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%	0.001

ubic.basecode.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestByteArrayConverter	17	0	0	0	100%	0.116

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ConfigUtilsTest	13	0	0	0	100%	0.206
	BatchIteratorTest	3	0	0	0	100%	0.001
	NetUtilsTest	4	0	0	0	100%	3.864
	StringUtilTest	6	0	0	0	100%	0.001
	DateUtilTest	6	0	0	0	100%	0.027
	PrettyPrinterTest	1	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.067
	SQLUtilsTest	1	0	0	0	100%	0.001
	TestStringUtil	8	0	0	0	100%	0.017

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParameterKeeperTest	1	0	0	0	100%	0.012
	ParamGrabberTest	1	0	0	0	100%	0

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.177

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixWriterTest	3	0	0	0	100%	0.008
	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
	NormalProbabilityComputerTest	4	0	0	0	100%	0.001
	UniformDensityComputerTest	1	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.024
	TestWishart	1	0	0	0	100%	0.001

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.049
	LeastSquaresFitTest	20	0	0	0	100%	9.982
	DesignMatrixTest	5	0	0	0	100%	0.008
	ModeratedTstatTest	6	0	0	0	100%	0.327

ubic.basecode.math.metaanalysis

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

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	1	0	0	1	0%	0.309
	JRIClientTest	1	0	0	1	0%	0

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologySearchTest	9	0	0	0	100%	7.956
	OntologyLoaderTest	2	0	0	0	100%	0.119
	UberonOntologySearchTest	2	0	0	0	100%	25.692
	JenaUtilsTest	1	0	0	0	100%	0.147

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.171

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DistanceTest	12	0	0	0	100%	0
	PrecisionRecallTest	5	0	0	0	100%	0
	TestRank	14	0	0	0	100%	0.015
	TestStats	14	0	0	0	100%	0
	TestDescriptiveWithMissing	38	0	0	0	100%	0.001
	RandomChooserTest	7	0	0	0	100%	0.915
	CorrelationStatsTest	18	0	0	0	100%	0.101
	TestMatrixRowStats	6	0	0	0	100%	0.001
	TestMatrixStats	15	0	0	0	100%	0.03
	MultipleTestCorrectionTest	5	0	0	0	100%	0.122
	StringDistanceTest	16	0	0	0	100%	0
	TestSpecFunc	7	0	0	0	100%	0
	TestWilcoxon	15	0	0	0	100%	2.019
	TestKSTest	2	0	0	0	100%	0
	TestMathUtil	5	0	0	0	100%	0.001
	KruskalWallisTest	1	0	0	0	100%	0
	TestROC	3	0	0	0	100%	0.032
	SingularValueDecompositionTest	1	0	0	0	100%	0.094
	TestMatrixNormalizer	2	0	0	0	100%	0.001

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	StringMatrixTest	4	0	0	0	100%	0
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.025
	MatrixUtilTest	7	0	0	0	100%	0.002
	RCDoubleMatrix1DTest	3	0	0	0	100%	0.001
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.002
	SparseDoubleMatrixTest	24	0	0	0	100%	0.009
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.001
	IntegerMatrixTest	16	0	0	0	100%	0.001
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.045
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.001
	DenseDoubleMatrixTest	39	0	0	0	100%	0.036

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStringMatrixReader	4	0	0	0	100%	0.002
	TestDoubleMatrixReader	15	0	0	0	100%	0.122
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.896
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.009
	TestMapReader	3	0	0	0	100%	0
	HistogramReaderTest	2	0	0	0	100%	0.001

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	1.498

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowNameFilter	4	0	0	0	100%	0.009
	TestRowAbsentFilter	9	0	0	0	100%	0.02
	TestRowLevelFilter	23	0	0	0	100%	0.077
	TestRowAffyNameFilter	2	0	0	0	100%	0.002
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowMissingFilter	11	0	0	0	100%	0.023

ubic.basecode.dataStructure

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.531

Test Cases

[Summary] [Package List] [Test Cases]

