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%	0.001

ubic.basecode.math.linalg

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	QRDecompositionTest	5	0	0	0	100%	0.002

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	PrettyPrinterTest	1	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.308
	TestStringUtil	8	0	0	0	100%	0
	NetUtilsTest	4	0	0	0	100%	2.608
	ConfigUtilsTest	13	0	0	0	100%	0.122
	DateUtilTest	6	0	0	0	100%	0.001
	BatchIteratorTest	3	0	0	0	100%	0
	StringUtilTest	6	0	0	0	100%	0.001
	SQLUtilsTest	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%	0.122
	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%	0.775

ubic.basecode.io.writer

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixWriterTest	3	0	0	0	100%	0
	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%	0.001

ubic.basecode.math.distribution

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	HistogramSamplerTest	1	0	0	0	100%	0.019
	TestWishart	1	0	0	0	100%	0
	HistogramTest	2	0	0	0	100%	0
	UniformDensityComputerTest	1	0	0	0	100%	0.001
	NormalProbabilityComputerTest	4	0	0	0	100%	0

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%	0.001

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.028
	LeastSquaresFitTest	20	0	0	0	100%	10.093
	ModeratedTstatTest	6	0	0	0	100%	0.036
	DesignMatrixTest	5	0	0	0	100%	0.01

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

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyLoaderTest	2	0	0	0	100%	0.093
	OntologySearchTest	9	0	0	0	100%	4.638
	UberonOntologySearchTest	2	0	0	0	100%	20.372
	JenaUtilsTest	1	0	0	0	100%	0.148

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.001

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	PrecisionRecallTest	5	0	0	0	100%	0
	DistanceTest	12	0	0	0	100%	0.001
	TestMatrixNormalizer	2	0	0	0	100%	0.007
	TestMatrixRowStats	6	0	0	0	100%	0
	TestROC	3	0	0	0	100%	0
	KruskalWallisTest	1	0	0	0	100%	0
	TestKSTest	2	0	0	0	100%	0.001
	TestSpecFunc	7	0	0	0	100%	0
	TestWilcoxon	15	0	0	0	100%	2.434
	StringDistanceTest	16	0	0	0	100%	0.001
	RandomChooserTest	7	0	0	0	100%	0.586
	TestMathUtil	5	0	0	0	100%	0.001
	TestMatrixStats	15	0	0	0	100%	0.013
	TestRank	14	0	0	0	100%	0.001
	TestStats	14	0	0	0	100%	0
	MultipleTestCorrectionTest	5	0	0	0	100%	0.163
	CorrelationStatsTest	18	0	0	0	100%	0.002
	TestDescriptiveWithMissing	38	0	0	0	100%	0.001
	SingularValueDecompositionTest	1	0	0	0	100%	0.03

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DenseDoubleMatrixTest	39	0	0	0	100%	0.384
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	StringMatrixTest	4	0	0	0	100%	0.001
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.013
	MatrixUtilTest	7	0	0	0	100%	0.001
	IntegerMatrixTest	16	0	0	0	100%	0.002
	SparseDoubleMatrixTest	24	0	0	0	100%	0.002
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.001
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.002
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.093
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDoubleMatrixReader	15	0	0	0	100%	0.039
	TestStringMatrixReader	4	0	0	0	100%	0
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0
	HistogramReaderTest	2	0	0	0	100%	0
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.734
	TestMapReader	3	0	0	0	100%	0

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAbsentFilter	9	0	0	0	100%	0.001
	TestRowLevelFilter	23	0	0	0	100%	0.06
	TestRowMissingFilter	11	0	0	0	100%	0.003
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowNameFilter	4	0	0	0	100%	0.002
	TestRowAffyNameFilter	2	0	0	0	100%	0.003

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	5.015

ubic.basecode.dataStructure

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	CountingMapTest	6	0	0	0	100%	0
	StringToStringSetMapTest	6	0	0	0	100%	0
	DoubleAddingMapTest	1	0	0	0	100%	0.002
	BitUtilTest	5	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%	0.193

Test Cases

[Summary] [Package List] [Test Cases]

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0.001
	testSmallNumbers	0.019
	testReadInputStreamMissingSpaces	0.007
	testReadBad	0.001
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.002
	testReadBlankCorner	0.002
	testReadInputStreamMissing	0.002
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0.002

CountingMapTest

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

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

PrettyPrinterTest

testPrintBeans

0

DistanceTest

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

HistogramSamplerTest

testNextSample

0.018

TestRowAbsentFilter

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

DenseDoubleMatrixTest

	testConstructFromArray	0.287
	testSubsetRows	0.006
	testToArray	0.004
	testSortByColumnAbsoluteValue	0.017
	testGet	0.002
	testSet	0.003
	testRows2	0.003
	testCopy	0.004
	testGet2	0.003
	testRows	0.003
	testSet2	0.002
	testSize	0.002
	testToString	0.002
	testGetRowByNameFail	0.003
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0.001
	testSubsetColumns	0.002
	testViewRow	0.002
	testColumns	0.002
	testGetColRange	0.002
	testGetByKeys	0.002
	testGetColObj	0.002
	testGetColumn	0.001
	testIsMissing	0.004
	testViewColumn	0.001
	testGetColObj2	0.002
	testGetObject	0.001
	testGetRow	0.002
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.002
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.002
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.001
	testViewRow2	0.002

