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%	0.032

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.164

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	PrettyPrinterTest	1	0	0	0	100%	0.007
	SQLUtilsTest	1	0	0	0	100%	0
	DateUtilTest	6	0	0	0	100%	0.009
	StringUtilTest	6	0	0	0	100%	0.003
	NetUtilsTest	4	0	0	0	100%	3.833
	FileToolsTest	32	0	0	0	100%	0.062
	TestStringUtil	8	0	0	0	100%	0.02
	ConfigUtilsTest	13	0	0	0	100%	0.249
	BatchIteratorTest	3	0	0	0	100%	0

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParamGrabberTest	1	0	0	0	100%	0
	ParameterKeeperTest	1	0	0	0	100%	0.002

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.674

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%	0.009

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
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0
	TestWishart	1	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.021

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	1	0	0	1	0%	0.33
	JRIClientTest	1	0	0	1	0%	0

ubic.basecode.math.metaanalysis

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

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ModeratedTstatTest	6	0	0	0	100%	0.157
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.055
	LeastSquaresFitTest	20	0	0	0	100%	8.834
	DesignMatrixTest	5	0	0	0	100%	0.006

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	23.971
	OntologySearchTest	9	0	0	0	100%	5.944
	OntologyLoaderTest	2	0	0	0	100%	0.199
	JenaUtilsTest	1	0	0	0	100%	0.166

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.038

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMatrixNormalizer	2	0	0	0	100%	0
	TestDescriptiveWithMissing	38	0	0	0	100%	0.002
	TestKSTest	2	0	0	0	100%	0
	StringDistanceTest	16	0	0	0	100%	0
	PrecisionRecallTest	5	0	0	0	100%	0.001
	TestWilcoxon	15	0	0	0	100%	3.043
	TestStats	14	0	0	0	100%	0.001
	KruskalWallisTest	1	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.105
	TestSpecFunc	7	0	0	0	100%	0
	TestMathUtil	5	0	0	0	100%	0.001
	TestRank	14	0	0	0	100%	0.012
	SingularValueDecompositionTest	1	0	0	0	100%	0.089
	CorrelationStatsTest	18	0	0	0	100%	0.074
	TestROC	3	0	0	0	100%	0.033
	RandomChooserTest	7	0	0	0	100%	1.209
	TestMatrixStats	15	0	0	0	100%	0.015
	DistanceTest	12	0	0	0	100%	0
	TestMatrixRowStats	6	0	0	0	100%	0.001

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.002
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.006
	MatrixUtilTest	7	0	0	0	100%	0.004
	StringMatrixTest	4	0	0	0	100%	0.001
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.038
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.048
	IntegerMatrixTest	16	0	0	0	100%	0.003
	RCDoubleMatrix1DTest	3	0	0	0	100%	0.001
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.052
	SparseDoubleMatrixTest	24	0	0	0	100%	0.016

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.958
	TestMapReader	3	0	0	0	100%	0.001
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.576
	TestStringMatrixReader	4	0	0	0	100%	0.014
	HistogramReaderTest	2	0	0	0	100%	0
	TestDoubleMatrixReader	15	0	0	0	100%	0.102

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAffyNameFilter	2	0	0	0	100%	0.002
	TestItemLevelFilter	1	0	0	0	100%	0.002
	TestRowLevelFilter	23	0	0	0	100%	0.109
	TestRowNameFilter	4	0	0	0	100%	0.003
	TestRowAbsentFilter	9	0	0	0	100%	0.028
	TestRowMissingFilter	11	0	0	0	100%	0.026

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	3.325

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
	DoubleAddingMapTest	1	0	0	0	100%	0.001
	CountingMapTest	6	0	0	0	100%	0
	BitUtilTest	5	0	0	0	100%	0.002
	StringToStringSetMapTest	6	0	0	0	100%	0.001

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.488

Test Cases

[Summary] [Package List] [Test Cases]

RServeClientTest

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

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

BinaryTreeTest

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

ExcelUtilTest

	testGetSheetFromFile	0.472
	testGetSet	0.003
	testSetFormula	0.013

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0.013
	test1	0.013
	test3	0.006
	test2NoPivoting	0

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

CompressedNamedBitMatrixTest

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

TestMeanDifferenceMetaAnalysis

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

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0

UniformDensityComputerTest

testDensity

0

TestDescriptiveWithMissing

	testRankInterpolated	0
	testKurtosis	0
	testCorrelationA	0
	testCorrelationB	0
	testQuantileInverse	0
	testStandardize	0.001
	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

PrettyPrinterTest

testPrintBeans

0.006

SQLUtilsTest

testBlobToString

0

MatrixUtilTest

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

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	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

