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%	0.071

ubic.basecode.math.linalg

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	QRDecompositionTest	5	0	0	0	100%	0.004

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	PrettyPrinterTest	1	0	0	0	100%	0.01
	StringUtilTest	6	0	0	0	100%	0.001
	NetUtilsTest	4	0	0	0	100%	4.84
	DateUtilTest	6	0	0	0	100%	0.011
	ConfigUtilsTest	13	0	0	0	100%	0.18
	TestStringUtil	8	0	0	0	100%	0.02
	BatchIteratorTest	3	0	0	0	100%	0
	FileToolsTest	32	0	0	0	100%	0.068
	SQLUtilsTest	1	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%	0.182

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.168

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

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
	NormalProbabilityComputerTest	4	0	0	0	100%	0.001
	HistogramTest	2	0	0	0	100%	0
	UniformDensityComputerTest	1	0	0	0	100%	0
	TestWishart	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.02

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	JRIClientTest	1	0	0	1	0%	0
	RServeClientTest	1	0	0	1	0%	0.318

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DesignMatrixTest	5	0	0	0	100%	0.001
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.764
	ModeratedTstatTest	6	0	0	0	100%	0.253
	LeastSquaresFitTest	20	0	0	0	100%	12.227

ubic.basecode.math.metaanalysis

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

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	22.416
	JenaUtilsTest	1	0	0	0	100%	0.146
	OntologySearchTest	9	0	0	0	100%	5.3
	OntologyLoaderTest	2	0	0	0	100%	0.199

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.264

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SparseDoubleMatrixTest	24	0	0	0	100%	0.005
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.024
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.029
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.092
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.001
	MatrixUtilTest	7	0	0	0	100%	0.002
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.029
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	IntegerMatrixTest	16	0	0	0	100%	0
	StringMatrixTest	4	0	0	0	100%	0.001

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	PrecisionRecallTest	5	0	0	0	100%	0.001
	DistanceTest	12	0	0	0	100%	0
	CorrelationStatsTest	18	0	0	0	100%	0.084
	KruskalWallisTest	1	0	0	0	100%	0.001
	TestRank	14	0	0	0	100%	0
	TestKSTest	2	0	0	0	100%	0
	TestMatrixRowStats	6	0	0	0	100%	0.005
	TestSpecFunc	7	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.137
	TestROC	3	0	0	0	100%	0.014
	TestWilcoxon	15	0	0	0	100%	2.896
	TestMatrixStats	15	0	0	0	100%	0.039
	RandomChooserTest	7	0	0	0	100%	0.819
	TestMathUtil	5	0	0	0	100%	0.002
	StringDistanceTest	16	0	0	0	100%	0.003
	TestMatrixNormalizer	2	0	0	0	100%	0.006
	TestDescriptiveWithMissing	38	0	0	0	100%	0.075
	TestStats	14	0	0	0	100%	0.001
	SingularValueDecompositionTest	1	0	0	0	100%	0.088

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramReaderTest	2	0	0	0	100%	0.001
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.737
	TestMapReader	3	0	0	0	100%	0.001
	TestDoubleMatrixReader	15	0	0	0	100%	0.04
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.001
	TestStringMatrixReader	4	0	0	0	100%	0

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowMissingFilter	11	0	0	0	100%	0.032
	TestRowAffyNameFilter	2	0	0	0	100%	0.002
	TestRowNameFilter	4	0	0	0	100%	0.014
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowAbsentFilter	9	0	0	0	100%	0.036
	TestRowLevelFilter	23	0	0	0	100%	0.1

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	4.272

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%	0.001
	DoubleAddingMapTest	1	0	0	0	100%	0
	CountingMapTest	6	0	0	0	100%	0.001
	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%	0.19

Test Cases

[Summary] [Package List] [Test Cases]

PrettyPrinterTest

testPrintBeans

0.01

SparseDoubleMatrixTest

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

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0.001
	testInvalidVariance	0
	testProbabilityDouble	0

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0.001

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

TestRowMissingFilter

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

CorrelationStatsTest

	testSpearmanPvalueA	0.002
	testSpearmanPvalueB	0.002
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.035
	testSpearmanPvalueF	0.001
	testSpearmanPvalueG	0.024
	testCorrelationForPvalue	0.002
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0.001
	testCorrel	0
	testCorrelAsByte	0.001
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0.001
	testSpearmanPvalueEh	0
	testSpearmanPvalueEm	0.015
	testSpearmanPvalueG2	0

TestHistogramWriter

testWriter

0

JRIClientTest

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

ParamGrabberTest

test

0

BinaryTreeTest

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

ExcelUtilTest

	testGetSheetFromFile	0.187
	testGetSet	0.001
	testSetFormula	0.002

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0.002
	testFilter	0.006
	testFilterStringExclude	0.004