ParameterKeeperTest

test

0.122

MatrixWriterTest

	testWriteMatrixB	0
	testWriteMatrix	0
	testWrite3DMatrix	0

TestMatrixNormalizer

	testQuantileNormalize	0.004
	testQuantileNormalizeWithMissing	0.003

TestRowLevelFilter

	testFilterMinHigh	0.057
	testFilterFractionMaxRemoveHighAndLowBothFraction	0
	testFilterMaxTooHigh	0
	testFilterMedian	0
	testFilterNoFilter	0
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0
	testFilterFractionMaxRemoveNegHigh	0
	testFilterMax	0
	testFilterMin	0
	testFilterMaxFractionNoneRemoveNeg	0
	testFilterMedianHigh	0
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.001
	testFilterFractionMaxRemoveNeg	0
	testFilterMaxFractionAll	0
	testFilterFractionMaxRemoveHighAndLowBothLevels	0
	testFilterMaxFraction	0
	testFilterBadFraction	0
	testFilterMaxFractionHigh	0
	testFilterMaxFractionNone	0
	testFilterFractionMaxRemoveHighAndLow	0
	testFilterMeanHigh	0
	testFilterMean	0
	testFilterMaxHigh	0.001

MatrixDisplayTest

	testWriteOutAsPNG2	0.691
	testWriteOutAsPNG	0.009
	testSaveImage	0.006
	testSaveImageStandardize	0.019

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0

FileToolsTest

	testHasImageExtension	0
	testTestDir	0
	testGetWithoutExtension	0
	testGetLines	0
	testTouch	0
	testListDirectoryFiles	0
	testAddImageExtension	0.001
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.283
	testCleanFileName	0
	testgetStringListFromFile	0
	testGetWithoutExtensionB	0
	testGetWithoutExtensionC	0
	testResourcetoPath	0
	testCleanFileNameErr	0
	testIsGZipped	0.001
	testUnGzipFile	0
	testCopyFileFailOnDirectoryOutput	0
	testTestFileString	0
	testGetCompressedFile	0
	testCopyFile	0
	testGetExtension	0
	testCheckPathIsReadableFile	0
	testIsZipped	0
	testAddDataExtension	0
	testGetCompressedFileZip	0.001
	testTestFileFile	0.002
	testCheckPathIsReadableFileNot	0.002
	testCopyFileFailOnDirectoryInput	0.002
	testGetInputStreamFromPlainOrCompressedFile	0.002
	testHasXMLExtension	0.002
	testUnzipFile	0.01

JRIClientTest

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

ExcelUtilTest

	testGetSheetFromFile	0.19
	testGetSet	0
	testSetFormula	0.003

MeanVarianceEstimatorTest

	testVoom	0
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.023
	testInterpolate	0.001
	testMeanVarianceNoDesignWithMissing	0.003

TestRowMissingFilter

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

MetaAnalysisTest

	testFisherCombinePvaluesB	0
	testFisherCombinePvalues	0

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

TestMeanDifferenceMetaAnalysis

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

TestMatrixRowStats

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

TestWishart

testNextDoubleMatrix

0

StringMatrixTest

	testToString	0
	testSubsetColumns	0.001
	testGetColObj	0
	testSubset	0

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0

TestItemLevelFilter

testFilter

0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

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
	testIsMissing	0
	testViewColumn	0
	testGetColObj2	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testIsMissing2	0.001
	testGetColByNameFail	0.002
	testGetColByNameNull	0.002
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.001
	testViewRow2	0.002

TestStringUtil

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

StringToStringSetMapTest

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

TestROC

	testBig	0
	testAroc	0
	testArocPvalue	0

MatrixUtilTest

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

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.164
	testThreeWaySingular	0.05
	testEstrogen	3.994
	testVectorWeightedRegress	0.001
	testNHBE	5.608
	testLSFTwoLevels2	0.047
	testLSFTwoLevels3	0.096
	testSingular2	0.041
	testVectorWeightedRegressWithMissing	0.006
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.005
	testTwoWayAnovaWithInteractions	0.009
	testLSFTwoLevels	0.01
	testOneWayAnova	0.023
	testTwoWayTwoLevelsOneContinousInteractionC	0.009
	testLSFThreeLevelsOnecontinous2	0.004
	testMatrixWeightedRegress	0
	testSingular	0.016
	testLSFTwoLevelsOneContinuous	0.006
	testLSFOneContinuousWithMissing3	0.004

