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

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.029

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	NetUtilsTest	4	0	0	0	100%	3.685
	PrettyPrinterTest	1	0	0	0	100%	0
	SQLUtilsTest	1	0	0	0	100%	0
	StringUtilTest	6	0	0	0	100%	0.001
	TestStringUtil	8	0	0	0	100%	0.008
	BatchIteratorTest	3	0	0	0	100%	0
	ConfigUtilsTest	13	0	0	0	100%	0.097
	DateUtilTest	6	0	0	0	100%	0.016
	FileToolsTest	32	0	0	0	100%	0.023

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%	0.078

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.217

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixWriterTest	3	0	0	0	100%	0.003
	TestHistogramWriter	1	0	0	0	100%	0

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
	HistogramSamplerTest	1	0	0	0	100%	0.008
	HistogramTest	2	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	TestWishart	1	0	0	0	100%	0.004
	UniformDensityComputerTest	1	0	0	0	100%	0

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DesignMatrixTest	5	0	0	0	100%	0.002
	LeastSquaresFitTest	20	0	0	0	100%	2.753
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.031
	ModeratedTstatTest	6	0	0	0	100%	0.065

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
	TestMeanDifferenceMetaAnalysis	8	0	0	0	100%	0.001

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JRIClientTest	1	0	0	1	0%	0.214
	RServeClientTest	1	0	0	1	0%	0.301

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JenaUtilsTest	1	0	0	0	100%	0.21
	OntologyLoaderTest	2	0	0	0	100%	0.247
	OntologySearchTest	9	0	0	0	100%	3.178
	UberonOntologySearchTest	2	0	0	0	100%	6.712

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.127

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.002
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.04
	DenseDouble3dMatrixTest	4	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.023
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.021
	IntegerMatrixTest	16	0	0	0	100%	0.001
	MatrixUtilTest	7	0	0	0	100%	0.007
	RCDoubleMatrix1DTest	3	0	0	0	100%	0.002
	SparseDoubleMatrixTest	24	0	0	0	100%	0.009
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.004
	StringMatrixTest	4	0	0	0	100%	0

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CorrelationStatsTest	18	0	0	0	100%	0.031
	DistanceTest	12	0	0	0	100%	0
	KruskalWallisTest	1	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.028
	PrecisionRecallTest	5	0	0	0	100%	0
	RandomChooserTest	7	0	0	0	100%	0.229
	SingularValueDecompositionTest	1	0	0	0	100%	0.1
	StringDistanceTest	16	0	0	0	100%	0
	TestDescriptiveWithMissing	38	0	0	0	100%	0
	TestKSTest	2	0	0	0	100%	0
	TestMathUtil	5	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0
	TestMatrixRowStats	6	0	0	0	100%	0
	TestMatrixStats	15	0	0	0	100%	0.005
	TestROC	3	0	0	0	100%	0.013
	TestRank	14	0	0	0	100%	0
	TestSpecFunc	7	0	0	0	100%	0
	TestStats	14	0	0	0	100%	0
	TestWilcoxon	15	0	0	0	100%	1.027

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramReaderTest	2	0	0	0	100%	0
	TestDoubleMatrixReader	15	0	0	0	100%	0.016
	TestMapReader	3	0	0	0	100%	0
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.193
	TestStringMatrixReader	4	0	0	0	100%	0

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	0.292

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestItemLevelFilter	1	0	0	0	100%	0
	TestRowAbsentFilter	9	0	0	0	100%	0.011
	TestRowAffyNameFilter	2	0	0	0	100%	0
	TestRowLevelFilter	23	0	0	0	100%	0.015
	TestRowMissingFilter	11	0	0	0	100%	0.003
	TestRowNameFilter	4	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

ubic.basecode.dataStructure

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.062

Test Cases

[Summary] [Package List] [Test Cases]

NetUtilsTest

	testFtpFileSize	0.723
	testCheckForFile	0.723
	testFtpFileSizeDoesntExist	1.256
	testDownloadFile	0.982

PrettyPrinterTest

testPrintBeans

0

SQLUtilsTest

testBlobToString

0

StringUtilTest

	testMakeUnique	0
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0
	testCommonSuffix	0
	testMakeNames	0.001

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.007
	testCsvSplitB	0.001
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0
	testTwoStringHashKeyB	0

