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%	0.012

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	15	0	0	0	100%	0.088

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ConfigUtilsTest	13	0	0	0	100%	0.137
	FileToolsTest	32	0	0	0	100%	0.04
	StringUtilTest	5	0	0	0	100%	0.003
	PrettyPrinterTest	1	0	0	0	100%	0.011
	NetUtilsTest	4	0	0	0	100%	4.708
	SQLUtilsTest	1	0	0	0	100%	0.001
	TestStringUtil	8	0	0	0	100%	0.007
	DateUtilTest	6	0	0	0	100%	0.011
	BatchIteratorTest	3	0	0	0	100%	0.001

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParamGrabberTest	1	0	0	0	100%	0.001
	ParameterKeeperTest	1	0	0	0	100%	0.238

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.634

ubic.basecode.ontology.search

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologySearchTest	11	0	0	0	100%	5.715

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestHistogramWriter	1	0	0	0	100%	0
	MatrixWriterTest	3	0	0	0	100%	0.008

ubic.basecode.ontology.ncbo

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

ubic.basecode.math.distribution

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestWishart	1	0	0	0	100%	0.002
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.026
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0.008

ubic.basecode.ontology.providers

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ObiServiceTest	1	0	0	0	100%	5.716
	AbstractOntologyServiceTest	4	0	0	1	75%	0.164

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	21	0	0	0	100%	7.42
	JRIClientTest	21	0	0	0	100%	0.01

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.108
	LeastSquaresFitTest	20	0	0	0	100%	7.35
	ModeratedTstatTest	6	0	0	0	100%	0.227
	DesignMatrixTest	5	0	0	0	100%	0.007

ubic.basecode.math.metaanalysis

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MetaAnalysisTest	2	0	0	0	100%	0.001
	TestCorrelationEffectMetaAnalysis	9	0	0	0	100%	0.004
	TestMeanDifferenceMetaAnalysis	8	0	0	0	100%	0

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.227

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.093
	MatrixUtilTest	7	0	0	0	100%	0.066
	DenseDoubleMatrixTest	39	0	0	0	100%	0.061
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.005
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.029
	RCDoubleMatrix1DTest	3	0	0	0	100%	0.001
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.074
	SparseDoubleMatrixTest	24	0	0	0	100%	0.024
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.004
	IntegerMatrixTest	16	0	0	0	100%	0.01
	StringMatrixTest	4	0	0	0	100%	0.012

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStats	14	0	0	0	100%	0.001
	TestSpecFunc	7	0	0	0	100%	0
	TestDescriptiveWithMissing	44	0	0	0	100%	0.005
	TestRank	14	0	0	0	100%	0.005
	RandomChooserTest	7	0	0	0	100%	0.922
	TestMathUtil	5	0	0	0	100%	0.001
	TestMatrixStats	15	0	0	0	100%	0.025
	KruskalWallisTest	1	0	0	0	100%	0.001
	TestMatrixRowStats	6	0	0	0	100%	0.001
	StringDistanceTest	16	0	0	0	100%	0.005
	TestKSTest	2	0	0	0	100%	0
	TestROC	3	0	0	0	100%	0.045
	SingularValueDecompositionTest	1	0	0	0	100%	0.104
	CorrelationStatsTest	18	0	0	0	100%	0.107
	TestWilcoxon	15	0	0	0	100%	3.266
	PrecisionRecallTest	5	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0.006
	MultipleTestCorrectionTest	5	0	0	0	100%	0.108
	DistanceTest	12	0	0	0	100%	0.001

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMapReader	3	0	0	0	100%	0.001
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.566
	TestDoubleMatrixReader	15	0	0	0	100%	0.024
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.001
	TestStringMatrixReader	4	0	0	0	100%	0.001
	HistogramReaderTest	2	0	0	0	100%	0.002

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	7	0	0	0	100%	29.022

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%	0.006
	TestRowLevelFilter	23	0	0	0	100%	0.073
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowAbsentFilter	9	0	0	0	100%	0.031
	TestRowMissingFilter	11	0	0	0	100%	0.021

ubic.basecode.dataStructure

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

ubic.basecode.dataStructure.tree

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	BinaryTreeTest	7	0	0	0	100%	0.005

