Surefire Report

Summary

[Summary] [Package List] [Test Cases]


Tests Errors Failures Skipped Success Rate Time
691 1 0 5 99.132% 203.995

Note: failures are anticipated and checked for with assertions while errors are unanticipated.


Package List

[Summary] [Package List] [Test Cases]


Package Tests Errors Failures Skipped Success Rate Time
ubic.basecode.math.linalg 5 0 0 0 100% 0.005
ubic.basecode.io 17 0 0 0 100% 0.129
ubic.basecode.util 74 0 0 0 100% 4.716
ubic.basecode.dataStructure.params 2 0 0 0 100% 0.008
ubic.basecode.graphics 4 0 0 0 100% 0.187
ubic.basecode.io.writer 4 0 0 0 100% 0.044
ubic.basecode.ontology.ncbo 3 0 0 3 0% 0.001
ubic.basecode.math.distribution 9 0 0 0 100% 0.042
ubic.basecode.util.r 2 0 0 2 0% 0.309
ubic.basecode.math.linearmodels 36 0 0 0 100% 9.057
ubic.basecode.math.metaanalysis 19 0 0 0 100% 0.002
ubic.basecode.ontology.jena 14 1 0 0 92.857% 180.011
ubic.basecode.dataStructure.graph 11 0 0 0 100% 0.341
ubic.basecode.dataStructure.matrix 193 0 0 0 100% 0.118
ubic.basecode.math 186 0 0 0 100% 3.145
ubic.basecode.io.reader 29 0 0 0 100% 1.964
ubic.basecode.datafilter 50 0 0 0 100% 0.125
ubic.basecode.ontology 5 0 0 0 100% 3.261
ubic.basecode.dataStructure.tree 7 0 0 0 100% 0
ubic.basecode.dataStructure 18 0 0 0 100% 0.003
ubic.basecode.io.excel 3 0 0 0 100% 0.527

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% 0.005

ubic.basecode.io

Class Tests Errors Failures Skipped Success Rate Time
 TestByteArrayConverter 17 0 0 0 100% 0.129

ubic.basecode.util

Class Tests Errors Failures Skipped Success Rate Time
 SQLUtilsTest 1 0 0 0 100% 0
 TestStringUtil 8 0 0 0 100% 0.012
 FileToolsTest 32 0 0 0 100% 0.099
 PrettyPrinterTest 1 0 0 0 100% 0.018
 DateUtilTest 6 0 0 0 100% 0.017
 NetUtilsTest 4 0 0 0 100% 4.354
 BatchIteratorTest 3 0 0 0 100% 0.001
 StringUtilTest 6 0 0 0 100% 0.008
 ConfigUtilsTest 13 0 0 0 100% 0.207

ubic.basecode.dataStructure.params

Class Tests Errors Failures Skipped Success Rate Time
 ParameterKeeperTest 1 0 0 0 100% 0.008
 ParamGrabberTest 1 0 0 0 100% 0

ubic.basecode.graphics

Class Tests Errors Failures Skipped Success Rate Time
 MatrixDisplayTest 4 0 0 0 100% 0.187

ubic.basecode.io.writer

Class Tests Errors Failures Skipped Success Rate Time
 MatrixWriterTest 3 0 0 0 100% 0.044
 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
 NormalProbabilityComputerTest 4 0 0 0 100% 0
 TestWishart 1 0 0 0 100% 0.001
 HistogramSamplerTest 1 0 0 0 100% 0.04
 UniformDensityComputerTest 1 0 0 0 100% 0.001
 HistogramTest 2 0 0 0 100% 0

ubic.basecode.util.r

Class Tests Errors Failures Skipped Success Rate Time
 RServeClientTest 1 0 0 1 0% 0.307
 JRIClientTest 1 0 0 1 0% 0.002

ubic.basecode.math.linearmodels

Class Tests Errors Failures Skipped Success Rate Time
 DesignMatrixTest 5 0 0 0 100% 0.018
 LeastSquaresFitTest 20 0 0 0 100% 8.546
 MeanVarianceEstimatorTest 5 0 0 0 100% 0.052
 ModeratedTstatTest 6 0 0 0 100% 0.441

ubic.basecode.math.metaanalysis

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

ubic.basecode.ontology.jena

Class Tests Errors Failures Skipped Success Rate Time
 OntologySearchTest 9 1 0 0 88.889% 159.578
 OntologyLoaderTest 2 0 0 0 100% 0.136
 JenaUtilsTest 1 0 0 0 100% 0.111
 UberonOntologySearchTest 2 0 0 0 100% 20.186

