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%	0.107

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
	FileToolsTest	32	0	0	0	100%	0.049
	NetUtilsTest	4	0	0	0	100%	4.542
	PrettyPrinterTest	1	0	0	0	100%	0.03
	StringUtilTest	6	0	0	0	100%	0.001
	ConfigUtilsTest	13	0	0	0	100%	0.353
	SQLUtilsTest	1	0	0	0	100%	0.005
	TestStringUtil	8	0	0	0	100%	0.025
	BatchIteratorTest	3	0	0	0	100%	0
	DateUtilTest	6	0	0	0	100%	0.011

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%	0.001

ubic.basecode.graphics

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MatrixDisplayTest	4	0	0	0	100%	0.175

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%	0.04

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
	HistogramTest	2	0	0	0	100%	0
	NormalProbabilityComputerTest	4	0	0	0	100%	0
	TestWishart	1	0	0	0	100%	0
	HistogramSamplerTest	1	0	0	0	100%	0.022
	UniformDensityComputerTest	1	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%	0.331

ubic.basecode.math.linearmodels

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MeanVarianceEstimatorTest	5	0	0	0	100%	0.078
	ModeratedTstatTest	6	0	0	0	100%	1.289
	DesignMatrixTest	5	0	0	0	100%	0.015
	LeastSquaresFitTest	20	0	0	0	100%	8.78

ubic.basecode.math.metaanalysis

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MetaAnalysisTest	2	0	0	0	100%	0.053
	TestCorrelationEffectMetaAnalysis	9	0	0	0	100%	0.003
	TestMeanDifferenceMetaAnalysis	8	0	0	0	100%	0.002

ubic.basecode.ontology.jena

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	UberonOntologySearchTest	2	0	0	0	100%	20.825
	OntologySearchTest	9	0	0	0	100%	4.945
	OntologyLoaderTest	2	0	0	0	100%	0.087
	JenaUtilsTest	1	0	0	0	100%	0.115

ubic.basecode.dataStructure.graph

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

ubic.basecode.dataStructure.matrix

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	RCDoubleMatrix1DTest	3	0	0	0	100%	0
	SparseRaggedDoubleMatrixTest	10	0	0	0	100%	0.005
	DenseDoubleMatrixTest	39	0	0	0	100%	0.066
	CompressedNamedBitMatrixTest	9	0	0	0	100%	0.002
	FastRowAccessDoubleMatrixTest	39	0	0	0	100%	0.026
	MatrixUtilTest	7	0	0	0	100%	0.008
	IntegerMatrixTest	16	0	0	0	100%	0.001
	SparseDoubleMatrixTest	24	0	0	0	100%	0.003
	StringMatrixTest	4	0	0	0	100%	0
	CompressedSparseDoubleMatrixTest	38	0	0	0	100%	0.078
	DenseDouble3dMatrixTest	4	0	0	0	100%	0.001

ubic.basecode.math

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SingularValueDecompositionTest	1	0	0	0	100%	0.102
	TestStats	14	0	0	0	100%	0.001
	CorrelationStatsTest	18	0	0	0	100%	0.074
	TestROC	3	0	0	0	100%	0.054
	KruskalWallisTest	1	0	0	0	100%	0
	DistanceTest	12	0	0	0	100%	0.002
	StringDistanceTest	16	0	0	0	100%	0.001
	TestRank	14	0	0	0	100%	0.002
	PrecisionRecallTest	5	0	0	0	100%	0.001
	TestMatrixStats	15	0	0	0	100%	0.03
	RandomChooserTest	7	0	0	0	100%	0.792
	TestDescriptiveWithMissing	38	0	0	0	100%	0.014
	TestMatrixRowStats	6	0	0	0	100%	0.001
	TestMathUtil	5	0	0	0	100%	0.001
	TestKSTest	2	0	0	0	100%	0
	TestMatrixNormalizer	2	0	0	0	100%	0.005
	MultipleTestCorrectionTest	5	0	0	0	100%	0.145
	TestSpecFunc	7	0	0	0	100%	0.001
	TestWilcoxon	15	0	0	0	100%	1.937

ubic.basecode.io.reader

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestMapReader	3	0	0	0	100%	0.001
	TestSparseRaggedDouble2DNamedMatrixReader	3	0	0	0	100%	0.859
	TestSparseDoubleMatrixReader	2	0	0	0	100%	0.008
	TestStringMatrixReader	4	0	0	0	100%	0.001
	TestDoubleMatrixReader	15	0	0	0	100%	0.091
	HistogramReaderTest	2	0	0	0	100%	0.002