KruskalWallisTest

testKW

0

TestCorrelationEffectMetaAnalysis

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

IntegerMatrixTest

	testGetEntry	0
	testGet	0
	testSet	0
	testRows	0
	testSize	0
	testColumns	0
	testSetByKeys	0
	testToInteger	0
	testGetByKeys	0
	testGetColObj	0
	testGetColumn	0.001
	testIsMissing	0
	testGetObject	0
	testGetRow	0
	testGetRowObj	0
	testSetObj	0

OntologyLoaderTest

	testCacheOntologyToDisk	0.075
	testHasChanged	0.006

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

OntologySearchTest

	testPersistence	0.377
	testOmitDefinitions2	0.183
	testOmitDefinitions3	0.046
	testOmitDefinitions4	1.023
	testOmitBadPredicates2	0.042
	testOmitBadPredicates	2.084
	testIndexing	0.563
	testOmitDefinitions	0.042
	testStemming	0.248

NetUtilsTest

	testFtpFileSize	0
	testCheckForFile	0.022
	testFtpFileSizeDoesntExist	1.462
	testDownloadFile	1.123

DoubleAddingMapTest

test

0

ConfigUtilsTest

	testLoadConfigURL	0
	testGetConfigBuilderFile	0.018
	testGetConfigBuilderString	0
	testGetConfigBuilderURLNew	0
	testGetConfigBuilderStringNew	0
	testLoadConfigString	0
	testLoadConfigURLNew	0
	testLoadConfigStringNewName	0.091
	testGetConfigBuilderURL	0.002
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.002
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.002

SparseDoubleMatrixTest

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

CompressedNamedBitMatrixTest

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

TestSpecFunc

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

UniformDensityComputerTest

testDensity

0

CompressedSparseDoubleMatrixTest

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

DateUtilTest

	testgetRelative5yearsFromnow	0
	testRange	0
	testgetRelative5yearsago	0
	testgetRelativeTomorrow	0
	testgetRelativeDateDayago	0
	testRangeBad	0

TestDirectedGraph

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

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	2.412
	testWilxcoxonPGaussB	0.002
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0.001
	testCGaussian	0
	testDVolume	0.001
	testAExact	0.01
	testWilxcoxonPWithTies	0.001
	testEVolume	0

StringDistanceTest

	testWeightedHammingA	0.001
	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

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.093
	testgetcolobj	0
	testgetrowobj	0

RandomChooserTest

	testChooseRandomDeck	0
	testRepeatSubset	0.105
	testChooserandomInts	0.024
	testChooserandomWrep	0.001
	testRandomSubset	0.001
	testChooserandomInt	0.059
	testRepeat	0.396

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0

UberonOntologySearchTest

	testScore	0.11
	testOmitDefinition	0.023

TestMatrixStats

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

RServeClientTest

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

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

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

ParamGrabberTest

test

0

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.029
	testBenjaminiHochbergCut	0.045
	testBenjaminiHochberg	0.035
	testBenjaminiHochbergM	0.031
	testBonferroniCut	0.022

CorrelationStatsTest

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

ModeratedTstatTest

	testLimmaMissing	0.036
	testFdist	0
	testLimma	0
	testSqueezeVarB	0
	testSqueezeVar	0
	testSqueezeVarWMissing	0

DesignMatrixTest

	testInteractionC	0
	test2	0
	testA	0
	testB	0
	testInteractionAndRelevel	0

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0
	testByteArrayToBooleans	0
	testStringToDoubleArrayConversionSpeed	0
	testByteArrayToDoubleConversionSpeed	0
	testByteArrayToTabbedString	0
	testDoubleArrayToBytes	0
	testIntsToBytes	0
	testBooleansToLongArray	0
	testByteArrayToSquareDoubleMatrix	0
	testByteArrayToDoubles	0
	testStringArrayToBytes	0
	testDoubleArrayToDelimitedStringConversionSpeed	0
	testStringArrayToTabbedBytes	0
	testObjectToBytes	0
	testBooleansToByteArray	0
	testByteArrayToLongs	0
	testByteArrayToDoubleMatrix	0

SparseRaggedDoubleMatrixTest

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

TestHistogramWriter

testWriter

0

BinaryTreeTest

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

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

StringUtilTest

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

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	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
	testTrimmedMean	0
	testDurbinWatsonShort	0

SingularValueDecompositionTest

testSingularValueDecomposition

0.03

TestRowAffyNameFilter

	testStringFilter	0.002
	testFilter	0

OntologyTermTest

	testGetParentsHasProperPart	2.055
	testGetChildren	1.439
	testGetChildrenHasProperPart	0.047
	testGetParents	0.839
	testRejectNonEnglish	0.606

SQLUtilsTest

testBlobToString

0

JenaUtilsTest

testInferenceCapabilities

0.147

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.001
	test2NoPivoting	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0
	testReadInputStream	0
	testReadStreamAdjListBig	0.734

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	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
	ubic.basecode.util.r.RServeClientTest
	skipped: got: <java.io.IOException: Could not connect to Rserve>, expected: 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.