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%	0.097

ubic.basecode.math.linalg

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

ubic.basecode.util

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SQLUtilsTest	1	0	0	0	100%	0.001
	StringUtilTest	6	0	0	0	100%	0.001
	FileToolsTest	32	0	0	0	100%	0.074
	PrettyPrinterTest	1	0	0	0	100%	0.001
	DateUtilTest	6	0	0	0	100%	0.01
	NetUtilsTest	4	0	0	0	100%	4.109
	TestStringUtil	8	0	0	0	100%	0.029
	BatchIteratorTest	3	0	0	0	100%	0
	ConfigUtilsTest	13	0	0	0	100%	0.235

ubic.basecode.dataStructure.params

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParameterKeeperTest	1	0	0	0	100%	0.003
	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%	0.37

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%	0.004

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%	0.027
	HistogramTest	2	0	0	0	100%	0.001
	TestWishart	1	0	0	0	100%	0.001
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	UniformDensityComputerTest	1	0	0	0	100%	0

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.068
	DesignMatrixTest	5	0	0	0	100%	0.032
	ModeratedTstatTest	6	0	0	0	100%	0.219
	LeastSquaresFitTest	20	0	0	0	100%	9.048

ubic.basecode.util.r

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RServeClientTest	1	0	0	1	0%	0.306
	JRIClientTest	1	0	0	1	0%	0.001

ubic.basecode.math.metaanalysis

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

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyLoaderTest	2	0	0	0	100%	0.193
	OntologySearchTest	9	0	0	0	100%	4.79
	UberonOntologySearchTest	2	0	0	0	100%	22.466
	JenaUtilsTest	1	0	0	0	100%	0.152

ubic.basecode.dataStructure.graph

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestDirectedGraph	11	0	0	0	100%	0.041

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestStats	14	0	0	0	100%	0.001
	CorrelationStatsTest	18	0	0	0	100%	0.066
	KruskalWallisTest	1	0	0	0	100%	0.093
	TestRank	14	0	0	0	100%	0.006
	TestMathUtil	5	0	0	0	100%	0
	StringDistanceTest	16	0	0	0	100%	0.001
	TestWilcoxon	15	0	0	0	100%	3.155
	TestSpecFunc	7	0	0	0	100%	0.028
	SingularValueDecompositionTest	1	0	0	0	100%	0.096
	TestKSTest	2	0	0	0	100%	0
	TestMatrixRowStats	6	0	0	0	100%	0.022
	MultipleTestCorrectionTest	5	0	0	0	100%	0.332
	TestMatrixNormalizer	2	0	0	0	100%	0.793
	TestROC	3	0	0	0	100%	0.03
	PrecisionRecallTest	5	0	0	0	100%	0
	RandomChooserTest	7	0	0	0	100%	1.386
	DistanceTest	12	0	0	0	100%	0.002
	TestMatrixStats	15	0	0	0	100%	0.025
	TestDescriptiveWithMissing	38	0	0	0	100%	0.003

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixUtilTest	7	0	0	0	100%	0.001
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0
	IntegerMatrixTest	16	0	0	0	100%	0
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.001
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.032
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.062
	SparseDoubleMatrixTest	24	0	0	0	100%	0.002
	StringMatrixTest	4	0	0	0	100%	0
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	DenseDoubleMatrixTest	39	0	0	0	100%	0.026
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.001

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMapReader	3	0	0	0	100%	0.001
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.002
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.626
	TestDoubleMatrixReader	15	0	0	0	100%	0.057
	TestStringMatrixReader	4	0	0	0	100%	0
	HistogramReaderTest	2	0	0	0	100%	0.001

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowAbsentFilter	9	0	0	0	100%	0.028
	TestRowMissingFilter	11	0	0	0	100%	0.023
	TestItemLevelFilter	1	0	0	0	100%	0.001
	TestRowAffyNameFilter	2	0	0	0	100%	0.001
	TestRowNameFilter	4	0	0	0	100%	0.006
	TestRowLevelFilter	23	0	0	0	100%	0.121

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	4.079

ubic.basecode.dataStructure

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

ubic.basecode.dataStructure.tree

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

ubic.basecode.io.excel

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ExcelUtilTest	3	0	0	0	100%	0.366

Test Cases

[Summary] [Package List] [Test Cases]

