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%	0.054

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.144

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ConfigUtilsTest	13	0	0	0	100%	0.211
	BatchIteratorTest	3	0	0	0	100%	0
	NetUtilsTest	4	0	0	0	100%	5.582
	StringUtilTest	6	0	0	0	100%	0
	SQLUtilsTest	1	0	0	0	100%	0
	FileToolsTest	32	0	0	0	100%	0.09
	DateUtilTest	6	0	0	0	100%	0.013
	TestStringUtil	8	0	0	0	100%	0.025
	PrettyPrinterTest	1	0	0	0	100%	0.002

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParameterKeeperTest	1	0	0	0	100%	0.023
	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%	0.412

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%	0.054

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
	HistogramTest	2	0	0	0	100%	0.001
	UniformDensityComputerTest	1	0	0	0	100%	0.001
	HistogramSamplerTest	1	0	0	0	100%	0.029
	TestWishart	1	0	0	0	100%	0.001
	NormalProbabilityComputerTest	4	0	0	0	100%	0

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.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	LeastSquaresFitTest	20	0	0	0	100%	9.01
	DesignMatrixTest	5	0	0	0	100%	0.008
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.088
	ModeratedTstatTest	6	0	0	0	100%	0.432

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%	0.005

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	21.826
	JenaUtilsTest	1	0	0	0	100%	0.182
	OntologySearchTest	9	0	0	0	100%	22.482
	OntologyLoaderTest	2	0	0	0	100%	0.149

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.045

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.002
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.058
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.066
	StringMatrixTest	4	0	0	0	100%	0.001
	SparseDoubleMatrixTest	24	0	0	0	100%	0.03
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.007
	MatrixUtilTest	7	0	0	0	100%	0.007
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.086
	IntegerMatrixTest	16	0	0	0	100%	0.001
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.002

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMatrixNormalizer	2	0	0	0	100%	0
	StringDistanceTest	16	0	0	0	100%	0.008
	PrecisionRecallTest	5	0	0	0	100%	0
	SingularValueDecompositionTest	1	0	0	0	100%	0.104
	TestMatrixStats	15	0	0	0	100%	0.027
	DistanceTest	12	0	0	0	100%	0.001
	RandomChooserTest	7	0	0	0	100%	0.824
	TestROC	3	0	0	0	100%	0.05
	TestDescriptiveWithMissing	38	0	0	0	100%	0.006
	KruskalWallisTest	1	0	0	0	100%	0
	CorrelationStatsTest	18	0	0	0	100%	0.072
	TestRank	14	0	0	0	100%	0.009
	TestKSTest	2	0	0	0	100%	0.001
	TestWilcoxon	15	0	0	0	100%	2.196
	TestMatrixRowStats	6	0	0	0	100%	0.001
	MultipleTestCorrectionTest	5	0	0	0	100%	0.137
	TestSpecFunc	7	0	0	0	100%	0
	TestMathUtil	5	0	0	0	100%	0.001
	TestStats	14	0	0	0	100%	0

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMapReader	3	0	0	0	100%	0.015
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.927
	TestStringMatrixReader	4	0	0	0	100%	0.006
	TestDoubleMatrixReader	15	0	0	0	100%	0.192
	HistogramReaderTest	2	0	0	0	100%	0.003
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.013

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowNameFilter	4	0	0	0	100%	0.017
	TestRowMissingFilter	11	0	0	0	100%	0.054
	TestRowAffyNameFilter	2	0	0	0	100%	0.005
	TestRowLevelFilter	23	0	0	0	100%	0.153
	TestRowAbsentFilter	9	0	0	0	100%	0.089
	TestItemLevelFilter	1	0	0	0	100%	0.002

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	3.772

ubic.basecode.dataStructure

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

ubic.basecode.dataStructure.tree

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	1.154

Test Cases

[Summary] [Package List] [Test Cases]

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

TestCorrelationEffectMetaAnalysis

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

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0.001

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.