ubic.basecode.dataStructure.graph

Class Tests Errors Failures Skipped Success Rate Time
 TestDirectedGraph 11 0 0 0 100% 0.341

ubic.basecode.dataStructure.matrix

Class Tests Errors Failures Skipped Success Rate Time
 CompressedSparseDoubleMatrixTest 38 0 0 0 100% 0.046
 FastRowAccessDoubleMatrixTest 39 0 0 0 100% 0.022
 SparseRaggedDoubleMatrixTest 10 0 0 0 100% 0.004
 SparseDoubleMatrixTest 24 0 0 0 100% 0.008
 CompressedNamedBitMatrixTest 9 0 0 0 100% 0
 IntegerMatrixTest 16 0 0 0 100% 0.001
 StringMatrixTest 4 0 0 0 100% 0
 RCDoubleMatrix1DTest 3 0 0 0 100% 0.002
 DenseDoubleMatrixTest 39 0 0 0 100% 0.032
 DenseDouble3dMatrixTest 4 0 0 0 100% 0.002
 MatrixUtilTest 7 0 0 0 100% 0.001

ubic.basecode.math

Class Tests Errors Failures Skipped Success Rate Time
 MultipleTestCorrectionTest 5 0 0 0 100% 0.075
 TestRank 14 0 0 0 100% 0.001
 TestMatrixNormalizer 2 0 0 0 100% 0
 TestROC 3 0 0 0 100% 0.029
 KruskalWallisTest 1 0 0 0 100% 0
 StringDistanceTest 16 0 0 0 100% 0.003
 SingularValueDecompositionTest 1 0 0 0 100% 0.101
 TestDescriptiveWithMissing 38 0 0 0 100% 0.001
 TestMathUtil 5 0 0 0 100% 0.001
 PrecisionRecallTest 5 0 0 0 100% 0.001
 TestWilcoxon 15 0 0 0 100% 1.975
 TestSpecFunc 7 0 0 0 100% 0
 TestKSTest 2 0 0 0 100% 0.001
 TestMatrixStats 15 0 0 0 100% 0.02
 CorrelationStatsTest 18 0 0 0 100% 0.133
 TestStats 14 0 0 0 100% 0.001
 RandomChooserTest 7 0 0 0 100% 0.8
 TestMatrixRowStats 6 0 0 0 100% 0
 DistanceTest 12 0 0 0 100% 0.003

ubic.basecode.io.reader

Class Tests Errors Failures Skipped Success Rate Time
 HistogramReaderTest 2 0 0 0 100% 0.002
 TestSparseDoubleMatrixReader 2 0 0 0 100% 0.001
 TestDoubleMatrixReader 15 0 0 0 100% 0.944
 TestMapReader 3 0 0 0 100% 0.007
 TestStringMatrixReader 4 0 0 0 100% 0
 TestSparseRaggedDouble2DNamedMatrixReader 3 0 0 0 100% 1.01

ubic.basecode.datafilter

Class Tests Errors Failures Skipped Success Rate Time
 TestRowLevelFilter 23 0 0 0 100% 0.076
 TestRowMissingFilter 11 0 0 0 100% 0.014
 TestRowAffyNameFilter 2 0 0 0 100% 0.003
 TestItemLevelFilter 1 0 0 0 100% 0.002
 TestRowNameFilter 4 0 0 0 100% 0.002
 TestRowAbsentFilter 9 0 0 0 100% 0.028

ubic.basecode.ontology

Class Tests Errors Failures Skipped Success Rate Time
 OntologyTermTest 5 0 0 0 100% 3.261

ubic.basecode.dataStructure.tree

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

ubic.basecode.dataStructure

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

ubic.basecode.io.excel

Class Tests Errors Failures Skipped Success Rate Time
 ExcelUtilTest 3 0 0 0 100% 0.527

Test Cases

[Summary] [Package List] [Test Cases]

CompressedSparseDoubleMatrixTest

 testSubsetRows 0.004
 testToArray 0.001
 testSortByColumnAbsoluteValue 0.006
 testGet 0.001
 testSet 0.001
 testRows2 0.001
 testCopy 0.002
 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
 testSubsetColumns 0.002
 testViewRow 0.001
 testColumns 0.001
 testGetColRange 0.001
 testGetByKeys 0
 testGetColObj 0.001
 testGetColumn 0.001
 testIsMissing 0.001
 testViewColumn 0.001
 testGetColObj2 0.001
 testGetObject 0.001
 testGetRow 0.001
 testGetRowObj 0.001
 testGetRowRange 0.001
 testGetRowByName 0.001
 testIsMissing2 0.001
 testGetColByNameFail 0.001
 testGetColByNameNull 0
 testGetRowObj2 0.001
 testGetColByName 0.001
 testGetRowArrayList2 0.001
 testViewRow2 0.001

