	testBenjaminiHochbergM	0.03
	testBonferroniCut	0.026

NetUtilsTest

	testFtpFileSize	0.861
	testCheckForFile	0.715
	testFtpFileSizeDoesntExist	1.295
	testDownloadFile	0.995

SparseRaggedDoubleMatrixTest

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

SingularValueDecompositionTest

testSingularValueDecomposition

0.086

TestMatrixRowStats

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

ExcelUtilTest

	testGetSheetFromFile	0.976
	testGetSet	0.005
	testSetFormula	0.027

CountingMapTest

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

MeanVarianceEstimatorTest

	testVoom	0.038
	testMeanVarianceNoDesignWithColsRowAllMissing	0.002
	testDuplicateRows	0.02
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.002

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

ParameterKeeperTest

test

0.023

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.015
	testReadInputStream	0.032
	testReadStreamAdjListBig	1.525

PrettyPrinterTest

testPrintBeans

0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

TestRowLevelFilter

	testFilterMinHigh	0.006
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.012
	testFilterMaxTooHigh	0.01
	testFilterMedian	0.012
	testFilterNoFilter	0.01
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.009
	testFilterFractionMaxRemoveNegHigh	0.01
	testFilterMax	0.01
	testFilterMin	0.009
	testFilterMaxFractionNoneRemoveNeg	0.01
	testFilterMedianHigh	0.012
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.012
	testFilterFractionMaxRemoveNeg	0.01
	testFilterMaxFractionAll	0.01
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.01
	testFilterMaxFraction	0.012
	testFilterBadFraction	0.011
	testFilterMaxFractionHigh	0.009
	testFilterMaxFractionNone	0.01
	testFilterFractionMaxRemoveHighAndLow	0.01
	testFilterMeanHigh	0.009
	testFilterMean	0.014
	testFilterMaxHigh	0.009

FileToolsTest

	testHasImageExtension	1.525
	testTestDir	0.003
	testGetWithoutExtension	0.002
	testGetLines	0.012
	testTouch	0.003
	testListDirectoryFiles	0.024
	testAddImageExtension	0.003
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.036
	testCleanFileName	0.006
	testgetStringListFromFile	0.005
	testGetWithoutExtensionB	0.003
	testGetWithoutExtensionC	0.004
	testResourcetoPath	0.003
	testCleanFileNameErr	0.002
	testIsGZipped	0.009
	testUnGzipFile	0.007
	testCopyFileFailOnDirectoryOutput	0.003
	testTestFileString	0.005
	testGetCompressedFile	0.003
	testCopyFile	0.006
	testGetExtension	0.004
	testCheckPathIsReadableFile	0
	testIsZipped	0.004
	testAddDataExtension	0
	testGetCompressedFileZip	0.004
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0.002
	testCopyFileFailOnDirectoryInput	0.002
	testGetInputStreamFromPlainOrCompressedFile	0.002
	testHasXMLExtension	0.001
	testUnzipFile	0.021

TestROC

	testBig	0.093
	testAroc	0.003
	testArocPvalue	0.024

OntologyLoaderTest

	testCacheOntologyToDisk	0.158
	testHasChanged	0.01

OntologySearchTest

	testPersistence	1.168
	matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	2.131
	testOmitDefinitions2	0.224
	testOmitDefinitions3	0.053
	testOmitDefinitions4	2.508
	testOmitBadPredicates2	0.483
	testOmitBadPredicates	0.22
	testIndexing	1.201
	matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.01
	matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.007
	testOmitDefinitions	0.092

TestHistogramWriter

testWriter

0.005

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	0.001
	testWeightedSuffixHammingB	0
	testWeightedSuffixHammingC	0

MatrixDisplayTest

	testWriteOutAsPNG2	0.513
	testWriteOutAsPNG	0.015
	testSaveImage	0.01
	testSaveImageStandardize	0.025