TestStats

	testNormalizeDoubleArrayListdouble	0
	testCdf	0
	testRange	0
	testMeanAboveQuantile	0
	testCv	0.001
	testCumulateRight	0
	testQuantile	0
	testIsValidFraction	0
	testIsValidFraction2	0
	testNumberOfDistinctValues	0
	testCumulate	0
	testQuantile75	0
	testNormalizeDoubleArrayList	0
	testNumberOfDistinctValuesNonNA	0

MatrixUtilTest

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

SQLUtilsTest

testBlobToString

0

CompressedNamedBitMatrixTest

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

MeanVarianceEstimatorTest

	testVoom	0.047
	testMeanVarianceNoDesignWithColsRowAllMissing	0.001
	testDuplicateRows	0.018
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.002

StringUtilTest

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

CorrelationStatsTest

	testSpearmanPvalueA	0.003
	testSpearmanPvalueB	0.001
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.023
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.026
	testCorrelationForPvalue	0.001
	testCorrelTooSmall	0
	testInverseFisherTransform	0
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.01
	testSpearmanPvalueG2	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

KruskalWallisTest

testKW

0.02

OntologyLoaderTest

	testCacheOntologyToDisk	0.181
	testHasChanged	0.006

TestHistogramWriter

testWriter

0

TestRank

	testRankTransformMapDesc	0
	testRankTransformDoubleArrayListDesc	0
	testRankTransformMap	0
	testOrder	0.003
	testRankWithTies	0
	testWithNaNs	0.001
	testRankTransformDoubleArrayList	0
	testRankWithTiesB	0
	testRankWithTiesC	0.001
	testRankWithTiesD	0
	testRankWithTiesE	0
	testWithNaNs2	0.001
	testWithNaNs3	0
	testOrderB	0

OntologySearchTest

	testPersistence	0.388
	testOmitDefinitions2	0.139
	testOmitDefinitions3	0.037
	testOmitDefinitions4	1.069
	testOmitBadPredicates2	0.045
	testOmitBadPredicates	2.047
	testIndexing	0.606
	testOmitDefinitions	0.042
	testStemming	0.389

TestRowAbsentFilter

	testFilterKeepMarginal	0.001
	testFilterPresentCountInvalid	0
	testFilterWithMissing	0.005
	testFilterNullFlags	0.003
	testFilterWithMissingLessStringent	0.004
	testFilterFractionInvalid	0.003
	testFilterStringMatrix	0.004
	testFilterFraction	0.003
	testFilter	0.005

StringToStringSetMapTest

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

ParameterKeeperTest

test

0.003

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	0

TestMapReader

	testRead	0.001
	testReadNoHeader	0
	testReadNoHeaderFile	0

TestRowMissingFilter

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

DesignMatrixTest

	testInteractionC	0.015
	test2	0.003
	testA	0.001
	testB	0.003
	testInteractionAndRelevel	0.01

TestSparseDoubleMatrixReader

	testReadStream	0
	testReadJW	0.001

MatrixWriterTest

	testWriteMatrixB	0
	testWriteMatrix	0
	testWrite3DMatrix	0.004

FileToolsTest

	testHasImageExtension	0
	testTestDir	0
	testGetWithoutExtension	0
	testGetLines	0.001
	testTouch	0.002
	testListDirectoryFiles	0.006
	testAddImageExtension	0.002
	testChangeExtension	0.002
	testDeleteFilesAndDir	0.005
	testCleanFileName	0.002
	testgetStringListFromFile	0.003
	testGetWithoutExtensionB	0.002
	testGetWithoutExtensionC	0.002
	testResourcetoPath	0.002
	testCleanFileNameErr	0.002
	testIsGZipped	0.005
	testUnGzipFile	0.002
	testCopyFileFailOnDirectoryOutput	0.002
	testTestFileString	0.001
	testGetCompressedFile	0.002
	testCopyFile	0.003
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.005
	testIsZipped	0.002
	testAddDataExtension	0.002
	testGetCompressedFileZip	0.003
	testTestFileFile	0.002
	testCheckPathIsReadableFileNot	0.001
	testCopyFileFailOnDirectoryInput	0.002
	testGetInputStreamFromPlainOrCompressedFile	0.001
	testHasXMLExtension	0.002
	testUnzipFile	0.007

SparseRaggedDoubleMatrixTest

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

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.003
	testReadInputStream	0.004
	testReadStreamAdjListBig	0.619

