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.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.292

ubic.basecode.math.linalg

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	QRDecompositionTest	5	0	0	0	100%	0.008

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.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	BatchIteratorTest	3	0	0	0	100%	0.001
	DateUtilTest	6	0	0	0	100%	0.011
	SQLUtilsTest	1	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.085
	StringUtilTest	6	0	0	0	100%	0
	ConfigUtilsTest	13	0	0	0	100%	0.136
	NetUtilsTest	4	0	0	0	100%	3.912
	TestStringUtil	8	0	0	0	100%	0.015
	PrettyPrinterTest	1	0	0	0	100%	0

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.152

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixWriterTest	3	0	0	0	100%	0.045
	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%	0.002

ubic.basecode.math.distribution

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.022
	TestWishart	1	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ModeratedTstatTest	6	0	0	0	100%	0.238
	LeastSquaresFitTest	20	0	0	0	100%	8.628
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.046
	DesignMatrixTest	5	0	0	0	100%	0.006

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	1	0	0	1	0%	0.3
	JRIClientTest	1	0	0	1	0%	0

ubic.basecode.math.metaanalysis

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

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JenaUtilsTest	1	0	0	0	100%	0.126
	OntologySearchTest	9	0	0	0	100%	11.966
	OntologyLoaderTest	2	0	0	0	100%	0.109
	UberonOntologySearchTest	2	0	0	0	100%	20.441

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.186

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestROC	3	0	0	0	100%	0.031
	StringDistanceTest	16	0	0	0	100%	0
	TestMathUtil	5	0	0	0	100%	0.001
	CorrelationStatsTest	18	0	0	0	100%	0.118
	TestWilcoxon	15	0	0	0	100%	2.44
	TestSpecFunc	7	0	0	0	100%	0.001
	PrecisionRecallTest	5	0	0	0	100%	0
	RandomChooserTest	7	0	0	0	100%	0.74
	TestKSTest	2	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0.001
	KruskalWallisTest	1	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.073
	DistanceTest	12	0	0	0	100%	0.001
	TestRank	14	0	0	0	100%	0.03
	TestMatrixStats	15	0	0	0	100%	0.044
	TestMatrixRowStats	6	0	0	0	100%	0
	TestStats	14	0	0	0	100%	0
	SingularValueDecompositionTest	1	0	0	0	100%	0.088
	TestDescriptiveWithMissing	38	0	0	0	100%	0.002

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.002
	SparseDoubleMatrixTest	24	0	0	0	100%	0.009
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.001
	IntegerMatrixTest	16	0	0	0	100%	0.001
	StringMatrixTest	4	0	0	0	100%	0
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0
	MatrixUtilTest	7	0	0	0	100%	0.004
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.059
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.012
	DenseDoubleMatrixTest	39	0	0	0	100%	0.016

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDoubleMatrixReader	15	0	0	0	100%	0.105
	TestStringMatrixReader	4	0	0	0	100%	0.017
	HistogramReaderTest	2	0	0	0	100%	0.002
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.506
	TestMapReader	3	0	0	0	100%	0.001
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	1.008

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAbsentFilter	9	0	0	0	100%	0.046
	TestRowLevelFilter	23	0	0	0	100%	0.126
	TestRowMissingFilter	11	0	0	0	100%	0.034
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowNameFilter	4	0	0	0	100%	0.011
	TestRowAffyNameFilter	2	0	0	0	100%	0.01

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	3.37

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.dataStructure.tree

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.41

Test Cases

[Summary] [Package List] [Test Cases]

TestROC

	testBig	0.027
	testAroc	0.001
	testArocPvalue	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.

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.002
	testgetcolobj	0
	testgetrowobj	0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.008
	testReadInputStreamRowCount	0.006
	testReadInputStreamGotColName	0.003
	testReadInputStreamGotRowName	0.003
	testSmallNumbers	0.06
	testReadInputStreamMissingSpaces	0.009
	testReadBad	0.002
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.002
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0.002
	testReadChooseRows	0.002
	testReadInputStreamColumnCount	0.002

MatrixWriterTest

	testWriteMatrixB	0.037
	testWriteMatrix	0.002
	testWrite3DMatrix	0.005

CountingMapTest

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

SparseDoubleMatrixTest

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

UniformDensityComputerTest

testDensity

0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

ModeratedTstatTest

	testLimmaMissing	0.019
	testFdist	0.001
	testLimma	0.027
	testSqueezeVarB	0.188
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0.001

TestRowAbsentFilter

	testFilterKeepMarginal	0.004
	testFilterPresentCountInvalid	0.004
	testFilterWithMissing	0.004
	testFilterNullFlags	0.004
	testFilterWithMissingLessStringent	0.006
	testFilterFractionInvalid	0.005
	testFilterStringMatrix	0.005
	testFilterFraction	0.006
	testFilter	0.006