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.206

Test Cases

[Summary] [Package List] [Test Cases]

RServeClientTest

	testExec	1.242
	testListEvalA	0.306
	testListEvalB	0.305
	testExecError	0.307
	testDataFrameA	0.305
	testAssignAndRetrieveMatrix	0.304
	testAnovaA	0.303
	testAnovaB	0.304
	testAnovaC	0.304
	testAnovaD	0.304
	testAnovaE	0.307
	testAnovaF	0.307
	testLimmaA	0.304
	testExecDoubleArray	0.303
	testAssignAndRetrieveMatrixB	0.304
	testAssignAndRetrieveMatrixD	0.306
	testLinearModelA	0.303
	testLinearModelB	0.303
	testLinearModelC	0.305
	testLinearModelD	0.303
	testStringListEvalB	0.302

JRIClientTest

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

ConfigUtilsTest

	testLoadConfigURL	0.05
	testGetConfigBuilderFile	0.066
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.003
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.001
	testLoadConfigStringNewName	0.008
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.001
	testLoadConfigFile	0.002
	testGetConfigBuilderFileNew	0
	testLoadConfigFileNew	0

FileToolsTest

	testHasImageExtension	0.002
	testTestDir	0
	testGetWithoutExtension	0.001
	testGetLines	0.002
	testTouch	0
	testListDirectoryFiles	0.002
	testAddImageExtension	0.001
	testChangeExtension	0.01
	testDeleteFilesAndDir	0.003
	testCleanFileName	0.001
	testgetStringListFromFile	0.001
	testGetWithoutExtensionB	0
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0
	testCleanFileNameErr	0.001
	testIsGZipped	0.002
	testUnGzipFile	0.001
	testCopyFileFailOnDirectoryOutput	0.001
	testTestFileString	0
	testGetCompressedFile	0.001
	testCopyFile	0.001
	testGetExtension	0
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.001
	testAddDataExtension	0
	testGetCompressedFileZip	0.001
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0
	testHasXMLExtension	0.001
	testUnzipFile	0.002

StringUtilTest

	testMakeRnames	0.002
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0

PrettyPrinterTest

testPrintBeans

0.011

NetUtilsTest

	testFtpFileSize	1.007
	testCheckForFile	0.872
	testFtpFileSizeDoesntExist	1.663
	testDownloadFile	1.165

SQLUtilsTest

testBlobToString

0.001

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.006
	testCsvSplitB	0.001
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0
	testTwoStringHashKeyB	0

DateUtilTest

	testgetRelative5yearsFromnow	0.003
	testRange	0.003
	testgetRelative5yearsago	0.001
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0
	testRangeBad	0

BatchIteratorTest

	testBatches	0.001
	testBatchIterator	0
	testConcurrentModificationException	0

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.012
	testToArray	0.001
	testSortByColumnAbsoluteValue	0.015
	testGet	0.002
	testSet	0.001
	testRows2	0.002
	testCopy	0.002
	testGet2	0.001
	testRows	0.001
	testSet2	0.001
	testSize	0.001
	testToString	0.003
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.002
	testSetIntIntObject	0.003
	testGetRow2	0.002
	testSubsetColumns	0.005
	testViewRow	0.006
	testColumns	0.002
	testGetColRange	0.002
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.002
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0.002
	testGetObject	0.002
	testGetRow	0.001
	testGetRowObj	0.002
	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	0.002

MatrixUtilTest

	testSelectColumnsAndRowsBad	0.003
	testSelectColumns	0.002
	testDropColumn	0.002
	testSelectColumnsAndRows	0.053
	testRemoveMissing1	0.002
	testRemoveMissing2	0.001
	testSelectRows	0.002