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	3.022
	testWilxcoxonPGaussB	0.001
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0.001
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.01
	testWilxcoxonPWithTies	0.001
	testEVolume	0.001

ModeratedTstatTest

	testLimmaMissing	0.014
	testFdist	0.001
	testLimma	0.023
	testSqueezeVarB	0.118
	testSqueezeVar	0
	testSqueezeVarWMissing	0

TestStats

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

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.011
	testReadInputStream	0.006
	testReadStreamAdjListBig	0.941

JRIClientTest

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

StringMatrixTest

	testToString	0
	testSubsetColumns	0.001
	testGetColObj	0
	testSubset	0

KruskalWallisTest

testKW

0

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.006
	testBenjaminiHochbergCut	0.02
	testBenjaminiHochberg	0.033
	testBenjaminiHochbergM	0.029
	testBonferroniCut	0.017

TestHistogramWriter

testWriter

0

TestMapReader

	testRead	0.001
	testReadNoHeader	0
	testReadNoHeaderFile	0

DateUtilTest

	testgetRelative5yearsFromnow	0.004
	testRange	0.003
	testgetRelative5yearsago	0.001
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0
	testRangeBad	0

TestSpecFunc

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

DoubleAddingMapTest

test

0

SparseRaggedDoubleMatrixTest

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

UberonOntologySearchTest

	testScore	0.017
	testOmitDefinition	0.011

MeanVarianceEstimatorTest

	testVoom	0.037
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.016
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.002

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.026
	testThreeWaySingular	0.138
	testEstrogen	3.853
	testVectorWeightedRegress	0.001
	testNHBE	4.618
	testLSFTwoLevels2	0.058
	testLSFTwoLevels3	0.054
	testSingular2	0.009
	testVectorWeightedRegressWithMissing	0.005
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.008
	testTwoWayAnovaWithInteractions	0.006
	testLSFTwoLevels	0.005
	testOneWayAnova	0.024
	testTwoWayTwoLevelsOneContinousInteractionC	0.004
	testLSFThreeLevelsOnecontinous2	0.003
	testMatrixWeightedRegress	0.001
	testSingular	0.012
	testLSFTwoLevelsOneContinuous	0.005
	testLSFOneContinuousWithMissing3	0.004

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.

DenseDoubleMatrixTest

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

StringUtilTest

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

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

CompressedSparseDoubleMatrixTest

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

OntologySearchTest

	testPersistence	0.746
	testOmitDefinitions2	0.166
	testOmitDefinitions3	0.043
	testOmitDefinitions4	1.388
	testOmitBadPredicates2	0.057
	testOmitBadPredicates	2.435
	testIndexing	0.668
	testOmitDefinitions	0.043
	testStemming	0.37

CountingMapTest

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

TestRank

	testRankTransformMapDesc	0.009
	testRankTransformDoubleArrayListDesc	0.001
	testRankTransformMap	0
	testOrder	0
	testRankWithTies	0
	testWithNaNs	0
	testRankTransformDoubleArrayList	0
	testRankWithTiesB	0.001
	testRankWithTiesC	0
	testRankWithTiesD	0
	testRankWithTiesE	0
	testWithNaNs2	0
	testWithNaNs3	0
	testOrderB	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	0.001

TestItemLevelFilter

testFilter

0

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.038

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.185
	testHasChanged	0.007

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0.001

MatrixWriterTest

	testWriteMatrixB	0.001
	testWriteMatrix	0.002
	testWrite3DMatrix	0.006

MatrixDisplayTest

	testWriteOutAsPNG2	0.564
	testWriteOutAsPNG	0.015
	testSaveImage	0.008
	testSaveImageStandardize	0.024

StringToStringSetMapTest

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

TestRowLevelFilter

	testFilterMinHigh	0.006
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.006
	testFilterMaxTooHigh	0.003
	testFilterMedian	0.004
	testFilterNoFilter	0.002
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.004
	testFilterFractionMaxRemoveNegHigh	0.004
	testFilterMax	0.004
	testFilterMin	0.003
	testFilterMaxFractionNoneRemoveNeg	0.004
	testFilterMedianHigh	0.005
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.005
	testFilterFractionMaxRemoveNeg	0.005
	testFilterMaxFractionAll	0.007
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.006
	testFilterMaxFraction	0.005
	testFilterBadFraction	0.004
	testFilterMaxFractionHigh	0.004
	testFilterMaxFractionNone	0.004
	testFilterFractionMaxRemoveHighAndLow	0.005
	testFilterMeanHigh	0.005
	testFilterMean	0.005
	testFilterMaxHigh	0.004