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

JRIClientTest

	testExec	0.005
	testListEvalA	0.001
	testListEvalB	0.002
	testExecError	0.002
	testDataFrameA	0
	testAssignAndRetrieveMatrix	0.001
	testAnovaA	0.001
	testAnovaB	0.001
	testAnovaC	0.002
	testAnovaD	0.002
	testAnovaE	0
	testAnovaF	0
	testLimmaA	0
	testExecDoubleArray	0
	testAssignAndRetrieveMatrixB	0
	testAssignAndRetrieveMatrixD	0.004
	testLinearModelA	0
	testLinearModelB	0.004
	testLinearModelC	0
	testLinearModelD	0
	testStringListEvalB	0

TestRowAbsentFilter

	testFilterKeepMarginal	0.008
	testFilterPresentCountInvalid	0.008
	testFilterWithMissing	0.01
	testFilterNullFlags	0.008
	testFilterWithMissingLessStringent	0.01
	testFilterFractionInvalid	0.011
	testFilterStringMatrix	0.007
	testFilterFraction	0.01
	testFilter	0.009

ModeratedTstatTest

	testLimmaMissing	0.162
	testFdist	0.001
	testLimma	0.083
	testSqueezeVarB	0.25
	testSqueezeVar	0
	testSqueezeVarWMissing	0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.034
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.055
	testCorrelationForPvalue	0.001
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0.001
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.01
	testSpearmanPvalueG2	0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	6.723
	testWilxcoxonPGaussB	0.005
	testBGaussian	0
	testFVolume	0.002
	testWilxcoxonPVolume	0.009
	testBig	0.001
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.003
	testAExact	0.008
	testWilxcoxonPWithTies	0.001
	testEVolume	0.002

MatrixWriterTest

	testWriteMatrixB	0.017
	testWriteMatrix	0.006
	testWrite3DMatrix	0.01

UniformDensityComputerTest

testDensity

0

TestRowNameFilter

	testFilterString	0.03
	testFilterExclude	0.01
	testFilter	0.008
	testFilterStringExclude	0.008

TestStringUtil

	testTwoStringHashKey	0.011
	testCsvSplitA	0.014
	testCsvSplitB	0.001
	testCsvSplitC	0.001
	testCsvSplitD	0.001
	testCsvSplitE	0
	testCsvSplitF	0.002
	testTwoStringHashKeyB	0

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

RServeClientTest

	testExec	0.341
	testListEvalA	0.311
	testListEvalB	0.308
	testExecError	0.308
	testDataFrameA	0.306
	testAssignAndRetrieveMatrix	0.307
	testAnovaA	0.307
	testAnovaB	0.309
	testAnovaC	0.306
	testAnovaD	0.306
	testAnovaE	0.307
	testAnovaF	0.307
	testLimmaA	0.313
	testExecDoubleArray	0.307
	testAssignAndRetrieveMatrixB	0.321
	testAssignAndRetrieveMatrixD	0.307
	testLinearModelA	0.307
	testLinearModelB	0.307
	testLinearModelC	0.309
	testLinearModelD	0.307
	testStringListEvalB	0.311

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

DateUtilTest

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

TestSpecFunc

	testdBinom	0
	testCumHyperGeometricB	0
	testTrigammaInverse	0.027
	testCumHyperGeometric	0
	testTrigammaInverseB	0.001
	testHypergeometric	0
	testCumHyperGeometricUT	0.001

HistogramSamplerTest

testNextSample

0.032

BinaryTreeTest

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

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

IntegerMatrixTest

	testGetEntry	0
	testGet	0.005
	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

TestItemLevelFilter

testFilter

0.002

SQLUtilsTest

testBlobToString

0

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0.004
	testToArray	0.004
	testSortByColumnAbsoluteValue	0.013
	testGet	0.004
	testSet	0.003
	testRows2	0.004
	testCopy	0.007
	testGet2	0.001
	testRows	0.002
	testSet2	0.003
	testSize	0.004
	testToString	0.003
	testGetRowByNameFail	0.003
	testGetRowByNameNull	0.003
	testSetIntIntObject	0.004
	testGetRow2	0.003
	testSubsetColumns	0.003
	testViewRow	0.003
	testColumns	0.002
	testGetColRange	0.002
	testGetByKeys	0.003
	testGetColObj	0.002
	testGetColumn	0.003
	testIsMissing	0.004
	testViewColumn	0.002
	testGetColObj2	0.002
	testGetObject	0.002
	testGetRow	0.002
	testGetRowObj	0.002
	testGetRowRange	0.003
	testGetRowByName	0.002
	testIsMissing2	0.004
	testGetColByNameFail	0.003
	testGetColByNameNull	0.002
	testGetRowObj2	0.003
	testGetColByName	0.003
	testGetRowArrayList2	0.002
	testViewRow2	0.003