OntologyTermTest

	testGetParentsHasProperPart	1.358
	testGetChildren	1.312
	testGetChildrenHasProperPart	0.063
	testGetParents	0.657
	testRejectNonEnglish	0.65

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0
	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0.001
	testSmallNumbers	0.035
	testReadInputStreamMissingSpaces	0.009
	testReadBad	0.001
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.001
	testReadBlankCorner	0.001
	testReadInputStreamMissing	0.002
	testReadChooseRows	0.001
	testReadInputStreamColumnCount	0.002

ExcelUtilTest

	testGetSheetFromFile	0.355
	testGetSet	0.002
	testSetFormula	0.008

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	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

ParamGrabberTest

test

0

FastRowAccessDoubleMatrixTest

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

HistogramSamplerTest

testNextSample

0.026

RServeClientTest

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

TestItemLevelFilter

testFilter

0

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	3.136
	testWilxcoxonPGaussB	0
	testBGaussian	0
	testFVolume	0.001
	testWilxcoxonPVolume	0.005
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0.001
	testDVolume	0.001
	testAExact	0.009
	testWilxcoxonPWithTies	0
	testEVolume	0.001

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.002
	testByteArrayToBooleans	0.003
	testStringToDoubleArrayConversionSpeed	0.006
	testByteArrayToDoubleConversionSpeed	0.006
	testByteArrayToTabbedString	0.004
	testDoubleArrayToBytes	0.004
	testIntsToBytes	0.008
	testBooleansToLongArray	0.004
	testByteArrayToSquareDoubleMatrix	0.004
	testByteArrayToDoubles	0.003
	testStringArrayToBytes	0.003
	testDoubleArrayToDelimitedStringConversionSpeed	0.015
	testStringArrayToTabbedBytes	0.003
	testObjectToBytes	0.006
	testBooleansToByteArray	0.008
	testByteArrayToLongs	0.009
	testByteArrayToDoubleMatrix	0.007

PrettyPrinterTest

testPrintBeans

0

TestSpecFunc

	testdBinom	0
	testCumHyperGeometricB	0
	testTrigammaInverse	0.026
	testCumHyperGeometric	0
	testTrigammaInverseB	0.001
	testHypergeometric	0
	testCumHyperGeometricUT	0

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0

DateUtilTest

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

ModeratedTstatTest

	testLimmaMissing	0.029
	testFdist	0
	testLimma	0.048
	testSqueezeVarB	0.141
	testSqueezeVar	0
	testSqueezeVarWMissing	0

JRIClientTest

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

MatrixDisplayTest

	testWriteOutAsPNG2	0.33
	testWriteOutAsPNG	0.01
	testSaveImage	0.006
	testSaveImageStandardize	0.024

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0.001
	testTreeView	0.039

NetUtilsTest

	testFtpFileSize	0.817
	testCheckForFile	0.734
	testFtpFileSizeDoesntExist	1.508
	testDownloadFile	1.049

DoubleAddingMapTest

test

0

SingularValueDecompositionTest

testSingularValueDecomposition

0.096

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestMatrixRowStats

	testSumOfSquaresDoubleMatrixNamed	0.002
	testMeans	0.004
	testSums	0.004
	testMeans2	0.006
	testStandardDeviations	0.003
	testSumOfSquaresDoubleMatrixNamedDoubleArrayList	0.003

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.004
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.007
	testGet	0.002
	testSet	0.001
	testRows2	0.002
	testCopy	0.002
	testGet2	0
	testRows	0.001
	testSet2	0.001
	testSize	0.001
	testToString	0.002
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0.002
	testSubsetColumns	0.001
	testViewRow	0.002
	testColumns	0.001
	testGetColRange	0.003
	testGetByKeys	0.003
	testGetColObj	0.001
	testGetColumn	0.001
	testIsMissing	0.002
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.002
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.001
	testGetColByNameFail	0.002
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.026
	testCsvSplitB	0.001
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0
	testCsvSplitF	0.001
	testTwoStringHashKeyB	0

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.032
	testThreeWaySingular	0.147
	testEstrogen	4.144
	testVectorWeightedRegress	0.001
	testNHBE	4.553
	testLSFTwoLevels2	0.033
	testLSFTwoLevels3	0.028
	testSingular2	0.006
	testVectorWeightedRegressWithMissing	0.004
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.006
	testTwoWayAnovaWithInteractions	0.006
	testLSFTwoLevels	0.005
	testOneWayAnova	0.028
	testTwoWayTwoLevelsOneContinousInteractionC	0.009
	testLSFThreeLevelsOnecontinous2	0.004
	testMatrixWeightedRegress	0.001
	testSingular	0.026
	testLSFTwoLevelsOneContinuous	0.009
	testLSFOneContinuousWithMissing3	0.006

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
	testIsMissing	0
	testViewColumn	0
	testGetObject	0
	testGetRow	0.001
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testGetColByName	0

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.076
	testBenjaminiHochbergCut	0.071
	testBenjaminiHochberg	0.109
	testBenjaminiHochbergM	0.061
	testBonferroniCut	0.014

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	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.