ubic.basecode.ontology

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	OntologyTermTest	5	0	0	0	100%	3.535

ubic.basecode.datafilter

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	TestRowNameFilter	4	0	0	0	100%	0.002
	TestRowAffyNameFilter	2	0	0	0	100%	0.002
	TestRowMissingFilter	11	0	0	0	100%	0.011
	TestRowAbsentFilter	9	0	0	0	100%	0.024
	TestRowLevelFilter	23	0	0	0	100%	0.074
	TestItemLevelFilter	1	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.dataStructure

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	DoubleAddingMapTest	1	0	0	0	100%	0
	BitUtilTest	5	0	0	0	100%	0
	StringToStringSetMapTest	6	0	0	0	100%	0.001
	CountingMapTest	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%	0.47

Test Cases

[Summary] [Package List] [Test Cases]

FileToolsTest

	testHasImageExtension	0
	testTestDir	0
	testGetWithoutExtension	0
	testGetLines	0.003
	testTouch	0.001
	testListDirectoryFiles	0.004
	testAddImageExtension	0.001
	testChangeExtension	0.001
	testDeleteFilesAndDir	0.004
	testCleanFileName	0.002
	testgetStringListFromFile	0.002
	testGetWithoutExtensionB	0.001
	testGetWithoutExtensionC	0.001
	testResourcetoPath	0.001
	testCleanFileNameErr	0.001
	testIsGZipped	0.001
	testUnGzipFile	0.002
	testCopyFileFailOnDirectoryOutput	0.001
	testTestFileString	0.002
	testGetCompressedFile	0.001
	testCopyFile	0.002
	testGetExtension	0.001
	testCheckPathIsReadableFile	0.001
	testIsZipped	0.001
	testAddDataExtension	0.001
	testGetCompressedFileZip	0.003
	testTestFileFile	0.001
	testCheckPathIsReadableFileNot	0.001
	testCopyFileFailOnDirectoryInput	0.001
	testGetInputStreamFromPlainOrCompressedFile	0.001
	testHasXMLExtension	0.001
	testUnzipFile	0.005

TestMapReader

	testRead	0
	testReadNoHeader	0
	testReadNoHeaderFile	0

OntologyTermTest

	testGetParentsHasProperPart	1.236
	testGetChildren	1.401
	testGetChildrenHasProperPart	0.046
	testGetParents	0.345
	testRejectNonEnglish	0.48

RCDoubleMatrix1DTest

	testZSum	0
	testAssignAr	0
	testAssign	0

ParamGrabberTest

test

0

SparseRaggedDoubleMatrixTest

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

NetUtilsTest

	testFtpFileSize	0.983
	testCheckForFile	0.76
	testFtpFileSizeDoesntExist	1.344
	testDownloadFile	1.453

ExcelUtilTest

	testGetSheetFromFile	0.458
	testGetSet	0.003
	testSetFormula	0.009

BinaryTreeTest

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

SingularValueDecompositionTest

testSingularValueDecomposition

0.102

TestRowNameFilter

	testFilterString	0.002
	testFilterExclude	0
	testFilter	0
	testFilterStringExclude	0

JRIClientTest

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

DenseDoubleMatrixTest

	testConstructFromArray	0
	testSubsetRows	0
	testToArray	0.001
	testSortByColumnAbsoluteValue	0.011
	testGet	0.001
	testSet	0.001
	testRows2	0.001
	testCopy	0.002
	testGet2	0.001
	testRows	0.002
	testSet2	0.002
	testSize	0.002
	testToString	0.002
	testGetRowByNameFail	0.002
	testGetRowByNameNull	0.001
	testSetIntIntObject	0.002
	testGetRow2	0.002
	testSubsetColumns	0.002
	testViewRow	0.002
	testColumns	0.002
	testGetColRange	0.001
	testGetByKeys	0.001
	testGetColObj	0.002
	testGetColumn	0.001
	testIsMissing	0.003
	testViewColumn	0.001
	testGetColObj2	0.001
	testGetObject	0.001
	testGetRow	0.001
	testGetRowObj	0.001
	testGetRowRange	0.002
	testGetRowByName	0.002
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.001
	testGetColByName	0.002
	testGetRowArrayList2	0.001
	testViewRow2	0.001

