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%	0.001

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	15	0	0	0	100%	0.063

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ConfigUtilsTest	13	0	0	0	100%	0.108
	FileToolsTest	32	0	0	0	100%	0.044
	StringUtilTest	5	0	0	0	100%	0.002
	PrettyPrinterTest	1	0	0	0	100%	0.042
	NetUtilsTest	4	0	0	0	100%	7.616
	SQLUtilsTest	1	0	0	0	100%	0.001
	TestStringUtil	8	0	0	0	100%	0.007
	DateUtilTest	6	0	0	0	100%	0.012
	BatchIteratorTest	3	0	0	0	100%	0.002

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%	0.528

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.431

ubic.basecode.ontology.search

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologySearchTest	11	0	0	0	100%	3.236

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%	0.003

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
	TestWishart	1	0	0	0	100%	0.001
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.017
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0

ubic.basecode.ontology.providers

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ObiServiceTest	1	0	0	0	100%	6.126
	AbstractOntologyServiceTest	3	0	0	0	100%	4.053

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	21	0	0	0	100%	6.651
	JRIClientTest	21	0	0	0	100%	0.002

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.061
	LeastSquaresFitTest	20	0	0	0	100%	4.636
	ModeratedTstatTest	6	0	0	0	100%	0.098
	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
	TestCorrelationEffectMetaAnalysis	9	0	0	0	100%	0.001
	TestMeanDifferenceMetaAnalysis	8	0	0	0	100%	0.001

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.237

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.1
	MatrixUtilTest	7	0	0	0	100%	0.017
	DenseDoubleMatrixTest	39	0	0	0	100%	0.061
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.016
	RCDoubleMatrix1DTest	3	0	0	0	100%	0.001
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.049
	SparseDoubleMatrixTest	24	0	0	0	100%	0.012
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.002
	IntegerMatrixTest	16	0	0	0	100%	0.005
	StringMatrixTest	4	0	0	0	100%	0.004

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStats	14	0	0	0	100%	0
	TestSpecFunc	7	0	0	0	100%	0
	TestDescriptiveWithMissing	44	0	0	0	100%	0
	TestRank	14	0	0	0	100%	0.001
	RandomChooserTest	7	0	0	0	100%	0.432
	TestMathUtil	5	0	0	0	100%	0
	TestMatrixStats	15	0	0	0	100%	0.012
	KruskalWallisTest	1	0	0	0	100%	0
	TestMatrixRowStats	6	0	0	0	100%	0
	StringDistanceTest	16	0	0	0	100%	0.001
	TestKSTest	2	0	0	0	100%	0
	TestROC	3	0	0	0	100%	0.041
	SingularValueDecompositionTest	1	0	0	0	100%	0.103
	CorrelationStatsTest	18	0	0	0	100%	0.068
	TestWilcoxon	15	0	0	0	100%	2.699
	PrecisionRecallTest	5	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0.003
	MultipleTestCorrectionTest	5	0	0	0	100%	0.07
	DistanceTest	12	0	0	0	100%	0

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMapReader	3	0	0	0	100%	0
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.316
	TestDoubleMatrixReader	15	0	0	0	100%	0.028
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.005
	TestStringMatrixReader	4	0	0	0	100%	0.002
	HistogramReaderTest	2	0	0	0	100%	0.001

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	0.395

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowNameFilter	4	0	0	0	100%	0.005
	TestRowAffyNameFilter	2	0	0	0	100%	0.003
	TestRowLevelFilter	23	0	0	0	100%	0.035
	TestItemLevelFilter	1	0	0	0	100%	0
	TestRowAbsentFilter	9	0	0	0	100%	0.015
	TestRowMissingFilter	11	0	0	0	100%	0.01

ubic.basecode.dataStructure

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CountingMapTest	6	0	0	0	100%	0.001
	StringToStringSetMapTest	6	0	0	0	100%	0
	DoubleAddingMapTest	1	0	0	0	100%	0.001
	BitUtilTest	5	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%	0.129

Test Cases

[Summary] [Package List] [Test Cases]