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

SparseRaggedDoubleMatrixTest

	testSubsetRows	0.012
	testSubsetRowsFail	0.002
	testRows	0.001
	testGetRowMatrix1D	0.001
	testGetRowArrayList	0.001
	testColumns	0.002
	testGetColRange	0.001
	testAddrow	0.001
	testGetRow	0.002
	testGetRowRange	0.001

UberonOntologySearchTest

	testScore	0.027
	testOmitDefinition	0.018

TestItemLevelFilter

testFilter

0

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0
	testInteractionAndRelevel	0

TestDirectedGraph

	testDeleteLeaf1	0.004
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0.001
	testAddChild	0
	testTopoSort	0
	testAddParent	0.001
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.25

StringUtilTest

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

TestCorrelationEffectMetaAnalysis

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

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0.001
	testGet	0.001
	testSet	0.001
	testRows2	0
	testCopy	0.001
	testGet2	0.001
	testRows	0.001
	testSet2	0
	testSize	0.001
	testToString	0.001
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0.001
	testSubsetColumns	0.001
	testViewRow	0.001
	testColumns	0
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0
	testGetColumn	0
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0
	testGetObject	0.001
	testGetRow	0.001
	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

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.013
	testToArray	0.004
	testSortByColumnAbsoluteValue	0.022
	testGet	0.003
	testSet	0.003
	testRows2	0.004
	testCopy	0.004
	testGet2	0.003
	testRows	0.003
	testSet2	0.002
	testSize	0.002
	testToString	0.003
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0.001
	testSubsetColumns	0.001
	testViewRow	0.001
	testColumns	0.001
	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
	testIsMissing2	0.002
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

DoubleAddingMapTest

test

0

OntologyTermTest

	testGetParentsHasProperPart	1.508
	testGetChildren	1.615
	testGetChildrenHasProperPart	0.056
	testGetParents	0.358
	testRejectNonEnglish	0.703

MatrixDisplayTest

	testWriteOutAsPNG2	0.14
	testWriteOutAsPNG	0.008
	testSaveImage	0.005
	testSaveImageStandardize	0.015

TestRowAbsentFilter

	testFilterKeepMarginal	0.001
	testFilterPresentCountInvalid	0.003
	testFilterWithMissing	0.005
	testFilterNullFlags	0.003
	testFilterWithMissingLessStringent	0.005
	testFilterFractionInvalid	0.004
	testFilterStringMatrix	0.004
	testFilterFraction	0.005
	testFilter	0.005

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

MatrixUtilTest

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

KruskalWallisTest

testKW

0

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.003
	testByteArrayToBooleans	0.005
	testStringToDoubleArrayConversionSpeed	0.009
	testByteArrayToDoubleConversionSpeed	0.006
	testByteArrayToTabbedString	0.005
	testDoubleArrayToBytes	0.004
	testIntsToBytes	0.005
	testBooleansToLongArray	0.003
	testByteArrayToSquareDoubleMatrix	0.004
	testByteArrayToDoubles	0.002
	testStringArrayToBytes	0.003
	testDoubleArrayToDelimitedStringConversionSpeed	0.007
	testStringArrayToTabbedBytes	0.003
	testObjectToBytes	0.004
	testBooleansToByteArray	0.003
	testByteArrayToLongs	0.003
	testByteArrayToDoubleMatrix	0.002

MatrixWriterTest

	testWriteMatrixB	0
	testWriteMatrix	0
	testWrite3DMatrix	0

CompressedNamedBitMatrixTest

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

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

UniformDensityComputerTest

testDensity

0

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestMatrixRowStats

	testSumOfSquaresDoubleMatrixNamed	0
	testMeans	0
	testSums	0
	testMeans2	0.001
	testStandardDeviations	0.001
	testSumOfSquaresDoubleMatrixNamedDoubleArrayList	0.001

NetUtilsTest

	testFtpFileSize	0.839
	testCheckForFile	0.995
	testFtpFileSizeDoesntExist	1.602
	testDownloadFile	1.404

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.

TestSpecFunc

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

TestWishart

testNextDoubleMatrix

0

DateUtilTest

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

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.031
	testBenjaminiHochbergCut	0.028
	testBenjaminiHochberg	0.035
	testBenjaminiHochbergM	0.031
	testBonferroniCut	0.012

TestROC

	testBig	0.013
	testAroc	0
	testArocPvalue	0.001

HistogramSamplerTest

testNextSample

0.02

RServeClientTest

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

TestMeanDifferenceMetaAnalysis

	testRunRandomE	0
	testRunRandomZ	0
	testRunFixedE	0
	testRunFixedQ	0
	testRunFixedZ	0.001
	testRunRandomBSV	0
	testRunRandomVar	0
	testRunFixedVar	0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	2.875
	testWilxcoxonPGaussB	0
	testBGaussian	0.001
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0.001
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.002
	testAExact	0.01
	testWilxcoxonPWithTies	0
	testEVolume	0.001