HistogramTest

	testGetBiggestBinSize	0
	testGetApproximateQuantile	0

TestDirectedGraph

	testDeleteLeaf1	0
	testDeleteLeafFail	0
	testGetChildren	0
	testToString	0
	testAddChild	0
	testTopoSort	0
	testAddParent	0
	testDeleteLeafNotLeaf	0
	testAddChildFail	0
	testAddParentFail	0
	testTreeView	0.185

TestStats

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

PrettyPrinterTest

testPrintBeans

0.03

TestByteArrayConverter

	testDoubleArrayToByteArrayConversionSpeed	0.023
	testByteArrayToBooleans	0.008
	testStringToDoubleArrayConversionSpeed	0.012
	testByteArrayToDoubleConversionSpeed	0.006
	testByteArrayToTabbedString	0.006
	testDoubleArrayToBytes	0.003
	testIntsToBytes	0.005
	testBooleansToLongArray	0.003
	testByteArrayToSquareDoubleMatrix	0.004
	testByteArrayToDoubles	0.003
	testStringArrayToBytes	0.002
	testDoubleArrayToDelimitedStringConversionSpeed	0.012
	testStringArrayToTabbedBytes	0.003
	testObjectToBytes	0.006
	testBooleansToByteArray	0.003
	testByteArrayToLongs	0.004
	testByteArrayToDoubleMatrix	0.004

MeanVarianceEstimatorTest

	testVoom	0.055
	testMeanVarianceNoDesignWithColsRowAllMissing	0
	testDuplicateRows	0.019
	testInterpolate	0
	testMeanVarianceNoDesignWithMissing	0.003

StringUtilTest

	testMakeUnique	0
	testCommonPrefixNone	0
	testCommonSuffixNone	0
	testCommonPrefix	0.001
	testCommonSuffix	0
	testMakeNames	0

MetaAnalysisTest

	testFisherCombinePvaluesB	0.012
	testFisherCombinePvalues	0

DoubleAddingMapTest

test

0

TestHistogramWriter

testWriter

0

CorrelationStatsTest

	testSpearmanPvalueA	0
	testSpearmanPvalueB	0
	testSpearmanPvalueD	0
	testSpearmanPvalueE	0.023
	testSpearmanPvalueF	0
	testSpearmanPvalueG	0.038
	testCorrelationForPvalue	0
	testCorrelTooSmall	0
	testInverseFisherTransform	0.001
	testSpearmanPvalueTDist	0
	testCorrel	0
	testCorrelAsByte	0
	testPvalue	0.001
	testSpearmanPvalueA2	0
	testSpearmanPvalueD2	0
	testSpearmanPvalueEh	0.001
	testSpearmanPvalueEm	0.01
	testSpearmanPvalueG2	0

TestSparseRaggedDouble2DNamedMatrixReader

	testReadStreamAdjList	0.008
	testReadInputStream	0.007
	testReadStreamAdjListBig	0.844

NormalProbabilityComputerTest

	testProbabilityDoubleBoolean	0
	testProbabilityDoubleBooleanLower	0
	testInvalidVariance	0
	testProbabilityDouble	0

RServeClientTest

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

TestROC

	testBig	0.052
	testAroc	0.001
	testArocPvalue	0

TestRowAffyNameFilter

	testStringFilter	0.001
	testFilter	0

KruskalWallisTest

testKW

0

CompressedNamedBitMatrixTest

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

BitUtilTest

	testGet	0
	testSet	0
	testClear	0
	testCount	0
	testToBool	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

FastRowAccessDoubleMatrixTest

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

UberonOntologySearchTest

	testScore	0.028
	testOmitDefinition	0.016

TestRank

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

TestRowMissingFilter

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

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
	testReadJW	0.008

StringToStringSetMapTest

	testExpandedValues	0
	testMatrix2	0
	testExpandedSize	0
	testWhereIs	0
	testMatrix	0.001
	testSeenValues	0