RServeClientTest

	testExec	0.431
	testListEvalA	0.315
	testListEvalB	0.312
	testExecError	0.31
	testDataFrameA	0.311
	testAssignAndRetrieveMatrix	0.309
	testAnovaA	0.309
	testAnovaB	0.309
	testAnovaC	0.306
	testAnovaD	0.307
	testAnovaE	0.308
	testAnovaF	0.308
	testLimmaA	0.308
	testExecDoubleArray	0.309
	testAssignAndRetrieveMatrixB	0.308
	testAssignAndRetrieveMatrixD	0.31
	testLinearModelA	0.308
	testLinearModelB	0.308
	testLinearModelC	0.304
	testLinearModelD	0.306
	testStringListEvalB	0.308

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
	testAssignAndRetrieveMatrixB	0
	testAssignAndRetrieveMatrixD	0
	testLinearModelA	0
	testLinearModelB	0
	testLinearModelC	0
	testLinearModelD	0
	testStringListEvalB	0

ConfigUtilsTest

	testLoadConfigURL	0.059
	testGetConfigBuilderFile	0.031
	testGetConfigBuilderString	0.001
	testGetConfigBuilderURLNew	0.002
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.001
	testLoadConfigURLNew	0.001
	testLoadConfigStringNewName	0.007
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.001

FileToolsTest

	testHasImageExtension	0.002
	testTestDir	0.001
	testGetWithoutExtension	0
	testGetLines	0.002
	testTouch	0.001
	testListDirectoryFiles	0.001
	testAddImageExtension	0.001
	testChangeExtension	0
	testDeleteFilesAndDir	0.001
	testCleanFileName	0.003
	testgetStringListFromFile	0.002
	testGetWithoutExtensionB	0
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0
	testCleanFileNameErr	0
	testIsGZipped	0.002
	testUnGzipFile	0.001
	testCopyFileFailOnDirectoryOutput	0
	testTestFileString	0
	testGetCompressedFile	0
	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	0.002
	testHasXMLExtension	0.001
	testUnzipFile	0.013

StringUtilTest

	testMakeRnames	0.001
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0

PrettyPrinterTest

testPrintBeans

0.042

NetUtilsTest

	testFtpFileSize	2.174
	testCheckForFile	1.272
	testFtpFileSizeDoesntExist	2.295
	testDownloadFile	1.874

SQLUtilsTest

testBlobToString

0.001

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.005
	testCsvSplitB	0
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0
	testTwoStringHashKeyB	0.001

DateUtilTest

	testgetRelative5yearsFromnow	0.002
	testRange	0.003
	testgetRelative5yearsago	0
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0
	testRangeBad	0.001

BatchIteratorTest

	testBatches	0.001
	testBatchIterator	0
	testConcurrentModificationException	0.001

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.013
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.019
	testGet	0.003
	testSet	0.001
	testRows2	0.002
	testCopy	0.003
	testGet2	0.002
	testRows	0.002
	testSet2	0.001
	testSize	0.002
	testToString	0.003
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0.002
	testSubsetColumns	0.004
	testViewRow	0.003
	testColumns	0.002
	testGetColRange	0.002
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.002
	testIsMissing	0.002
	testViewColumn	0.001
	testGetColObj2	0.002
	testGetObject	0.001
	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	0.002
	testViewRow2	0.001

MatrixUtilTest

	testSelectColumnsAndRowsBad	0
	testSelectColumns	0.001
	testDropColumn	0.002
	testSelectColumnsAndRows	0.013
	testRemoveMissing1	0
	testRemoveMissing2	0
	testSelectRows	0

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0.001
	testToArray	0.001
	testSortByColumnAbsoluteValue	0.011
	testGet	0
	testSet	0
	testRows2	0.001
	testCopy	0.002
	testGet2	0.002
	testRows	0.001
	testSet2	0.001
	testSize	0.002
	testToString	0.001
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0.001
	testSubsetColumns	0.001
	testViewRow	0.002
	testColumns	0.001
	testGetColRange	0.002
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.001
	testIsMissing	0.003
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.002
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.002
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.002

CompressedNamedBitMatrixTest

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

SparseRaggedDoubleMatrixTest

	testSubsetRows	0.009
	testSubsetRowsFail	0
	testRows	0.002
	testGetRowMatrix1D	0.002
	testGetRowArrayList	0
	testColumns	0
	testGetColRange	0
	testAddrow	0.001
	testGetRow	0
	testGetRowRange	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0.001
	testAssign	0