OntologyTermTest

	testGetParentsHasProperPart	0.064
	testGetChildren	0.635
	testGetChildrenHasProperPart	0.03
	testGetParents	0.316
	testRejectNonEnglish	0.432

OntologySearchTest

	testPersistence	0.783
	testOmitDefinitions2	0.137
	testOmitDefinitions3	0.047
	testOmitDefinitions4	1.507
	testOmitBadPredicates2	0.074
	testOmitBadPredicates	4.508
	testIndexing	0.491
	testOmitDefinitions	0.055
	testStemming	0.29

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.11
	testHasChanged	0.003

MeanVarianceEstimatorTest

	testVoom	0.032
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.015
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.002

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

UberonOntologySearchTest

	testScore	0.118
	testOmitDefinition	0.018

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

TestRank

	testRankTransformMapDesc	0.01
	testRankTransformDoubleArrayListDesc	0
	testRankTransformMap	0.001
	testOrder	0
	testRankWithTies	0.001
	testWithNaNs	0
	testRankTransformDoubleArrayList	0.001
	testRankWithTiesB	0
	testRankWithTiesC	0
	testRankWithTiesD	0
	testRankWithTiesE	0.001
	testWithNaNs2	0
	testWithNaNs3	0
	testOrderB	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

TestMeanDifferenceMetaAnalysis

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

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.001
	test2NoPivoting	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.001
	testThreeWaySingular	0.094
	testEstrogen	4.034
	testVectorWeightedRegress	0.001
	testNHBE	5.671
	testLSFTwoLevels2	0.045
	testLSFTwoLevels3	0.039
	testSingular2	0.009
	testVectorWeightedRegressWithMissing	0.003
	testVectorRegress	0.001
	testLSFThreeLevelsOneContinuousWithMissing3	0.005
	testTwoWayAnovaWithInteractions	0.005
	testLSFTwoLevels	0.005
	testOneWayAnova	0.021
	testTwoWayTwoLevelsOneContinousInteractionC	0.008
	testLSFThreeLevelsOnecontinous2	0.003
	testMatrixWeightedRegress	0.001
	testSingular	0.021
	testLSFTwoLevelsOneContinuous	0.008
	testLSFOneContinuousWithMissing3	0.006

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.014
	testByteArrayToBooleans	0.01
	testStringToDoubleArrayConversionSpeed	0.008
	testByteArrayToDoubleConversionSpeed	0.006
	testByteArrayToTabbedString	0.006
	testDoubleArrayToBytes	0.005
	testIntsToBytes	0.008
	testBooleansToLongArray	0.006
	testByteArrayToSquareDoubleMatrix	0.005
	testByteArrayToDoubles	0.004
	testStringArrayToBytes	0.004
	testDoubleArrayToDelimitedStringConversionSpeed	0.013
	testStringArrayToTabbedBytes	0.005
	testObjectToBytes	0.008
	testBooleansToByteArray	0.004
	testByteArrayToLongs	0.004
	testByteArrayToDoubleMatrix	0.004

RandomChooserTest

	testChooseRandomDeck	0.031
	testRepeatSubset	0.347
	testChooserandomInts	0.019
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.046
	testRepeat	0.471

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.017
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.07
	testCorrelationForPvalue	0
	testCorrelTooSmall	0.001
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0.001
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0
	testSpearmanPvalueEm	0.011
	testSpearmanPvalueG2	0.001

TestMatrixRowStats

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

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0.003
	testCorrelationMatrix	0.005
	testMax	0
	testMin	0.001
	testNan	0
	testColSumsWithMissing	0.001
	testLogTransform	0.001
	testDoubleStandardize	0.006
	testCov2Cor	0.006
	testConvertToLog2Cpm	0.001
	testConvertLog	0.001
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.003