CompressedNamedBitMatrixTest

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

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.006
	testToArray	0.001
	testSortByColumnAbsoluteValue	0.004
	testGet	0.001
	testSet	0.001
	testRows2	0
	testCopy	0.002
	testGet2	0
	testRows	0.001
	testSet2	0.001
	testSize	0
	testToString	0.001
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0
	testSubsetColumns	0.002
	testViewRow	0.001
	testColumns	0.001
	testGetColRange	0.001
	testGetByKeys	0
	testGetColObj	0.001
	testGetColumn	0
	testIsMissing	0.001
	testViewColumn	0
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

DenseDouble3dMatrixTest

	testget	0
	testtostring	0
	testgetcolobj	0
	testgetrowobj	0

DenseDoubleMatrixTest

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

FastRowAccessDoubleMatrixTest

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

IntegerMatrixTest

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

MatrixUtilTest

	testSelectColumnsAndRowsBad	0
	testSelectColumns	0
	testDropColumn	0
	testSelectColumnsAndRows	0.003
	testRemoveMissing1	0.001
	testRemoveMissing2	0.001
	testSelectRows	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0.001
	testAssign	0

SparseDoubleMatrixTest

	testSubsetCols	0.003
	testSubsetRows	0
	testToArray	0.001
	testGet	0
	testSet	0
	testCopy	0
	testRows	0
	testSize	0
	testToString	0
	testGetRowArrayList	0.001
	testViewRow	0
	testColumns	0
	testGetColRange	0
	testGetByKeys	0.001
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0
	testViewColumn	0
	testGetObject	0
	testGetRow	0.001
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testGetColByName	0

SparseRaggedDoubleMatrixTest

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

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

ParamGrabberTest

test

0.001

ParameterKeeperTest

test

0.078

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.127

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

CountingMapTest

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

DoubleAddingMapTest

test

0

StringToStringSetMapTest

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

JenaUtilsTest

testInferenceCapabilities

0.209

OntologyLoaderTest

	testCacheOntologyToDisk	0.24
	testHasChanged	0.001

OntologySearchTest

	testPersistence	0.247
	testOmitDefinitions2	0.079
	testOmitDefinitions3	0.023
	testOmitDefinitions4	0.593
	testOmitBadPredicates2	0.021
	testOmitBadPredicates	1.802
	testIndexing	0.25
	testOmitDefinitions	0.024
	testStemming	0.131

UberonOntologySearchTest

	testScore	0.005
	testOmitDefinition	0.003

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.

OntologyTermTest

	testGetParentsHasProperPart	0.015
	testGetChildren	0.124
	testGetChildrenHasProperPart	0.009
	testGetParents	0.062
	testRejectNonEnglish	0.081

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0
	testInteractionAndRelevel	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.023
	testThreeWaySingular	0.052
	testEstrogen	1.299
	testVectorWeightedRegress	0.001
	testNHBE	1.328
	testLSFTwoLevels2	0.012
	testLSFTwoLevels3	0.011
	testSingular2	0.003
	testVectorWeightedRegressWithMissing	0.002
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.002
	testTwoWayAnovaWithInteractions	0.001
	testLSFTwoLevels	0.002
	testOneWayAnova	0.005
	testTwoWayTwoLevelsOneContinousInteractionC	0.002
	testLSFThreeLevelsOnecontinous2	0.001
	testMatrixWeightedRegress	0
	testSingular	0.005
	testLSFTwoLevelsOneContinuous	0.002
	testLSFOneContinuousWithMissing3	0.002

MeanVarianceEstimatorTest

	testVoom	0.024
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.006
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.001

ModeratedTstatTest

	testLimmaMissing	0.009
	testFdist	0
	testLimma	0.009
	testSqueezeVarB	0.047
	testSqueezeVar	0
	testSqueezeVarWMissing	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

TestCorrelationEffectMetaAnalysis

	testRunUFEffect	0
	testRunZFEffect	0
	testRunZRQval	0
	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

HistogramSamplerTest

testNextSample

0.008

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

TestWishart

testNextDoubleMatrix

0

UniformDensityComputerTest

testDensity

0

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0
	test2NoPivoting	0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.009
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.019
	testCorrelationForPvalue	0
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0
	testSpearmanPvalueEm	0.003
	testSpearmanPvalueG2	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

KruskalWallisTest

testKW

0

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.004
	testBenjaminiHochbergCut	0.006
	testBenjaminiHochberg	0.008
	testBenjaminiHochbergM	0.006
	testBonferroniCut	0.004

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

RandomChooserTest

	testChooseRandomDeck	0.004
	testRepeatSubset	0.096
	testChooserandomInts	0.006
	testChooserandomWrep	0
	testRandomSubset	0
	testChooserandomInt	0.012
	testRepeat	0.111