DenseDoubleMatrixTest

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

CompressedNamedBitMatrixTest

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

SparseRaggedDoubleMatrixTest

	testSubsetRows	0.014
	testSubsetRowsFail	0
	testRows	0
	testGetRowMatrix1D	0.003
	testGetRowArrayList	0.002
	testColumns	0.002
	testGetColRange	0.002
	testAddrow	0
	testGetRow	0.001
	testGetRowRange	0.001

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0.006
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.006
	testGet	0.001
	testSet	0.002
	testRows2	0.001
	testCopy	0.009
	testGet2	0.001
	testRows	0.001
	testSet2	0.001
	testSize	0.001
	testToString	0.006
	testGetRowByNameFail	0
	testGetRowByNameNull	0
	testSetIntIntObject	0.002
	testGetRow2	0.002
	testSubsetColumns	0.002
	testViewRow	0.001
	testColumns	0.002
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.002
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0.002
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.002
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

SparseDoubleMatrixTest

	testSubsetCols	0.008
	testSubsetRows	0.001
	testToArray	0.001
	testGet	0.001
	testSet	0.001
	testCopy	0.001
	testRows	0
	testSize	0.001
	testToString	0.001
	testGetRowArrayList	0
	testViewRow	0.001
	testColumns	0
	testGetColRange	0
	testGetByKeys	0.001
	testGetColObj	0
	testGetColumn	0.001
	testIsMissing	0.001
	testViewColumn	0
	testGetObject	0.001
	testGetRow	0
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0.001
	testGetColByName	0

DenseDouble3dMatrixTest

	testget	0.004
	testtostring	0
	testgetcolobj	0
	testgetrowobj	0

IntegerMatrixTest

	testGetEntry	0.005
	testGet	0.001
	testSet	0
	testRows	0
	testSize	0
	testColumns	0
	testSetByKeys	0
	testToInteger	0.001
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testGetObject	0
	testGetRow	0.001
	testGetRowObj	0
	testSetObj	0

StringMatrixTest

	testToString	0.001
	testSubsetColumns	0.011
	testGetColObj	0
	testSubset	0

CountingMapTest

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

StringToStringSetMapTest

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

ParamGrabberTest

test

0.001

ParameterKeeperTest

test

0.238

TestDirectedGraph

	testDeleteLeaf1	0.016
	testDeleteLeafFail	0
	testGetChildren	0.001
	testToString	0.001
	testAddChild	0
	testTopoSort	0
	testAddParent	0.001
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0.001
	testTreeView	0.206

BinaryTreeTest

	testGetRight	0
	testInsertRight	0
	testGetLeft	0
	testGetRoot	0.001
	testInsertLeft	0
	testIsLeaf	0
	testIsEmpty	0

DoubleAddingMapTest

test

0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

ObiServiceTest

testLoadAndSearch

5.715

AbstractOntologyServiceTest

	testInitializeInBackgroundThread	0.002
	testReindexOnInitialize	0
	testCacheOntologyToDisk + - [ Detail ]	0
	This test was always broken, but the failure was obscured in a thread.
	testGenericOntologyServiceMem	0.161

OntologyTermTest

	testGetParentsHasProperPart	0.014
	testGetChildrenHasPart	16.405
	testGetChildren	0.157
	testGetChildrenHasProperPart	0.01
	testGetParents	0.241
	testRejectNonEnglish	0.085
	testGetParentsHasPart	12.109

OntologySearchTest

	testPersistence	0.24
	matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	1.034
	testOmitDefinitions2	0.443
	testOmitDefinitions3	0.102
	testOmitDefinitions4	2.937
	testOmitBadPredicates2	0.09
	testOmitBadPredicates	0.092
	testIndexing	0.652
	matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.003
	matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.004
	testOmitDefinitions	0.115

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.