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0.002
	testCorrelationMatrix	0.005
	testMax	0.001
	testMin	0.001
	testNan	0.001
	testColSumsWithMissing	0.001
	testLogTransform	0.002
	testDoubleStandardize	0.01
	testCov2Cor	0.006
	testConvertToLog2Cpm	0.002
	testConvertLog	0.001
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.006

RandomChooserTest

	testChooseRandomDeck	0.054
	testRepeatSubset	0.312
	testChooserandomInts	0.015
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.038
	testRepeat	0.398

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

JenaUtilsTest

testInferenceCapabilities

0.144

MeanVarianceEstimatorTest

	testVoom	0.705
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.022
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.002

DenseDoubleMatrixTest

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

StringDistanceTest

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

ParameterKeeperTest

test

0.182

OntologySearchTest

	testPersistence	0.502
	testOmitDefinitions2	0.129
	testOmitDefinitions3	0.045
	testOmitDefinitions4	1.297
	testOmitBadPredicates2	0.042
	testOmitBadPredicates	2.338
	testIndexing	0.532
	testOmitDefinitions	0.049
	testStemming	0.338

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0
	testReadInputStream	0.001
	testReadStreamAdjListBig	0.735

OntologyLoaderTest

	testCacheOntologyToDisk	0.187
	testHasChanged	0.005

ModeratedTstatTest

	testLimmaMissing	0.024
	testFdist	0.001
	testLimma	0.04
	testSqueezeVarB	0.186
	testSqueezeVar	0
	testSqueezeVarWMissing	0.001

TestMatrixNormalizer

	testQuantileNormalize	0.003
	testQuantileNormalizeWithMissing	0.003

ConfigUtilsTest

	testLoadConfigURL	0.091
	testGetConfigBuilderFile	0.067
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.001
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.001
	testLoadConfigURLNew	0.003
	testLoadConfigStringNewName	0.007
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.001

TestStringUtil

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

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

CountingMapTest

	testSummation	0
	testCount	0
	testSeen	0
	testIncrement	0.001
	testSortedKeyList	0
	testSortedKeyListBoolean	0

StringToStringSetMapTest

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

TestDescriptiveWithMissing

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

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testSmallNumbers	0.025
	testReadInputStreamMissingSpaces	0.007
	testReadBad	0.001
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.001
	testReadBlankCorner	0.002
	testReadInputStreamMissing	0.001
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0.001

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

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.066
	testThreeWaySingular	0.204
	testEstrogen	5.165
	testVectorWeightedRegress	0.001
	testNHBE	6.518
	testLSFTwoLevels2	0.053
	testLSFTwoLevels3	0.043
	testSingular2	0.012
	testVectorWeightedRegressWithMissing	0.006
	testVectorRegress	0.001
	testLSFThreeLevelsOneContinuousWithMissing3	0.006
	testTwoWayAnovaWithInteractions	0.01
	testLSFTwoLevels	0.044
	testOneWayAnova	0.03
	testTwoWayTwoLevelsOneContinousInteractionC	0.01
	testLSFThreeLevelsOnecontinous2	0.005
	testMatrixWeightedRegress	0.001
	testSingular	0.029
	testLSFTwoLevelsOneContinuous	0.011
	testLSFOneContinuousWithMissing3	0.009

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.004
	test2NoPivoting	0

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

TestRowLevelFilter

	testFilterMinHigh	0.001
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.004
	testFilterMaxTooHigh	0.004
	testFilterMedian	0.004
	testFilterNoFilter	0.003
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.004
	testFilterFractionMaxRemoveNegHigh	0.004
	testFilterMax	0.005
	testFilterMin	0.004
	testFilterMaxFractionNoneRemoveNeg	0.004
	testFilterMedianHigh	0.005
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.005
	testFilterFractionMaxRemoveNeg	0.005
	testFilterMaxFractionAll	0.005
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.005
	testFilterMaxFraction	0.005
	testFilterBadFraction	0.004
	testFilterMaxFractionHigh	0.004
	testFilterMaxFractionNone	0.005
	testFilterFractionMaxRemoveHighAndLow	0.004
	testFilterMeanHigh	0.006
	testFilterMean	0.004
	testFilterMaxHigh	0.004

SingularValueDecompositionTest

testSingularValueDecomposition

0.088

FileToolsTest

	testHasImageExtension	0
	testTestDir	0
	testGetWithoutExtension	0
	testGetLines	0
	testTouch	0
	testListDirectoryFiles	0.011
	testAddImageExtension	0.001
	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	0.001
	testTestFileString	0.001
	testGetCompressedFile	0.002
	testCopyFile	0.003
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.002
	testIsZipped	0.001
	testAddDataExtension	0.002
	testGetCompressedFileZip	0.003
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0.002
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.002
	testHasXMLExtension	0.001
	testUnzipFile	0.008

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	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

SQLUtilsTest

testBlobToString

0

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

Failure Details

[Summary] [Package List] [Test Cases]

	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.
	ubic.basecode.util.r.RServeClientTest
	skipped: got: <java.io.IOException: Could not connect to Rserve>, expected: null