SingularValueDecompositionTest

testSingularValueDecomposition

0.1

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

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
	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
	testSampleVariance	0
	testWeightedMean	0
	testCovariance	0
	testMedian	0
	testTrimmedMean	0
	testDurbinWatsonShort	0

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

TestMatrixRowStats

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

TestMatrixStats

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

TestROC

	testBig	0.011
	testAroc	0
	testArocPvalue	0.001

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

TestSpecFunc

	testdBinom	0
	testCumHyperGeometricB	0
	testTrigammaInverse	0
	testCumHyperGeometric	0
	testTrigammaInverseB	0
	testHypergeometric	0
	testCumHyperGeometricUT	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	1.022
	testWilxcoxonPGaussB	0
	testBGaussian	0
	testFVolume	0
	testWilxcoxonPVolume	0.002
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.001
	testWilxcoxonPWithTies	0
	testEVolume	0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testSmallNumbers	0.01
	testReadInputStreamMissingSpaces	0.003
	testReadBad	0
	testBadFileName	0
	testReadChooseRowsSkipcols	0.001
	testReadBlankCorner	0
	testReadInputStreamMissing	0.001
	testReadChooseRows	0
	testReadInputStreamColumnCount	0

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0
	testReadInputStream	0
	testReadStreamAdjListBig	0.192

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0

ExcelUtilTest

	testGetSheetFromFile	0.059
	testGetSet	0.001
	testSetFormula	0.001

MatrixWriterTest

	testWriteMatrixB	0.001
	testWriteMatrix	0.001
	testWrite3DMatrix	0

TestHistogramWriter

testWriter

0

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.001
	testByteArrayToBooleans	0.001
	testStringToDoubleArrayConversionSpeed	0.003
	testByteArrayToDoubleConversionSpeed	0.002
	testByteArrayToTabbedString	0.002
	testDoubleArrayToBytes	0.002
	testIntsToBytes	0.001
	testBooleansToLongArray	0.001
	testByteArrayToSquareDoubleMatrix	0.002
	testByteArrayToDoubles	0.001
	testStringArrayToBytes	0.001
	testDoubleArrayToDelimitedStringConversionSpeed	0.004
	testStringArrayToTabbedBytes	0.001
	testObjectToBytes	0.002
	testBooleansToByteArray	0.002
	testByteArrayToLongs	0.001
	testByteArrayToDoubleMatrix	0.001

TestItemLevelFilter

testFilter

0

TestRowAbsentFilter

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

TestRowAffyNameFilter

	testStringFilter	0
	testFilter	0

TestRowLevelFilter

	testFilterMinHigh	0
	testFilterFractionMaxRemoveHighAndLowBothFraction	0
	testFilterMaxTooHigh	0.001
	testFilterMedian	0.001
	testFilterNoFilter	0.001
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.001
	testFilterFractionMaxRemoveNegHigh	0.001
	testFilterMax	0.001
	testFilterMin	0.001
	testFilterMaxFractionNoneRemoveNeg	0
	testFilterMedianHigh	0.001
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.001
	testFilterFractionMaxRemoveNeg	0
	testFilterMaxFractionAll	0.001
	testFilterFractionMaxRemoveHighAndLowBothLevels	0
	testFilterMaxFraction	0
	testFilterBadFraction	0
	testFilterMaxFractionHigh	0.001
	testFilterMaxFractionNone	0.001
	testFilterFractionMaxRemoveHighAndLow	0
	testFilterMeanHigh	0.001
	testFilterMean	0
	testFilterMaxHigh	0.001

TestRowMissingFilter

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

TestRowNameFilter

	testFilterString	0
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0.001

MatrixDisplayTest

	testWriteOutAsPNG2	0.206
	testWriteOutAsPNG	0.003
	testSaveImage	0.002
	testSaveImageStandardize	0.006

JRIClientTest

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

RServeClientTest

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

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

ConfigUtilsTest

	testLoadConfigURL	0.047
	testGetConfigBuilderFile	0.04
	testGetConfigBuilderString	0
	testGetConfigBuilderURLNew	0.001
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0
	testLoadConfigURLNew	0.001
	testLoadConfigStringNewName	0.003
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0
	testLoadConfigFileNew	0.001

DateUtilTest

	testgetRelative5yearsFromnow	0.012
	testRange	0.002
	testgetRelative5yearsago	0
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0
	testRangeBad	0

FileToolsTest

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

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