TestStats

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

TestSpecFunc

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

MeanVarianceEstimatorTest

	testVoom	0.087
	testMeanVarianceNoDesignWithColsRowAllMissing	0.001
	testDuplicateRows	0.019
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.001

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.035
	testThreeWaySingular	0.139
	testEstrogen	3.46
	testVectorWeightedRegress	0
	testNHBE	3.609
	testLSFTwoLevels2	0.029
	testLSFTwoLevels3	0.024
	testSingular2	0.004
	testVectorWeightedRegressWithMissing	0.002
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.004
	testTwoWayAnovaWithInteractions	0.002
	testLSFTwoLevels	0.003
	testOneWayAnova	0.015
	testTwoWayTwoLevelsOneContinousInteractionC	0.004
	testLSFThreeLevelsOnecontinous2	0.002
	testMatrixWeightedRegress	0
	testSingular	0.011
	testLSFTwoLevelsOneContinuous	0.004
	testLSFOneContinuousWithMissing3	0.003

ModeratedTstatTest

	testLimmaMissing	0.066
	testFdist	0
	testLimma	0.024
	testSqueezeVarB	0.136
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

DesignMatrixTest

	testInteractionC	0.001
	test2	0
	testA	0.001
	testB	0.001
	testInteractionAndRelevel	0.003

MetaAnalysisTest

	testFisherCombinePvaluesB	0.001
	testFisherCombinePvalues	0

TestCorrelationEffectMetaAnalysis

	testRunUFEffect	0.002
	testRunZFEffect	0
	testRunZRQval	0.001
	testRunUFZscore	0
	testRunZFZscore	0
	testRunUFVar	0
	testRunURBSV	0
	testRunZFVar	0
	testRunZRBSV	0

TestMeanDifferenceMetaAnalysis

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

TestDescriptiveWithMissing

	testRankInterpolated	0.001
	testKurtosis	0
	testCorrelationA	0
	testCorrelationB	0
	testQuantileInverse	0
	testStandardize	0
	testIncrementalWeightedUpdate	0.001
	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	0.001
	testMeanDoubleAr	0
	testSampleSkew	0
	testQuantile	0
	testVariance	0
	testQuantiles	0
	testSampleKurtosis	0
	testDurbinWatsonTwo	0
	testKurtosisList	0
	testSumOfSquaredDeviations	0
	testSampleStandardDeviation	0
	testMeanEff	0
	testSumOfPowers	0
	testSampleVariance	0
	testWeightedMean	0.001
	testCovariance	0
	testIncrementalUpdate	0
	testMedian	0
	testTrimmedMean	0
	testIncrementalUpdateSums	0
	testDurbinWatsonShort	0
	testAutoCorrelation	0

TestRank

	testRankTransformMapDesc	0.001
	testRankTransformDoubleArrayListDesc	0
	testRankTransformMap	0
	testOrder	0.002
	testRankWithTies	0
	testWithNaNs	0
	testRankTransformDoubleArrayList	0
	testRankWithTiesB	0
	testRankWithTiesC	0
	testRankWithTiesD	0
	testRankWithTiesE	0
	testWithNaNs2	0
	testWithNaNs3	0
	testOrderB	0

RandomChooserTest

	testChooseRandomDeck	0.022
	testRepeatSubset	0.522
	testChooserandomInts	0.027
	testChooserandomWrep	0
	testRandomSubset	0
	testChooserandomInt	0.037
	testRepeat	0.314

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

TestWishart

testNextDoubleMatrix

0.002

UniformDensityComputerTest

testDensity

0

HistogramSamplerTest

testNextSample

0.026

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

HistogramTest

	testGetBiggestBinSize	0.007
	testGetApproximateQuantile	0.001

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0.002
	testCorrelationMatrix	0.004
	testMax	0
	testMin	0.001
	testNan	0
	testColSumsWithMissing	0.001
	testLogTransform	0
	testDoubleStandardize	0.01
	testCov2Cor	0.003
	testConvertToLog2Cpm	0
	testConvertLog	0
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.002

KruskalWallisTest

testKW

0

TestMatrixRowStats

	testSumOfSquaresDoubleMatrixNamed	0
	testMeans	0
	testSums	0
	testMeans2	0
	testStandardDeviations	0.001
	testSumOfSquaresDoubleMatrixNamedDoubleArrayList	0