UberonOntologySearchTest

	testScore	0.03
	testOmitDefinition	0.016

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

UniformDensityComputerTest

testDensity

0

ConfigUtilsTest

	testLoadConfigURL	0.085
	testGetConfigBuilderFile	0.081
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.001
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.003
	testLoadConfigStringNewName	0.026
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.003
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.002

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.001
	testThreeWaySingular	0.082
	testEstrogen	4.117
	testVectorWeightedRegress	0
	testNHBE	4.661
	testLSFTwoLevels2	0.042
	testLSFTwoLevels3	0.026
	testSingular2	0.005
	testVectorWeightedRegressWithMissing	0.004
	testVectorRegress	0.001
	testLSFThreeLevelsOneContinuousWithMissing3	0.005
	testTwoWayAnovaWithInteractions	0.005
	testLSFTwoLevels	0.004
	testOneWayAnova	0.016
	testTwoWayTwoLevelsOneContinousInteractionC	0.007
	testLSFThreeLevelsOnecontinous2	0.003
	testMatrixWeightedRegress	0
	testSingular	0.017
	testLSFTwoLevelsOneContinuous	0.007
	testLSFOneContinuousWithMissing3	0.006

StringDistanceTest

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

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0.004
	testGet	0.002
	testSet	0.002
	testRows2	0.001
	testCopy	0.002
	testGet2	0.002
	testRows	0.001
	testSet2	0.002
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0.001
	testSubsetColumns	0.001
	testViewRow	0.001
	testColumns	0.001
	testGetColRange	0.002
	testGetByKeys	0.002
	testGetColObj	0.001
	testGetColumn	0.002
	testIsMissing	0.003
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.002
	testGetRow	0.001
	testGetRowObj	0.002
	testGetRowRange	0.001
	testGetRowByName	0.002
	testIsMissing2	0.001
	testGetColByNameFail	0.002
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.002
	testViewRow2	0.001

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

NetUtilsTest

	testFtpFileSize	0.998
	testCheckForFile	1.125
	testFtpFileSizeDoesntExist	1.987
	testDownloadFile	1.472

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0.003
	testFilter	0.005
	testFilterStringExclude	0.006

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

DoubleAddingMapTest

test

0

SingularValueDecompositionTest

testSingularValueDecomposition

0.104

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0
	testCorrelationMatrix	0
	testMax	0
	testMin	0
	testNan	0
	testColSumsWithMissing	0
	testLogTransform	0
	testDoubleStandardize	0.011
	testCov2Cor	0.006
	testConvertToLog2Cpm	0.002
	testConvertLog	0.002
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.005

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0.008
	testGet	0.002
	testSet	0.001
	testRows2	0.002
	testCopy	0.002
	testGet2	0.002
	testRows	0.001
	testSet2	0.002
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.002
	testSetIntIntObject	0.003
	testGetRow2	0.002
	testSubsetColumns	0.001
	testViewRow	0.002
	testColumns	0.001
	testGetColRange	0.002
	testGetByKeys	0.001
	testGetColObj	0.002
	testGetColumn	0.001
	testIsMissing	0.003
	testViewColumn	0.001
	testGetColObj2	0.002
	testGetObject	0.001
	testGetRow	0.002
	testGetRowObj	0.001
	testGetRowRange	0.002
	testGetRowByName	0.001
	testIsMissing2	0.002
	testGetColByNameFail	0.002
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.002
	testViewRow2	0.001

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0.001

MatrixDisplayTest

	testWriteOutAsPNG2	0.355
	testWriteOutAsPNG	0.02
	testSaveImage	0.01
	testSaveImageStandardize	0.026

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.006
	testFilterWithMissing	0.008
	testFilterWithMissingLessStringent	0.004
	testFilterFractionInvalid2	0.004
	testFilterFractionInvalid	0.005
	testFilterStringMatrix	0.005
	testFilterFraction	0.005
	testFilter	0.005
	testMaxFractionRemovedInvalid	0.005
	testFilterNoFiltering	0.006

TestHistogramWriter

testWriter

0

DistanceTest

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

TestMeanDifferenceMetaAnalysis

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

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0.003

RandomChooserTest

	testChooseRandomDeck	0.055
	testRepeatSubset	0.318
	testChooserandomInts	0.02
	testChooserandomWrep	0
	testRandomSubset	0.001
	testChooserandomInt	0.041
	testRepeat	0.388