ConfigUtilsTest

	testLoadConfigURL	0.088
	testGetConfigBuilderFile	0.217
	testGetConfigBuilderString	0.003
	testGetConfigBuilderURLNew	0.002
	testGetConfigBuilderStringNew	0.002
	testLoadConfigString	0.002
	testLoadConfigURLNew	0.005
	testLoadConfigStringNewName	0.024
	testGetConfigBuilderURL	0.001
	testLoadConfigStringNew	0.002
	testLoadConfigFile	0.002
	testGetConfigBuilderFileNew	0.002
	testLoadConfigFileNew	0.002

ParameterKeeperTest

test

0.001

SQLUtilsTest

testBlobToString

0.004

PrecisionRecallTest

	testAveragePrecisionB	0
	testAveragePrecisionWithTie	0
	testAveragePrecisionNotInOrder	0
	testAveragePrecision	0
	testAveragePrecisionBNotInOrder	0

CountingMapTest

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

TestStringMatrixReader

	testReadInputStreamRowCount	0
	testReadInputStreamGotColName	0.001
	testReadInputStreamGotRowName	0
	testReadInputStreamColumnCount	0

QRDecompositionTest

	testScaledDesign	0
	testSingular2	0
	test1	0
	test3	0.004
	test2NoPivoting	0

MatrixUtilTest

	testSelectColumnsAndRowsBad	0
	testSelectColumns	0
	testDropColumn	0
	testSelectColumnsAndRows	0.003
	testRemoveMissing1	0.001
	testRemoveMissing2	0.002
	testSelectRows	0.002

IntegerMatrixTest

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

TestMatrixStats

	testRbfNormalize	0
	testSelfSquare	0
	testStandardize	0
	testCorrelationMatrix	0.002
	testMax	0.002
	testMin	0
	testNan	0
	testColSumsWithMissing	0.001
	testLogTransform	0.001
	testDoubleStandardize	0.008
	testCov2Cor	0.004
	testConvertToLog2Cpm	0.001
	testConvertLog	0.002
	testCountsPerMillionWithMissing	0.001
	testCorrelationMatrixThreshold	0.006

RandomChooserTest

	testChooseRandomDeck	0.03
	testRepeatSubset	0.35
	testChooserandomInts	0.02
	testChooserandomWrep	0
	testRandomSubset	0.001
	testChooserandomInt	0.04
	testRepeat	0.351

TestDescriptiveWithMissing

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

TestRowAbsentFilter

	testFilterKeepMarginal	0.001
	testFilterPresentCountInvalid	0
	testFilterWithMissing	0.001
	testFilterNullFlags	0.003
	testFilterWithMissingLessStringent	0.01
	testFilterFractionInvalid	0
	testFilterStringMatrix	0.001
	testFilterFraction	0.004
	testFilter	0.003

TestRowLevelFilter

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

TestMatrixRowStats

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

TestDoubleMatrixReader

	testReadChooseRowsBadfileName	0
	testReadInputStreamMissingBad	0
	testReadInputStreamGotColNameSkipColumn	0.002
	testReadInputStreamRowCount	0.001
	testReadInputStreamGotColName	0.002
	testReadInputStreamGotRowName	0.003
	testSmallNumbers	0.053
	testReadInputStreamMissingSpaces	0.012
	testReadBad	0.002
	testBadFileName	0.001
	testReadChooseRowsSkipcols	0.002
	testReadBlankCorner	0.004
	testReadInputStreamMissing	0.002
	testReadChooseRows	0.002
	testReadInputStreamColumnCount	0.003

ModeratedTstatTest

	testLimmaMissing	0.919
	testFdist	0.004
	testLimma	0.073
	testSqueezeVarB	0.29
	testSqueezeVar	0.002
	testSqueezeVarWMissing	0

TestStringUtil

	testTwoStringHashKey	0
	testCsvSplitA	0.022
	testCsvSplitB	0.001
	testCsvSplitC	0
	testCsvSplitD	0
	testCsvSplitE	0.001
	testCsvSplitF	0
	testTwoStringHashKeyB	0

TestMathUtil

	testMax	0
	testSumArray	0
	testFillRangeDown	0
	testFillRange	0
	testFillRangeNo	0

HistogramReaderTest

	testHistogramReaderIs	0
	testHistogramReaderString	0.002

OntologySearchTest

	testPersistence	0.505
	testOmitDefinitions2	0.167
	testOmitDefinitions3	0.04
	testOmitDefinitions4	1.089
	testOmitBadPredicates2	0.044
	testOmitBadPredicates	2.191
	testIndexing	0.579
	testOmitDefinitions	0.037
	testStemming	0.263