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0.002
	testSubsetRows	0.001
	testToArray	0.003
	testSortByColumnAbsoluteValue	0.004
	testGet	0.001
	testSet	0.001
	testRows2	0.002
	testCopy	0.001
	testGet2	0.001
	testRows	0.002
	testSet2	0.001
	testSize	0.001
	testToString	0.005
	testGetRowByNameFail	0
	testGetRowByNameNull	0
	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	0.002
	testViewColumn	0
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.001
	testGetColByNameFail	0.002
	testGetColByNameNull	0.001
	testGetRowObj2	0
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

SparseDoubleMatrixTest

	testSubsetCols	0.002
	testSubsetRows	0
	testToArray	0.001
	testGet	0
	testSet	0.001
	testCopy	0
	testRows	0
	testSize	0
	testToString	0.001
	testGetRowArrayList	0
	testViewRow	0.001
	testColumns	0
	testGetColRange	0.001
	testGetByKeys	0
	testGetColObj	0.001
	testGetColumn	0.001
	testIsMissing	0
	testViewColumn	0.001
	testGetObject	0
	testGetRow	0
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0
	testGetColByName	0.001

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

IntegerMatrixTest

	testGetEntry	0.002
	testGet	0
	testSet	0
	testRows	0.001
	testSize	0
	testColumns	0
	testSetByKeys	0
	testToInteger	0.001
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testSetObj	0.001

StringMatrixTest

	testToString	0.001
	testSubsetColumns	0.001
	testGetColObj	0.001
	testSubset	0.001

CountingMapTest

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

StringToStringSetMapTest

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

ParamGrabberTest

test

0.001

ParameterKeeperTest

test

0.527

TestDirectedGraph

	testDeleteLeaf1	0.001
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0.001
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.235

BinaryTreeTest

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

DoubleAddingMapTest

test

0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

ObiServiceTest

testLoadAndSearch

6.126

AbstractOntologyServiceTest

	testReindexOnInitialize	0
	testCacheOntologyToDisk	3.035
	testGenericOntologyServiceMem	1.017

OntologyTermTest

	testGetParentsHasProperPart	0.013
	testGetChildren	0.153
	testGetChildrenHasProperPart	0.013
	testGetParents	0.134
	testRejectNonEnglish	0.082

OntologySearchTest

	testPersistence	0.129
	matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.621
	testOmitDefinitions2	0.115
	testOmitDefinitions3	0.062
	testOmitDefinitions4	1.662
	testOmitBadPredicates2	0.073
	testOmitBadPredicates	0.068
	testIndexing	0.436
	matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.002
	matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException	0.003
	testOmitDefinitions	0.065

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
	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	0.049
	testMeanVarianceNoDesignWithColsRowAllMissing	0.001
	testDuplicateRows	0.01
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.001

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.023
	testThreeWaySingular	0.113
	testEstrogen	2.042
	testVectorWeightedRegress	0
	testNHBE	2.37
	testLSFTwoLevels2	0.022
	testLSFTwoLevels3	0.021
	testSingular2	0.003
	testVectorWeightedRegressWithMissing	0.002
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.003
	testTwoWayAnovaWithInteractions	0.003
	testLSFTwoLevels	0.002
	testOneWayAnova	0.014
	testTwoWayTwoLevelsOneContinousInteractionC	0.003
	testLSFThreeLevelsOnecontinous2	0.001
	testMatrixWeightedRegress	0
	testSingular	0.009
	testLSFTwoLevelsOneContinuous	0.003
	testLSFOneContinuousWithMissing3	0.002

ModeratedTstatTest

	testLimmaMissing	0.009
	testFdist	0
	testLimma	0.013
	testSqueezeVarB	0.074
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

DesignMatrixTest

	testInteractionC	0
	test2	0.001
	testA	0.001
	testB	0.001
	testInteractionAndRelevel	0.004

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

TestCorrelationEffectMetaAnalysis

	testRunUFEffect	0
	testRunZFEffect	0
	testRunZRQval	0
	testRunUFZscore	0
	testRunZFZscore	0.001
	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
	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
	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
	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
	testRankWithTies	0.001
	testWithNaNs	0
	testRankTransformDoubleArrayList	0
	testRankWithTiesB	0
	testRankWithTiesC	0
	testRankWithTiesD	0
	testRankWithTiesE	0
	testWithNaNs2	0
	testWithNaNs3	0
	testOrderB	0