MatrixUtilTest

	testSelectColumnsAndRowsBad	0
	testSelectColumns	0
	testDropColumn	0.002
	testSelectColumnsAndRows	0.005
	testRemoveMissing1	0.003
	testRemoveMissing2	0.003
	testSelectRows	0.003

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0.006

OntologyTermTest

	testGetParentsHasProperPart	1.746
	testGetChildren	3.839
	testGetChildrenHasProperPart	0.116
	testGetParents	0.862
	testRejectNonEnglish	1.425

TestRowMissingFilter

	testFilterPresentCountInvalid	0.001
	testFilterWithMissingLowMaxFraction	0.008
	testFilterWithMissing	0.005
	testFilterWithMissingLessStringent	0.006
	testFilterFractionInvalid2	0.005
	testFilterFractionInvalid	0.009
	testFilterStringMatrix	0.009
	testFilterFraction	0.006
	testFilter	0.007
	testMaxFractionRemovedInvalid	0.005
	testFilterNoFiltering	0.006

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.

TestSparseDoubleMatrixReader

	testReadStream	0.034
	testReadJW	0.037

TestMapReader

	testRead	0.009
	testReadNoHeader	0.006
	testReadNoHeaderFile	0.006

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.002
	testThreeWaySingular	0.143
	testEstrogen	6.749
	testVectorWeightedRegress	0.001
	testNHBE	7.048
	testLSFTwoLevels2	0.038
	testLSFTwoLevels3	0.029
	testSingular2	0.008
	testVectorWeightedRegressWithMissing	0.007
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.007
	testTwoWayAnovaWithInteractions	0.009
	testLSFTwoLevels	0.005
	testOneWayAnova	0.02
	testTwoWayTwoLevelsOneContinousInteractionC	0.007
	testLSFThreeLevelsOnecontinous2	0.004
	testMatrixWeightedRegress	0.001
	testSingular	0.019
	testLSFTwoLevelsOneContinuous	0.008
	testLSFOneContinuousWithMissing3	0.006

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.046
	testByteArrayToBooleans	0.013
	testStringToDoubleArrayConversionSpeed	0.017
	testByteArrayToDoubleConversionSpeed	0.015
	testByteArrayToTabbedString	0.012
	testDoubleArrayToBytes	0.023
	testIntsToBytes	0.011
	testBooleansToLongArray	0.022
	testByteArrayToDoubles	0.017
	testStringToBytes	0.015
	testDoubleArrayToDelimitedStringConversionSpeed	0.038
	testObjectToBytes	0.028
	testBooleansToByteArray	0.009
	testByteArrayToLongs	0.007
	testByteArrayToDoubleMatrix	0.006

TestCorrelationEffectMetaAnalysis

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

RandomChooserTest

	testChooseRandomDeck	0.064
	testRepeatSubset	0.823
	testChooserandomInts	0.028
	testChooserandomWrep	0.002
	testRandomSubset	0
	testChooserandomInt	0.096
	testRepeat	0.496

DoubleAddingMapTest

test

0

StringToStringSetMapTest

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

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.002
	testReadInputStreamRowCount	0.007
	testReadInputStreamGotColName	0.007
	testReadInputStreamGotRowName	0.006
	testSmallNumbers	0.202
	testReadInputStreamMissingSpaces	0.038
	testReadBad	0.019
	testBadFileName	0.005
	testReadChooseRowsSkipcols	0.01
	testReadBlankCorner	0.006
	testReadInputStreamMissing	0.013
	testReadChooseRows	0.019
	testReadInputStreamColumnCount	0.018

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	0.001
	testGetColObj	0
	testGetColumn	0.002
	testIsMissing	0
	testViewColumn	0
	testGetObject	0.001
	testGetRow	0
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0.001
	testGetColByName	0

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0.003
	testInteractionAndRelevel	0.006

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.