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	17	0	0	0	100%	0.106

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ConfigUtilsTest	13	0	0	0	100%	0.197
	DateUtilTest	6	0	0	0	100%	0.013
	SQLUtilsTest	1	0	0	0	100%	0.001
	StringUtilTest	6	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.079
	BatchIteratorTest	3	0	0	0	100%	0
	PrettyPrinterTest	1	0	0	0	100%	0.001
	NetUtilsTest	4	0	0	0	100%	3.85
	TestStringUtil	8	0	0	0	100%	0.03

ubic.basecode.dataStructure.params

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

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.38

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestHistogramWriter	1	0	0	0	100%	0.001
	MatrixWriterTest	3	0	0	0	100%	0.017

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

ubic.basecode.math.metaanalysis

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

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DesignMatrixTest	5	0	0	0	100%	0.001
	ModeratedTstatTest	6	0	0	0	100%	0.15
	LeastSquaresFitTest	20	0	0	0	100%	9.105
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.001

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	1	0	0	1	0%	0.307
	JRIClientTest	1	0	0	1	0%	0.004

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	20.77
	JenaUtilsTest	1	0	0	0	100%	0.108
	OntologyLoaderTest	2	0	0	0	100%	0.133
	OntologySearchTest	9	0	0	0	100%	7.756

ubic.basecode.dataStructure.graph

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

ubic.basecode.dataStructure.matrix

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

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MultipleTestCorrectionTest	5	0	0	0	100%	0.041
	TestMathUtil	5	0	0	0	100%	0
	TestROC	3	0	0	0	100%	0
	TestStats	14	0	0	0	100%	0
	TestWilcoxon	15	0	0	0	100%	1.939
	TestMatrixStats	15	0	0	0	100%	0
	RandomChooserTest	7	0	0	0	100%	0.737
	TestSpecFunc	7	0	0	0	100%	0
	TestDescriptiveWithMissing	38	0	0	0	100%	0.003
	TestMatrixRowStats	6	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0
	TestRank	14	0	0	0	100%	0
	StringDistanceTest	16	0	0	0	100%	0
	SingularValueDecompositionTest	1	0	0	0	100%	0
	DistanceTest	12	0	0	0	100%	0.001
	TestKSTest	2	0	0	0	100%	0
	KruskalWallisTest	1	0	0	0	100%	0.001
	PrecisionRecallTest	5	0	0	0	100%	0
	CorrelationStatsTest	18	0	0	0	100%	0.001

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramReaderTest	2	0	0	0	100%	0
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.008
	TestMapReader	3	0	0	0	100%	0
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	1.139
	TestStringMatrixReader	4	0	0	0	100%	0.001
	TestDoubleMatrixReader	15	0	0	0	100%	0.081

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAffyNameFilter	2	0	0	0	100%	0.003
	TestRowNameFilter	4	0	0	0	100%	0.003
	TestRowAbsentFilter	9	0	0	0	100%	0.719
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowMissingFilter	11	0	0	0	100%	0.053
	TestRowLevelFilter	23	0	0	0	100%	0.129

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	1.171

ubic.basecode.dataStructure.tree

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	BinaryTreeTest	7	0	0	0	100%	0.001

ubic.basecode.dataStructure

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.46

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

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0
	testBenjaminiHochbergCut	0
	testBenjaminiHochberg	0.014
	testBenjaminiHochbergM	0.017
	testBonferroniCut	0.01

ConfigUtilsTest

	testLoadConfigURL	0.073
	testGetConfigBuilderFile	0.096
	testGetConfigBuilderString	0.003
	testGetConfigBuilderURLNew	0.002
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.001
	testLoadConfigStringNewName	0.01
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.002

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0.001

TestHistogramWriter

testWriter

0

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

TestROC

	testBig	0
	testAroc	0
	testArocPvalue	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

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	1.918
	testWilxcoxonPGaussB	0.002
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0.001
	testDVolume	0.001
	testAExact	0.009
	testWilxcoxonPWithTies	0.001
	testEVolume	0.001

MatrixUtilTest

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

TestRowAbsentFilter

	testFilterKeepMarginal	0.58
	testFilterPresentCountInvalid	0.012
	testFilterWithMissing	0.013
	testFilterNullFlags	0.007
	testFilterWithMissingLessStringent	0.011
	testFilterFractionInvalid	0.007
	testFilterStringMatrix	0.008
	testFilterFraction	0.008
	testFilter	0.007

TestMatrixStats

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

RandomChooserTest

	testChooseRandomDeck	0.009
	testRepeatSubset	0.293
	testChooserandomInts	0.029
	testChooserandomWrep	0
	testRandomSubset	0.001
	testChooserandomInt	0.062
	testRepeat	0.343