MatrixWriterTest

	testWriteMatrixB	0.002
	testWriteMatrix	0.002
	testWrite3DMatrix	0.004

FastRowAccessDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0
	testGet	0
	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
	testSubsetColumns	0.001
	testViewRow	0
	testColumns	0.001
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0
	testGetColumn	0.001
	testIsMissing	0.001
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0
	testGetRow	0
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0.001
	testIsMissing2	0
	testGetColByNameFail	0
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0
	testViewRow2	0.001

TestCorrelationEffectMetaAnalysis

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

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0
	testFilter	0.004
	testFilterStringExclude	0.003

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0.001
	testReadInputStreamColumnCount	0

MatrixUtilTest

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

TestHistogramWriter

testWriter

0

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

MatrixDisplayTest

	testWriteOutAsPNG2	0.143
	testWriteOutAsPNG	0.01
	testSaveImage	0.006
	testSaveImageStandardize	0.017

ConfigUtilsTest

	testLoadConfigURL	0.086
	testGetConfigBuilderFile	0.097
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.001
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.004
	testLoadConfigStringNewName	0.006
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.001

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.018
	testBenjaminiHochbergCut	0.023
	testBenjaminiHochberg	0.032
	testBenjaminiHochbergM	0.026
	testBonferroniCut	0.022

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.006
	testReadInputStreamRowCount	0.011
	testReadInputStreamGotColName	0.004
	testReadInputStreamGotRowName	0.006
	testSmallNumbers	0.066
	testReadInputStreamMissingSpaces	0.013
	testReadBad	0.002
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.002
	testReadBlankCorner	0.002
	testReadInputStreamMissing	0.003
	testReadChooseRows	0.002
	testReadInputStreamColumnCount	0.003

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

NetUtilsTest

	testFtpFileSize	0.731
	testCheckForFile	0.701
	testFtpFileSizeDoesntExist	1.369
	testDownloadFile	1.062

StringUtilTest

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

TestRowAbsentFilter

	testFilterKeepMarginal	0.001
	testFilterPresentCountInvalid	0
	testFilterWithMissing	0
	testFilterNullFlags	0
	testFilterWithMissingLessStringent	0.003
	testFilterFractionInvalid	0.003
	testFilterStringMatrix	0.004
	testFilterFraction	0.004
	testFilter	0.004

BinaryTreeTest

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

DateUtilTest

	testgetRelative5yearsFromnow	0.019
	testRange	0.005
	testgetRelative5yearsago	0.001
	testgetRelativeTomorrow	0.001
	testgetRelativeDateDayago	0.001
	testRangeBad	0

UniformDensityComputerTest

testDensity

0

ExcelUtilTest

	testGetSheetFromFile	0.514
	testGetSet	0.005
	testSetFormula	0.012

TestSpecFunc

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

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	1.999
	testWilxcoxonPGaussB	0.002
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0.001
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.005
	testWilxcoxonPWithTies	0.001
	testEVolume	0.002

TestRowLevelFilter

	testFilterMinHigh	0.001
	testFilterFractionMaxRemoveHighAndLowBothFraction	0
	testFilterMaxTooHigh	0
	testFilterMedian	0.004
	testFilterNoFilter	0.003
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.004
	testFilterFractionMaxRemoveNegHigh	0.005
	testFilterMax	0.003
	testFilterMin	0.003
	testFilterMaxFractionNoneRemoveNeg	0.004
	testFilterMedianHigh	0.004
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.004
	testFilterFractionMaxRemoveNeg	0.003
	testFilterMaxFractionAll	0.004
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.004
	testFilterMaxFraction	0.003
	testFilterBadFraction	0.004
	testFilterMaxFractionHigh	0.004
	testFilterMaxFractionNone	0.004
	testFilterFractionMaxRemoveHighAndLow	0.003
	testFilterMeanHigh	0.003
	testFilterMean	0.004
	testFilterMaxHigh	0.004

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.002
	testgetcolobj	0
	testgetrowobj	0

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0

JenaUtilsTest

testInferenceCapabilities

0.146

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0.001
	testB	0.002
	testInteractionAndRelevel	0.004