TestCorrelationEffectMetaAnalysis

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

DesignMatrixTest

	testInteractionC	0.002
	test2	0.001
	testA	0.001
	testB	0.003
	testInteractionAndRelevel	0.006

OntologyLoaderTest

	testCacheOntologyToDisk	0.078
	testHasChanged	0.003

TestKSTest

	testKSTestTwoSample	0
	testKSTestOneSample	0

TestWishart

testNextDoubleMatrix

0

MatrixWriterTest

	testWriteMatrixB	0.033
	testWriteMatrix	0.002
	testWrite3DMatrix	0.005

HistogramSamplerTest

testNextSample

0.022

LeastSquaresFitTest

	testTwoWayAnovaUnfittable	0.002
	testThreeWaySingular	0.156
	testEstrogen	3.946
	testVectorWeightedRegress	0
	testNHBE	4.549
	testLSFTwoLevels2	0.031
	testLSFTwoLevels3	0.024
	testSingular2	0.007
	testVectorWeightedRegressWithMissing	0.003
	testVectorRegress	0
	testLSFThreeLevelsOneContinuousWithMissing3	0.004
	testTwoWayAnovaWithInteractions	0.004
	testLSFTwoLevels	0.004
	testOneWayAnova	0.016
	testTwoWayTwoLevelsOneContinousInteractionC	0.006
	testLSFThreeLevelsOnecontinous2	0.003
	testMatrixWeightedRegress	0
	testSingular	0.014
	testLSFTwoLevelsOneContinuous	0.005
	testLSFOneContinuousWithMissing3	0.005

MatrixDisplayTest

	testWriteOutAsPNG2	0.146
	testWriteOutAsPNG	0.01
	testSaveImage	0.005
	testSaveImageStandardize	0.013

TestItemLevelFilter

testFilter

0

TestMatrixNormalizer

	testQuantileNormalize	0.001
	testQuantileNormalizeWithMissing	0.004

MultipleTestCorrectionTest

	testBenjaminiYekuteliCut	0.049
	testBenjaminiHochbergCut	0.035
	testBenjaminiHochberg	0.026
	testBenjaminiHochbergM	0.022
	testBonferroniCut	0.012

TestMeanDifferenceMetaAnalysis

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

TestSpecFunc

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

BatchIteratorTest

	testBatches	0
	testBatchIterator	0
	testConcurrentModificationException	0

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
	testGetRowObj	0
	testGetRowRange	0
	testGetRowByName	0
	testGetColByName	0

DateUtilTest

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

UniformDensityComputerTest

testDensity

0

StringMatrixTest

	testToString	0
	testSubsetColumns	0
	testGetColObj	0
	testSubset	0

CompressedSparseDoubleMatrixTest

	testSubsetRows	0.002
	testToArray	0.002
	testSortByColumnAbsoluteValue	0.009
	testGet	0.003
	testSet	0.002
	testRows2	0.002
	testCopy	0.003
	testGet2	0.002
	testRows	0.002
	testSet2	0.002
	testSize	0.001
	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	0.001
	testGetColumn	0.002
	testIsMissing	0.002
	testViewColumn	0.002
	testGetColObj2	0.002
	testGetObject	0.002
	testGetRow	0.001
	testGetRowObj	0.002
	testGetRowRange	0.001
	testGetRowByName	0.001
	testIsMissing2	0.001
	testGetColByNameFail	0.001
	testGetColByNameNull	0.001
	testGetRowObj2	0.002
	testGetColByName	0.001
	testGetRowArrayList2	0.001
	testViewRow2	0.001

TestWilcoxon

	testWilxcoxonPExactB	0
	testWilxcoxonPExactC	0
	testWilxcoxonPExactD	1.913
	testWilxcoxonPGaussB	0
	testBGaussian	0.001
	testFVolume	0.002
	testWilxcoxonPVolume	0.008
	testBig	0
	testWilxcoxonPGauss	0
	testWilcoxonPExactA	0
	testCGaussian	0
	testDVolume	0.002
	testAExact	0.007
	testWilxcoxonPWithTies	0.001
	testEVolume	0.002

JenaUtilsTest

testInferenceCapabilities

0.115

DenseDouble3dMatrixTest

	testget	0
	testtostring	0.001
	testgetcolobj	0
	testgetrowobj	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.