ParameterKeeperTest

test

0.001

MatrixDisplayTest

	testWriteOutAsPNG2	0.12
	testWriteOutAsPNG	0.01
	testSaveImage	0.006
	testSaveImageStandardize	0.016

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.022
	testSpearmanPvalueF	0.001
	testSpearmanPvalueG	0.073
	testCorrelationForPvalue	0.001
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0.001
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.017
	testSpearmanPvalueG2	0.001

TestStringMatrixReader

	testReadInputStreamRowCount	0.011
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0.002
	testReadInputStreamColumnCount	0.001

CompressedNamedBitMatrixTest

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

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	2.417
	testWilxcoxonPGaussB	0.002
	testBGaussian	0
	testFVolume	0.002
	testWilxcoxonPVolume	0.008
	testBig	0.001
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.002
	testAExact	0.004
	testWilxcoxonPWithTies	0.001
	testEVolume	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

TestSpecFunc

	testdBinom	0
	testCumHyperGeometricB	0.001
	testTrigammaInverse	0
	testCumHyperGeometric	0
	testTrigammaInverseB	0
	testHypergeometric	0
	testCumHyperGeometricUT	0

DoubleAddingMapTest

test

0

JRIClientTest

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

TestRowLevelFilter

	testFilterMinHigh	0.011
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.006
	testFilterMaxTooHigh	0.006
	testFilterMedian	0.007
	testFilterNoFilter	0.005
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.005
	testFilterFractionMaxRemoveNegHigh	0.006
	testFilterMax	0.005
	testFilterMin	0.006
	testFilterMaxFractionNoneRemoveNeg	0.004
	testFilterMedianHigh	0.005
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.005
	testFilterFractionMaxRemoveNeg	0.005
	testFilterMaxFractionAll	0.006
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.004
	testFilterMaxFraction	0.005
	testFilterBadFraction	0.004
	testFilterMaxFractionHigh	0.004
	testFilterMaxFractionNone	0.006
	testFilterFractionMaxRemoveHighAndLow	0.005
	testFilterMeanHigh	0.005
	testFilterMean	0.005
	testFilterMaxHigh	0.005

DateUtilTest

	testgetRelative5yearsFromnow	0.003
	testRange	0.006
	testgetRelative5yearsago	0.001
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0.001
	testRangeBad	0

HistogramSamplerTest

testNextSample

0.022

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.005
	testFilterWithMissing	0.002
	testFilterWithMissingLessStringent	0.003
	testFilterFractionInvalid2	0.004
	testFilterFractionInvalid	0.003
	testFilterStringMatrix	0.003
	testFilterFraction	0.003
	testFilter	0.002
	testMaxFractionRemovedInvalid	0.004
	testFilterNoFiltering	0.003

JenaUtilsTest

testInferenceCapabilities

0.124

TestItemLevelFilter

testFilter

0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0.002

SQLUtilsTest

testBlobToString

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

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.068
	testByteArrayToBooleans	0.01
	testStringToDoubleArrayConversionSpeed	0.011
	testByteArrayToDoubleConversionSpeed	0.011
	testByteArrayToTabbedString	0.016
	testDoubleArrayToBytes	0.007
	testIntsToBytes	0.006
	testBooleansToLongArray	0.007
	testByteArrayToSquareDoubleMatrix	0.01
	testByteArrayToDoubles	0.005
	testStringArrayToBytes	0.005
	testDoubleArrayToDelimitedStringConversionSpeed	0.019
	testStringArrayToTabbedBytes	0.034
	testObjectToBytes	0.009
	testBooleansToByteArray	0.005
	testByteArrayToLongs	0.006
	testByteArrayToDoubleMatrix	0.004

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

TestCorrelationEffectMetaAnalysis

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

TestWishart

testNextDoubleMatrix

0

SparseRaggedDoubleMatrixTest

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

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

FileToolsTest

	testHasImageExtension	0.004
	testTestDir	0.002
	testGetWithoutExtension	0.002
	testGetLines	0.003
	testTouch	0.002
	testListDirectoryFiles	0.014
	testAddImageExtension	0.003
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.005
	testCleanFileName	0.002
	testgetStringListFromFile	0.003
	testGetWithoutExtensionB	0.001
	testGetWithoutExtensionC	0.002
	testResourcetoPath	0.002
	testCleanFileNameErr	0.001
	testIsGZipped	0.002
	testUnGzipFile	0.002
	testCopyFileFailOnDirectoryOutput	0.002
	testTestFileString	0.001
	testGetCompressedFile	0.003
	testCopyFile	0.003
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.002
	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

StringToStringSetMapTest

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

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

MatrixUtilTest

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

BinaryTreeTest

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

StringUtilTest

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

RandomChooserTest

	testChooseRandomDeck	0.05
	testRepeatSubset	0.315
	testChooserandomInts	0.02
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.041
	testRepeat	0.313