BinaryTreeTest

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

StringUtilTest

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

MatrixWriterTest

	testWriteMatrixB	0.042
	testWriteMatrix	0.004
	testWrite3DMatrix	0.007

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0.014

TestROC

	testBig	0.046
	testAroc	0
	testArocPvalue	0.004

SparseDoubleMatrixTest

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

CountingMapTest

	testSummation	0
	testCount	0
	testSeen	0
	testIncrement	0
	testSortedKeyList	0
	testSortedKeyListBoolean	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	0.001
	testSumOfInversions	0
	testMean	0
	testSkew	0
	testDurbinWatson	0
	testMeanAboveQuantile	0
	testSumOfSquares	0
	testProduct	0
	testGeometricMean	0
	testMeanDoubleAr	0
	testSampleSkew	0
	testQuantile	0
	testQuantiles	0.001
	testSampleKurtosis	0
	testStandardizeNoVariance	0
	testDurbinWatsonTwo	0
	testKurtosisList	0.001
	testSumOfSquaredDeviations	0
	testMeanEff	0
	testSumOfPowers	0
	testSampleVariance	0.001
	testWeightedMean	0
	testCovariance	0
	testMedian	0
	testTrimmedMean	0
	testDurbinWatsonShort	0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0.001
	testB	0.002
	testInteractionAndRelevel	0.004

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.014
	testReadInputStream	0.005
	testReadStreamAdjListBig	0.908

JenaUtilsTest

testInferenceCapabilities

0.181

QRDecompositionTest

	testScaledDesign	0.022
	testSingular2	0.01
	test1	0.012
	test3	0.007
	test2NoPivoting	0.002

SparseRaggedDoubleMatrixTest

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

KruskalWallisTest

testKW

0

TestStringMatrixReader

	testReadInputStreamRowCount	0.002
	testReadInputStreamGotColName	0.002
	testReadInputStreamGotRowName	0.001
	testReadInputStreamColumnCount	0.001

SQLUtilsTest

testBlobToString

0

HistogramSamplerTest

testNextSample

0.029

TestRowLevelFilter

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

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.016
	testSpearmanPvalueF	0.001
	testSpearmanPvalueG	0.041
	testCorrelationForPvalue	0
	testCorrelTooSmall	0.001
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0.001
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0
	testSpearmanPvalueEm	0.01
	testSpearmanPvalueG2	0

TestRowAbsentFilter

	testFilterKeepMarginal	0.007
	testFilterPresentCountInvalid	0.01
	testFilterWithMissing	0.011
	testFilterNullFlags	0.008
	testFilterWithMissingLessStringent	0.012
	testFilterFractionInvalid	0.009
	testFilterStringMatrix	0.01
	testFilterFraction	0.011
	testFilter	0.01

ParameterKeeperTest

test

0.023

MatrixUtilTest

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

TestRank

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

JRIClientTest

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

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0.003
	testReadInputStreamMissingBad	0.004
	testReadInputStreamGotColNameSkipColumn	0.016
	testReadInputStreamRowCount	0.018
	testReadInputStreamGotColName	0.007
	testReadInputStreamGotRowName	0.007
	testSmallNumbers	0.097
	testReadInputStreamMissingSpaces	0.016
	testReadBad	0.004
	testBadFileName	0.002
	testReadChooseRowsSkipcols	0.004
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0.003
	testReadChooseRows	0.003
	testReadInputStreamColumnCount	0.003

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

OntologySearchTest

	testPersistence	0.63
	testOmitDefinitions2	0.142
	testOmitDefinitions3	0.048
	testOmitDefinitions4	1.428
	testOmitBadPredicates2	0.053
	testOmitBadPredicates	19.196
	testIndexing	0.591
	testOmitDefinitions	0.045
	testStemming	0.315

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	2.18
	testWilxcoxonPGaussB	0.001
	testBGaussian	0.001
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.002
	testAExact	0.004
	testWilxcoxonPWithTies	0
	testEVolume	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.134
	testHasChanged	0.006