DateUtilTest

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

TestSpecFunc

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

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

ParameterKeeperTest

test

0.001

DenseDoubleMatrixTest

	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
	testGetRowByNameNull	0
	testSetIntIntObject	0
	testGetRow2	0
	testSubsetColumns	0
	testViewRow	0
	testColumns	0
	testGetColRange	0
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testViewColumn	0
	testGetColObj2	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testIsMissing2	0
	testGetColByNameFail	0
	testGetColByNameNull	0
	testGetRowObj2	0
	testGetColByName	0
	testGetRowArrayList2	0
	testViewRow2	0

BinaryTreeTest

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

TestCorrelationEffectMetaAnalysis

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

UberonOntologySearchTest

	testScore	0.019
	testOmitDefinition	0.02

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.001
	test2NoPivoting	0

SQLUtilsTest

testBlobToString

0

CompressedSparseDoubleMatrixTest

	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
	testGetRowByNameNull	0
	testSetIntIntObject	0
	testGetRow2	0
	testSubsetColumns	0
	testViewRow	0
	testColumns	0
	testGetColRange	0
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testViewColumn	0
	testGetColObj2	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testIsMissing2	0
	testGetColByNameFail	0
	testGetColByNameNull	0
	testGetRowObj2	0
	testGetColByName	0
	testGetRowArrayList2	0.001
	testViewRow2	0

StringUtilTest

	testMakeUnique	0
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0
	testMakeNames	0

ParamGrabberTest

test

0

TestDescriptiveWithMissing

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

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.

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0
	testInteractionAndRelevel	0

FileToolsTest

	testHasImageExtension	0.003
	testTestDir	0.002
	testGetWithoutExtension	0.003
	testGetLines	0.005
	testTouch	0.002
	testListDirectoryFiles	0.006
	testAddImageExtension	0.002
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.004
	testCleanFileName	0.004
	testgetStringListFromFile	0.002
	testGetWithoutExtensionB	0.002
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0.002
	testCleanFileNameErr	0.002
	testIsGZipped	0.002
	testUnGzipFile	0.003
	testCopyFileFailOnDirectoryOutput	0.002
	testTestFileString	0.001
	testGetCompressedFile	0.002
	testCopyFile	0.003
	testGetExtension	0.002
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.002
	testAddDataExtension	0.001
	testGetCompressedFileZip	0.003
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0.002
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.002
	testHasXMLExtension	0.001
	testUnzipFile	0.008

DoubleAddingMapTest

test

0

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

TestMatrixRowStats

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

TestItemLevelFilter

testFilter

0

JenaUtilsTest

testInferenceCapabilities

0.107

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

TestDirectedGraph

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

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

UniformDensityComputerTest

testDensity

0

CompressedNamedBitMatrixTest

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

OntologyLoaderTest

	testCacheOntologyToDisk	0.125
	testHasChanged	0.003

ExcelUtilTest

	testGetSheetFromFile	0.447
	testGetSet	0.003
	testSetFormula	0.01

MatrixWriterTest

	testWriteMatrixB	0.006
	testWriteMatrix	0.004
	testWrite3DMatrix	0.006

TestWishart

testNextDoubleMatrix

0

OntologySearchTest

	testPersistence	2.098
	testOmitDefinitions2	0.217
	testOmitDefinitions3	0.092
	testOmitDefinitions4	1.637
	testOmitBadPredicates2	0.055
	testOmitBadPredicates	2.607
	testIndexing	0.633
	testOmitDefinitions	0.058
	testStemming	0.307

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

ModeratedTstatTest

	testLimmaMissing	0.015
	testFdist	0.001
	testLimma	0.02
	testSqueezeVarB	0.112
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

OntologyTermTest

	testGetParentsHasProperPart	0.059
	testGetChildren	0.45
	testGetChildrenHasProperPart	0.024
	testGetParents	0.247
	testRejectNonEnglish	0.379

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.007
	testFilterWithMissing	0.004
	testFilterWithMissingLessStringent	0.004
	testFilterFractionInvalid2	0.006
	testFilterFractionInvalid	0.004
	testFilterStringMatrix	0.005
	testFilterFraction	0.007
	testFilter	0.006
	testMaxFractionRemovedInvalid	0.004
	testFilterNoFiltering	0.005

RServeClientTest

	ubic.basecode.util.r.RServeClientTest + - [ Detail ]	0
	got: <java.io.IOException: Could not connect to Rserve>, expected: null