RandomChooserTest

	testChooseRandomDeck	0.023
	testRepeatSubset	0.196
	testChooserandomInts	0.011
	testChooserandomWrep	0
	testRandomSubset	0
	testChooserandomInt	0.028
	testRepeat	0.174

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

TestWishart

testNextDoubleMatrix

0.001

UniformDensityComputerTest

testDensity

0

HistogramSamplerTest

testNextSample

0.017

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

TestMatrixStats

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

KruskalWallisTest

testKW

0

TestMatrixRowStats

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

StringDistanceTest

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

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestROC

	testBig	0.04
	testAroc	0
	testArocPvalue	0.001

SingularValueDecompositionTest

testSingularValueDecomposition

0.101

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.001
	test2NoPivoting	0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.04
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.021
	testCorrelationForPvalue	0
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.006
	testSpearmanPvalueG2	0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	2.649
	testWilxcoxonPGaussB	0
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.002
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0.02
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.022
	testWilxcoxonPWithTies	0.003
	testEVolume	0.001

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

TestMatrixNormalizer

	testQuantileNormalize	0.001
	testQuantileNormalizeWithMissing	0.001

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.022
	testBenjaminiHochbergCut	0.011
	testBenjaminiHochberg	0.014
	testBenjaminiHochbergM	0.013
	testBonferroniCut	0.009

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

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0
	testReadInputStream	0
	testReadStreamAdjListBig	0.316

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0.002
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.001
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0.001
	testSmallNumbers	0.015
	testReadInputStreamMissingSpaces	0.003
	testReadBad	0.001
	testBadFileName	0
	testReadChooseRowsSkipcols	0
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0.005

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0.001

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0.001

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.005
	testByteArrayToBooleans	0.005
	testStringToDoubleArrayConversionSpeed	0.007
	testByteArrayToDoubleConversionSpeed	0.009
	testByteArrayToTabbedString	0.004
	testDoubleArrayToBytes	0.003
	testIntsToBytes	0.004
	testBooleansToLongArray	0.002
	testByteArrayToDoubles	0.003
	testStringToBytes	0.005
	testDoubleArrayToDelimitedStringConversionSpeed	0.005
	testObjectToBytes	0.003
	testBooleansToByteArray	0.003
	testByteArrayToLongs	0.002
	testByteArrayToDoubleMatrix	0.003

ExcelUtilTest

	testGetSheetFromFile	0.127
	testGetSet	0
	testSetFormula	0.002

TestHistogramWriter

testWriter

0

MatrixWriterTest

	testWriteMatrixB	0
	testWriteMatrix	0.001
	testWrite3DMatrix	0.001

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0.002
	testFilter	0.001
	testFilterStringExclude	0.001

TestRowAffyNameFilter

	testStringFilter	0
	testFilter	0.002

TestRowLevelFilter

	testFilterMinHigh	0.002
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.001
	testFilterMaxTooHigh	0.002
	testFilterMedian	0.001
	testFilterNoFilter	0.001
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.001
	testFilterFractionMaxRemoveNegHigh	0.002
	testFilterMax	0.001
	testFilterMin	0.001
	testFilterMaxFractionNoneRemoveNeg	0.001
	testFilterMedianHigh	0.003
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.001
	testFilterFractionMaxRemoveNeg	0.002
	testFilterMaxFractionAll	0.002
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.002
	testFilterMaxFraction	0.002
	testFilterBadFraction	0.001
	testFilterMaxFractionHigh	0.001
	testFilterMaxFractionNone	0.002
	testFilterFractionMaxRemoveHighAndLow	0.001
	testFilterMeanHigh	0.001
	testFilterMean	0.002
	testFilterMaxHigh	0.002

TestItemLevelFilter

testFilter

0

TestRowAbsentFilter

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

TestRowMissingFilter

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

MatrixDisplayTest

	testWriteOutAsPNG2	0.41
	testWriteOutAsPNG	0.005
	testSaveImage	0.004
	testSaveImageStandardize	0.011

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.