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

PrettyPrinterTest

testPrintBeans

0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

SparseDoubleMatrixTest

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

SparseRaggedDoubleMatrixTest

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

ModeratedTstatTest

	testLimmaMissing	0.123
	testFdist	0.001
	testLimma	0.036
	testSqueezeVarB	0.166
	testSqueezeVar	0.001
	testSqueezeVarWMissing	0

CountingMapTest

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

HistogramSamplerTest

testNextSample

0.024

RServeClientTest

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

IntegerMatrixTest

	testGetEntry	0.001
	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

KruskalWallisTest

testKW

0

TestROC

	testBig	0.031
	testAroc	0
	testArocPvalue	0.001

CompressedSparseDoubleMatrixTest

	testSubsetRows	0
	testToArray	0.001
	testSortByColumnAbsoluteValue	0.004
	testGet	0.002
	testSet	0.001
	testRows2	0.001
	testCopy	0.002
	testGet2	0.002
	testRows	0.001
	testSet2	0.001
	testSize	0.001
	testToString	0.001
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.001
	testGetRow2	0.001
	testSubsetColumns	0.001
	testViewRow	0
	testColumns	0.001
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0.001
	testIsMissing	0.001
	testViewColumn	0
	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
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

DoubleAddingMapTest

test

0

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0.001
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.17

JRIClientTest

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

TestItemLevelFilter

testFilter

0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.009
	testReadInputStream	0.005
	testReadStreamAdjListBig	0.882

ParameterKeeperTest

test

0.012

SingularValueDecompositionTest

testSingularValueDecomposition

0.094

CompressedNamedBitMatrixTest

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

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.

TestSparseDoubleMatrixReader

	testReadStream	0.001
	testReadJW	0.006

StringToStringSetMapTest

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

TestRowMissingFilter

	testFilterPresentCountInvalid	0
	testFilterWithMissingLowMaxFraction	0.002
	testFilterWithMissing	0
	testFilterWithMissingLessStringent	0.001
	testFilterFractionInvalid2	0.003
	testFilterFractionInvalid	0.002
	testFilterStringMatrix	0.003
	testFilterFraction	0.003
	testFilter	0.002
	testMaxFractionRemovedInvalid	0.003
	testFilterNoFiltering	0.003

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0.003
	testGet	0.001
	testSet	0.001
	testRows2	0
	testCopy	0.002
	testGet2	0.001
	testRows	0
	testSet2	0.001
	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	0.001
	testGetByKeys	0.001
	testGetColObj	0.001
	testGetColumn	0
	testIsMissing	0.002
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.001
	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
	testViewRow2	0.001

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

TestMatrixNormalizer

	testQuantileNormalize	0
	testQuantileNormalizeWithMissing	0.001

FileToolsTest

	testHasImageExtension	0.007
	testTestDir	0.001
	testGetWithoutExtension	0.001
	testGetLines	0.003
	testTouch	0.001
	testListDirectoryFiles	0.008
	testAddImageExtension	0.001
	testChangeExtension	0.001
	testDeleteFilesAndDir	0.005
	testCleanFileName	0.001
	testgetStringListFromFile	0.002
	testGetWithoutExtensionB	0.001
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0.002
	testCleanFileNameErr	0.001
	testIsGZipped	0.002
	testUnGzipFile	0.002
	testCopyFileFailOnDirectoryOutput	0.001
	testTestFileString	0.001
	testGetCompressedFile	0.002
	testCopyFile	0.002
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.001
	testAddDataExtension	0.001
	testGetCompressedFileZip	0.002
	testTestFileFile	0.002
	testCheckPathIsReadableFileNot	0.001
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.001
	testHasXMLExtension	0.001
	testUnzipFile	0.006

SQLUtilsTest

testBlobToString

0

ParamGrabberTest

test

0

TestWishart

testNextDoubleMatrix

0

TestStringUtil

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