MetaAnalysisTest

	testFisherCombinePvaluesB	0.001
	testFisherCombinePvalues	0

TestWishart

testNextDoubleMatrix

0

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

TestMatrixNormalizer

	testQuantileNormalize	0.785
	testQuantileNormalizeWithMissing	0.007

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0
	testSortByColumnAbsoluteValue	0
	testGet	0
	testSet	0
	testRows2	0
	testCopy	0
	testGet2	0
	testRows	0
	testSet2	0.001
	testSize	0.001
	testToString	0.001
	testGetRowByNameFail	0.001
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0
	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
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0
	testGetRowByName	0.002
	testIsMissing2	0
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.001
	testGetRowArrayList2	0
	testViewRow2	0

UberonOntologySearchTest

	testScore	0.035
	testOmitDefinition	0.017

TestCorrelationEffectMetaAnalysis

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

TestROC

	testBig	0.026
	testAroc	0
	testArocPvalue	0.004

TestRowNameFilter

	testFilterString	0.001
	testFilterExclude	0
	testFilter	0.001
	testFilterStringExclude	0.003

TestRowLevelFilter

	testFilterMinHigh	0.009
	testFilterFractionMaxRemoveHighAndLowBothFraction	0.007
	testFilterMaxTooHigh	0.007
	testFilterMedian	0.006
	testFilterNoFilter	0.006
	testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow	0.005
	testFilterFractionMaxRemoveNegHigh	0.006
	testFilterMax	0.005
	testFilterMin	0.007
	testFilterMaxFractionNoneRemoveNeg	0.007
	testFilterMedianHigh	0.006
	testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove	0.006
	testFilterFractionMaxRemoveNeg	0.006
	testFilterMaxFractionAll	0.004
	testFilterFractionMaxRemoveHighAndLowBothLevels	0.003
	testFilterMaxFraction	0.005
	testFilterBadFraction	0.004
	testFilterMaxFractionHigh	0.003
	testFilterMaxFractionNone	0.003
	testFilterFractionMaxRemoveHighAndLow	0.003
	testFilterMeanHigh	0.005
	testFilterMean	0.003
	testFilterMaxHigh	0.003

ConfigUtilsTest

	testLoadConfigURL	0.108
	testGetConfigBuilderFile	0.104
	testGetConfigBuilderString	0.002
	testGetConfigBuilderURLNew	0.002
	testGetConfigBuilderStringNew	0.001
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.002
	testLoadConfigStringNewName	0.009
	testGetConfigBuilderURL	0
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.001
	testGetConfigBuilderFileNew	0.001
	testLoadConfigFileNew	0.001

BinaryTreeTest

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

JenaUtilsTest

testInferenceCapabilities

0.15

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.008
	test2NoPivoting	0

TestMeanDifferenceMetaAnalysis

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

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

RandomChooserTest

	testChooseRandomDeck	0.052
	testRepeatSubset	0.644
	testChooserandomInts	0.021
	testChooserandomWrep	0.001
	testRandomSubset	0
	testChooserandomInt	0.082
	testRepeat	0.586

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	0

CountingMapTest

	testSummation	0
	testCount	0
	testSeen	0
	testIncrement	0
	testSortedKeyList	0
	testSortedKeyListBoolean	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

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0
	testCorrelationMatrix	0
	testMax	0
	testMin	0
	testNan	0
	testColSumsWithMissing	0
	testLogTransform	0
	testDoubleStandardize	0.011
	testCov2Cor	0.003
	testConvertToLog2Cpm	0.001
	testConvertLog	0.001
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.007

TestDescriptiveWithMissing

	testRankInterpolated	0
	testKurtosis	0.001
	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	0.001
	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

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

UniformDensityComputerTest

testDensity

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.