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.006
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.01
	testGet	0.002
	testSet	0.002
	testRows2	0.002
	testCopy	0.003
	testGet2	0.002
	testRows	0.002
	testSet2	0.001
	testSize	0.003
	testToString	0.002
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.002
	testSetIntIntObject	0.002
	testGetRow2	0.002
	testSubsetColumns	0.002
	testViewRow	0.002
	testColumns	0.002
	testGetColRange	0.001
	testGetByKeys	0.002
	testGetColObj	0.002
	testGetColumn	0.001
	testIsMissing	0.004
	testViewColumn	0.002
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.002
	testGetRowObj	0.002
	testGetRowRange	0.002
	testGetRowByName	0.001
	testIsMissing2	0.002
	testGetColByNameFail	0.002
	testGetColByNameNull	0.002
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.002
	testViewRow2	0.002

FileToolsTest

	testHasImageExtension	0.003
	testTestDir	0.002
	testGetWithoutExtension	0.001
	testGetLines	0.007
	testTouch	0.002
	testListDirectoryFiles	0.01
	testAddImageExtension	0.003
	testChangeExtension	0.001
	testDeleteFilesAndDir	0.007
	testCleanFileName	0.004
	testgetStringListFromFile	0.003
	testGetWithoutExtensionB	0.002
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0.002
	testCleanFileNameErr	0.001
	testIsGZipped	0.002
	testUnGzipFile	0.003
	testCopyFileFailOnDirectoryOutput	0.002
	testTestFileString	0.002
	testGetCompressedFile	0.003
	testCopyFile	0.003
	testGetExtension	0.002
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.001
	testAddDataExtension	0.002
	testGetCompressedFileZip	0.002
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0.002
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.002
	testHasXMLExtension	0.002
	testUnzipFile	0.007

TestMatrixRowStats

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

TestWishart

testNextDoubleMatrix

0

ExcelUtilTest

	testGetSheetFromFile	1.069
	testGetSet	0.003
	testSetFormula	0.013

MeanVarianceEstimatorTest

	testVoom	0.053
	testMeanVarianceNoDesignWithColsRowAllMissing	0.001
	testDuplicateRows	0.03
	testInterpolate	0.001
	testMeanVarianceNoDesignWithMissing	0.003

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.021
	testBenjaminiHochbergCut	0.025
	testBenjaminiHochberg	0.035
	testBenjaminiHochbergM	0.034
	testBonferroniCut	0.021

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0.002

TestSpecFunc

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

DateUtilTest

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

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0
	testByteArrayToBooleans	0.012
	testStringToDoubleArrayConversionSpeed	0.013
	testByteArrayToDoubleConversionSpeed	0.01
	testByteArrayToTabbedString	0.014
	testDoubleArrayToBytes	0.006
	testIntsToBytes	0.005
	testBooleansToLongArray	0.004
	testByteArrayToSquareDoubleMatrix	0.007
	testByteArrayToDoubles	0.005
	testStringArrayToBytes	0.004
	testDoubleArrayToDelimitedStringConversionSpeed	0.014
	testStringArrayToTabbedBytes	0.012
	testObjectToBytes	0.009
	testBooleansToByteArray	0.004
	testByteArrayToLongs	0.019
	testByteArrayToDoubleMatrix	0.004

CompressedNamedBitMatrixTest

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

ParamGrabberTest

test

0.001

OntologyTermTest

	testGetParentsHasProperPart	1.268
	testGetChildren	1.423
	testGetChildrenHasProperPart	0.058
	testGetParents	0.395
	testRejectNonEnglish	0.59

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

ModeratedTstatTest

	testLimmaMissing	0.175
	testFdist	0.002
	testLimma	0.058
	testSqueezeVarB	0.195
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.023
	testCsvSplitB	0
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0
	testTwoStringHashKeyB	0

TestItemLevelFilter

testFilter

0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	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

StringToStringSetMapTest

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

TestSparseDoubleMatrixReader

	testReadStream	0.003
	testReadJW	0.009

PrettyPrinterTest

testPrintBeans

0.001

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.045

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