StringDistanceTest

	testWeightedHammingA	0.001
	testWeightedHammingB	0
	testWeightedHammingC	0
	testHammingDistance	0
	testBadMatch	0.003
	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	0.04
	testAroc	0
	testArocPvalue	0.005

SingularValueDecompositionTest

testSingularValueDecomposition

0.104

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0.002
	test1	0.002
	test3	0.007
	test2NoPivoting	0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.054
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.034
	testCorrelationForPvalue	0
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.016
	testSpearmanPvalueG2	0.001

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	3.251
	testWilxcoxonPGaussB	0
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.006
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0.001
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.004
	testWilxcoxonPWithTies	0
	testEVolume	0.001

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

TestMatrixNormalizer

	testQuantileNormalize	0.004
	testQuantileNormalizeWithMissing	0.002

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.016
	testBenjaminiHochbergCut	0.016
	testBenjaminiHochberg	0.027
	testBenjaminiHochbergM	0.03
	testBonferroniCut	0.019

DistanceTest

	testSpearmanRankCorrelation	0.001
	testCorrelationOfStandardizedDoubleArrayDoubleArray	0
	testSpearmanRankCorrelation2	0
	testSpearmanRankCorrelation3	0
	testManhattanDistance	0
	testSpearmanRankCorrelationNaN	0
	testEuclDistance	0
	testSpearmanOneList1	0
	testSpearmanOneList2	0
	testSpearmanOneList3	0
	testSpearmanOneList4	0
	testCorrelationOfStandardizedDoubleArrayListDoubleArrayList	0

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0.001

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.002
	testReadInputStream	0
	testReadStreamAdjListBig	0.563

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0.001
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.001
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0.001
	testSmallNumbers	0.014
	testReadInputStreamMissingSpaces	0.003
	testReadBad	0
	testBadFileName	0
	testReadChooseRowsSkipcols	0
	testReadBlankCorner	0.001
	testReadInputStreamMissing	0
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0.001

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0.001

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0.001

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.011
	testByteArrayToBooleans	0.008
	testStringToDoubleArrayConversionSpeed	0.021
	testByteArrayToDoubleConversionSpeed	0.009
	testByteArrayToTabbedString	0.003
	testDoubleArrayToBytes	0.003
	testIntsToBytes	0.003
	testBooleansToLongArray	0.002
	testByteArrayToDoubles	0.003
	testStringToBytes	0.004
	testDoubleArrayToDelimitedStringConversionSpeed	0.009
	testObjectToBytes	0.002
	testBooleansToByteArray	0.003
	testByteArrayToLongs	0.003
	testByteArrayToDoubleMatrix	0.003

ExcelUtilTest

	testGetSheetFromFile	0.202
	testGetSet	0.001
	testSetFormula	0.003

TestHistogramWriter

testWriter

0

MatrixWriterTest

	testWriteMatrixB	0.004
	testWriteMatrix	0.003
	testWrite3DMatrix	0.001

TestRowNameFilter

	testFilterString	0.002
	testFilterExclude	0.003
	testFilter	0.003
	testFilterStringExclude	0.004

TestRowAffyNameFilter

	testStringFilter	0.002
	testFilter	0.003

TestRowLevelFilter

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

TestItemLevelFilter

testFilter

0

TestRowAbsentFilter

	testFilterKeepMarginal	0.006
	testFilterPresentCountInvalid	0.002
	testFilterWithMissing	0.003
	testFilterNullFlags	0.003
	testFilterWithMissingLessStringent	0.003
	testFilterFractionInvalid	0.002
	testFilterStringMatrix	0.004
	testFilterFraction	0.004
	testFilter	0.004

TestRowMissingFilter

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

MatrixDisplayTest

	testWriteOutAsPNG2	0.587
	testWriteOutAsPNG	0.012
	testSaveImage	0.009
	testSaveImageStandardize	0.026

Failure Details

[Summary] [Package List] [Test Cases]

	testCacheOntologyToDisk
	skipped: This test was always broken, but the failure was obscured in a thread.
	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.