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.012
	testThreeWaySingular	0.161
	testEstrogen	3.996
	testVectorWeightedRegress	0.001
	testNHBE	4.768
	testLSFTwoLevels2	0.037
	testLSFTwoLevels3	0.027
	testSingular2	0.005
	testVectorWeightedRegressWithMissing	0.002
	testVectorRegress	0.001
	testLSFThreeLevelsOneContinuousWithMissing3	0.012
	testTwoWayAnovaWithInteractions	0.005
	testLSFTwoLevels	0.003
	testOneWayAnova	0.015
	testTwoWayTwoLevelsOneContinousInteractionC	0.005
	testLSFThreeLevelsOnecontinous2	0.002
	testMatrixWeightedRegress	0.001
	testSingular	0.015
	testLSFTwoLevelsOneContinuous	0.005
	testLSFOneContinuousWithMissing3	0.004

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

TestMeanDifferenceMetaAnalysis

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

JRIClientTest

	ubic.basecode.util.r.JRIClientTest + - [ Detail ]	0
	got: <[R_HOME environment variable is not set., null]>, expected: every item is not null

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0
	testByteArrayToBooleans	0.003
	testStringToDoubleArrayConversionSpeed	0.007
	testByteArrayToDoubleConversionSpeed	0.008
	testByteArrayToTabbedString	0.006
	testDoubleArrayToBytes	0.005
	testIntsToBytes	0.006
	testBooleansToLongArray	0.005
	testByteArrayToSquareDoubleMatrix	0.012
	testByteArrayToDoubles	0.006
	testStringArrayToBytes	0.006
	testDoubleArrayToDelimitedStringConversionSpeed	0.017
	testStringArrayToTabbedBytes	0.006
	testObjectToBytes	0.006
	testBooleansToByteArray	0.003
	testByteArrayToLongs	0.003
	testByteArrayToDoubleMatrix	0.004

PrettyPrinterTest

testPrintBeans

0

SingularValueDecompositionTest

testSingularValueDecomposition

0

MeanVarianceEstimatorTest

	testVoom	0
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

StringToStringSetMapTest

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

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	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

MatrixDisplayTest

	testWriteOutAsPNG2	0.344
	testWriteOutAsPNG	0.011
	testSaveImage	0.006
	testSaveImageStandardize	0.019

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0.005

CountingMapTest

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

KruskalWallisTest

testKW

0.001

NetUtilsTest

	testFtpFileSize	0.777
	testCheckForFile	0.732
	testFtpFileSizeDoesntExist	1.31
	testDownloadFile	1.03

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.013
	testReadInputStream	0.009
	testReadStreamAdjListBig	1.116

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

SparseRaggedDoubleMatrixTest

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

CorrelationStatsTest

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

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.026
	testCsvSplitB	0.001
	testCsvSplitC	0
	testCsvSplitD	0.001
	testCsvSplitE	0.001
	testCsvSplitF	0
	testTwoStringHashKeyB	0

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

HistogramSamplerTest

testNextSample

0

TestRowLevelFilter

	testFilterMinHigh	0.002
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.002
	testFilterMaxTooHigh	0.008
	testFilterMedian	0.01
	testFilterNoFilter	0.009
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.007
	testFilterFractionMaxRemoveNegHigh	0.006
	testFilterMax	0.007
	testFilterMin	0.004
	testFilterMaxFractionNoneRemoveNeg	0.006
	testFilterMedianHigh	0.006
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.005
	testFilterFractionMaxRemoveNeg	0.005
	testFilterMaxFractionAll	0.006
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.005
	testFilterMaxFraction	0.004
	testFilterBadFraction	0.005
	testFilterMaxFractionHigh	0.005
	testFilterMaxFractionNone	0.004
	testFilterFractionMaxRemoveHighAndLow	0.005
	testFilterMeanHigh	0.004
	testFilterMean	0.005
	testFilterMaxHigh	0.004

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
	testGetRowByNameNull	0
	testSetIntIntObject	0
	testGetRow2	0
	testSubsetColumns	0
	testViewRow	0
	testColumns	0
	testGetColRange	0
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testViewColumn	0
	testGetColObj2	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testIsMissing2	0
	testGetColByNameFail	0
	testGetColByNameNull	0
	testGetRowObj2	0
	testGetColByName	0
	testGetRowArrayList2	0
	testViewRow2	0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0.002
	testSmallNumbers	0.047
	testReadInputStreamMissingSpaces	0.017
	testReadBad	0.002
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.001
	testReadBlankCorner	0.002
	testReadInputStreamMissing	0.003
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0.003

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.
	ubic.basecode.util.r.RServeClientTest
	skipped: got: <java.io.IOException: Could not connect to Rserve>, expected: null
	ubic.basecode.util.r.JRIClientTest
	skipped: got: <[R_HOME environment variable is not set., null]>, expected: every item is not null