TestSparseDoubleMatrixReader

	testReadStream	0.498
	testReadJW	0.007

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

OntologyTermTest

	testGetParentsHasProperPart	1.177
	testGetChildren	1.118
	testGetChildrenHasProperPart	0.049
	testGetParents	0.398
	testRejectNonEnglish	0.594

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

OntologySearchTest

	testPersistence	0.319
	testOmitDefinitions2	0.133
	testOmitDefinitions3	0.045
	testOmitDefinitions4	0.947
	testOmitBadPredicates2	0.055
	testOmitBadPredicates	9.525
	testIndexing	0.549
	testOmitDefinitions	0.053
	testStemming	0.311

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.045
	testThreeWaySingular	0.173
	testEstrogen	3.813
	testVectorWeightedRegress	0.001
	testNHBE	4.449
	testLSFTwoLevels2	0.033
	testLSFTwoLevels3	0.026
	testSingular2	0.005
	testVectorWeightedRegressWithMissing	0.003
	testVectorRegress	0.001
	testLSFThreeLevelsOneContinuousWithMissing3	0.005
	testTwoWayAnovaWithInteractions	0.005
	testLSFTwoLevels	0.004
	testOneWayAnova	0.02
	testTwoWayTwoLevelsOneContinousInteractionC	0.009
	testLSFThreeLevelsOnecontinous2	0.003
	testMatrixWeightedRegress	0.001
	testSingular	0.019
	testLSFTwoLevelsOneContinuous	0.007
	testLSFOneContinuousWithMissing3	0.005

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.094
	testHasChanged	0.005

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.005
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.008
	testGet	0.001
	testSet	0.001
	testRows2	0.001
	testCopy	0.002
	testGet2	0.002
	testRows	0.001
	testSet2	0.001
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0.002
	testSubsetColumns	0.001
	testViewRow	0.004
	testColumns	0.002
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.001
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0.001
	testTopoSort	0.001
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0.001
	testAddParentFail	0
	testTreeView	0.183

ConfigUtilsTest

	testLoadConfigURL	0.052
	testGetConfigBuilderFile	0.067
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.001
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.001
	testLoadConfigURLNew	0.002
	testLoadConfigStringNewName	0.006
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.001
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.001

KruskalWallisTest

testKW

0

UberonOntologySearchTest

	testScore	0.098
	testOmitDefinition	0.024

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.007
	testBenjaminiHochbergCut	0.013
	testBenjaminiHochberg	0.023
	testBenjaminiHochbergM	0.018
	testBonferroniCut	0.012

TestRowNameFilter

	testFilterString	0.002
	testFilterExclude	0.001
	testFilter	0.004
	testFilterStringExclude	0.003

ParamGrabberTest

test

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

TestMeanDifferenceMetaAnalysis

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

TestRank

	testRankTransformMapDesc	0.024
	testRankTransformDoubleArrayListDesc	0.001
	testRankTransformMap	0
	testOrder	0
	testRankWithTies	0.002
	testWithNaNs	0
	testRankTransformDoubleArrayList	0
	testRankWithTiesB	0
	testRankWithTiesC	0.001
	testRankWithTiesD	0
	testRankWithTiesE	0
	testWithNaNs2	0
	testWithNaNs3	0
	testOrderB	0.001

MeanVarianceEstimatorTest

	testVoom	0.031
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.014
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.001

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0.001
	testCorrelationMatrix	0.007
	testMax	0.001
	testMin	0.001
	testNan	0.001
	testColSumsWithMissing	0.003
	testLogTransform	0.002
	testDoubleStandardize	0.009
	testCov2Cor	0.007
	testConvertToLog2Cpm	0.002
	testConvertLog	0.002
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.005

TestHistogramWriter

testWriter

0

TestMatrixRowStats

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

NetUtilsTest

	testFtpFileSize	0.737
	testCheckForFile	0.722
	testFtpFileSizeDoesntExist	1.286
	testDownloadFile	1.166

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

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.009
	testReadInputStream	0.005
	testReadStreamAdjListBig	0.994

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	0.001
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0
	testGetRow	0.001
	testGetRowObj	0
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0
	testGetColByName	0.001
	testGetRowArrayList2	0
	testViewRow2	0.001

ExcelUtilTest

	testGetSheetFromFile	0.4
	testGetSet	0.003
	testSetFormula	0.007

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

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.007
	test2NoPivoting	0

SingularValueDecompositionTest

testSingularValueDecomposition

0.088

TestRowAffyNameFilter

	testStringFilter	0.006
	testFilter	0.003

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.013
	testCsvSplitB	0
	testCsvSplitC	0.001
	testCsvSplitD	0
	testCsvSplitE	0.001
	testCsvSplitF	0
	testTwoStringHashKeyB	0

DesignMatrixTest

	testInteractionC	0
	test2	0.001
	testA	0
	testB	0
	testInteractionAndRelevel	0.004

PrettyPrinterTest

testPrintBeans

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	0.001
	testTrimmedMean	0
	testDurbinWatsonShort	0

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