SingularValueDecompositionTest

testSingularValueDecomposition

0.089

TestSparseDoubleMatrixReader

	testReadStream	0.563
	testReadJW	0.012

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.027
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.035
	testCorrelationForPvalue	0.001
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.009
	testSpearmanPvalueG2	0.001

ParamGrabberTest

test

0

NetUtilsTest

	testFtpFileSize	0.722
	testCheckForFile	0.762
	testFtpFileSizeDoesntExist	1.305
	testDownloadFile	1.042

TestROC

	testBig	0.033
	testAroc	0
	testArocPvalue	0

RandomChooserTest

	testChooseRandomDeck	0.033
	testRepeatSubset	0.569
	testChooserandomInts	0.018
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.056
	testRepeat	0.532

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0

ParameterKeeperTest

test

0.002

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0
	testCorrelationMatrix	0
	testMax	0
	testMin	0
	testNan	0
	testColSumsWithMissing	0.001
	testLogTransform	0
	testDoubleStandardize	0.006
	testCov2Cor	0.002
	testConvertToLog2Cpm	0.001
	testConvertLog	0.001
	testCountsPerMillionWithMissing	0
	testCorrelationMatrixThreshold	0.003

TestCorrelationEffectMetaAnalysis

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

TestWishart

testNextDoubleMatrix

0

TestRowAbsentFilter

	testFilterKeepMarginal	0.002
	testFilterPresentCountInvalid	0
	testFilterWithMissing	0
	testFilterNullFlags	0.003
	testFilterWithMissingLessStringent	0.004
	testFilterFractionInvalid	0.003
	testFilterStringMatrix	0.005
	testFilterFraction	0.005
	testFilter	0.005

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.002
	testFilterWithMissing	0
	testFilterWithMissingLessStringent	0.003
	testFilterFractionInvalid2	0.004
	testFilterFractionInvalid	0.002
	testFilterStringMatrix	0.004
	testFilterFraction	0.003
	testFilter	0.003
	testMaxFractionRemovedInvalid	0.002
	testFilterNoFiltering	0.003

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.028
	testByteArrayToBooleans	0.02
	testStringToDoubleArrayConversionSpeed	0.028
	testByteArrayToDoubleConversionSpeed	0.013
	testByteArrayToTabbedString	0.004
	testDoubleArrayToBytes	0.004
	testIntsToBytes	0.003
	testBooleansToLongArray	0.004
	testByteArrayToSquareDoubleMatrix	0.007
	testByteArrayToDoubles	0.004
	testStringArrayToBytes	0.003
	testDoubleArrayToDelimitedStringConversionSpeed	0.015
	testStringArrayToTabbedBytes	0.007
	testObjectToBytes	0.005
	testBooleansToByteArray	0.005
	testByteArrayToLongs	0.006
	testByteArrayToDoubleMatrix	0.005

TestStringMatrixReader

	testReadInputStreamRowCount	0.008
	testReadInputStreamGotColName	0.002
	testReadInputStreamGotRowName	0.002
	testReadInputStreamColumnCount	0.001

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

JenaUtilsTest

testInferenceCapabilities

0.165

FileToolsTest

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

DistanceTest

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

FastRowAccessDoubleMatrixTest

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

OntologyTermTest

	testGetParentsHasProperPart	0.966
	testGetChildren	1.225
	testGetChildrenHasProperPart	0.044
	testGetParents	0.44
	testRejectNonEnglish	0.62

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.018
	testCsvSplitB	0
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0.001
	testTwoStringHashKeyB	0

ConfigUtilsTest

	testLoadConfigURL	0.1
	testGetConfigBuilderFile	0.078
	testGetConfigBuilderString	0.003
	testGetConfigBuilderURLNew	0
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.001
	testLoadConfigURLNew	0.003
	testLoadConfigStringNewName	0.056
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0.001
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.002

TestMatrixRowStats

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

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

SparseDoubleMatrixTest

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

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0
	testInteractionAndRelevel	0.005

HistogramSamplerTest

testNextSample

0.021

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0.002
	testReadInputStreamGotColNameSkipColumn	0.005
	testReadInputStreamRowCount	0.006
	testReadInputStreamGotColName	0.004
	testReadInputStreamGotRowName	0.004
	testSmallNumbers	0.05
	testReadInputStreamMissingSpaces	0.015
	testReadBad	0.003
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.001
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0.002
	testReadChooseRows	0.002
	testReadInputStreamColumnCount	0.002

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

Failure Details

[Summary] [Package List] [Test Cases]

	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
	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.