FastRowAccessDoubleMatrixTest

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

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

MultipleTestCorrectionTest

 testBenjaminiYekuteliCut 0.01
 testBenjaminiHochbergCut 0.014
 testBenjaminiHochberg 0.02
 testBenjaminiHochbergM 0.019
 testBonferroniCut 0.012

BinaryTreeTest

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

TestRank

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

TestWishart

 testNextDoubleMatrix 0

SQLUtilsTest

 testBlobToString 0

HistogramSamplerTest

 testNextSample 0.04

SparseRaggedDoubleMatrixTest

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

JRIClientTest

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

HistogramReaderTest

 testHistogramReaderIs 0
 testHistogramReaderString 0

TestMatrixNormalizer

 testQuantileNormalize 0
 testQuantileNormalizeWithMissing 0

SparseDoubleMatrixTest

 testSubsetCols 0
 testSubsetRows 0
 testToArray 0
 testGet 0
 testSet 0
 testCopy 0
 testRows 0
 testSize 0
 testToString 0
 testGetRowArrayList 0.001
 testViewRow 0
 testColumns 0
 testGetColRange 0
 testGetByKeys 0
 testGetColObj 0.001
 testGetColumn 0
 testIsMissing 0.001
 testViewColumn 0.001
 testGetObject 0
 testGetRow 0
 testGetRowObj 0.002
 testGetRowRange 0
 testGetRowByName 0.001
 testGetColByName 0

TestROC

 testBig 0.028
 testAroc 0
 testArocPvalue 0.001

TestStringUtil

 testTwoStringHashKey 0
 testCsvSplitA 0.009
 testCsvSplitB 0.001
 testCsvSplitC 0
 testCsvSplitD 0
 testCsvSplitE 0
 testCsvSplitF 0
 testTwoStringHashKeyB 0

DesignMatrixTest

 testInteractionC 0.006
 test2 0.001
 testA 0.001
 testB 0.002
 testInteractionAndRelevel 0.008

OntologySearchTest

 testPersistence 0.611
 testOmitDefinitions2 0.145
 testOmitDefinitions3 0.045
 testOmitDefinitions4 1.023
 testOmitBadPredicates2 0.044
 testOmitBadPredicates
+ [ Detail ]
 156.662
Failed to resolve import for http://semantic-mediawiki.org/swivt/1.0.
testIndexing 0.693
 testOmitDefinitions 0.043
 testStemming 0.287

KruskalWallisTest

 testKW 0

TestCorrelationEffectMetaAnalysis

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

StringDistanceTest

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

OntologyLoaderTest

 testCacheOntologyToDisk 0.121
 testHasChanged 0.006

QRDecompositionTest

 testScaledDesign 0
 testSingular2 0
 test1 0
 test3 0.005
 test2NoPivoting 0

SingularValueDecompositionTest

 testSingularValueDecomposition 0.101

StringToStringSetMapTest

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

CountingMapTest

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

ParameterKeeperTest

 test 0.008

TestSparseDoubleMatrixReader

 testReadStream 0
 testReadJW 0

TestDoubleMatrixReader

 testReadChooseRowsBadfileName 0.707
 testReadInputStreamMissingBad 0.01
 testReadInputStreamGotColNameSkipColumn 0.015
 testReadInputStreamRowCount 0.015
 testReadInputStreamGotColName 0.007
 testReadInputStreamGotRowName 0.006
 testSmallNumbers 0.101
 testReadInputStreamMissingSpaces 0.014
 testReadBad 0.003
 testBadFileName 0.002
 testReadChooseRowsSkipcols 0.003
 testReadBlankCorner 0.004
 testReadInputStreamMissing 0.005
 testReadChooseRows 0.003
 testReadInputStreamColumnCount 0.002

TestMapReader

 testRead 0.004
 testReadNoHeader 0
 testReadNoHeaderFile 0.002

FileToolsTest

 testHasImageExtension 0
 testTestDir 0
 testGetWithoutExtension 0
 testGetLines 0
 testTouch 0
 testListDirectoryFiles 0.034
 testAddImageExtension 0.002
 testChangeExtension 0.001
 testDeleteFilesAndDir 0.006
 testCleanFileName 0.002
 testgetStringListFromFile 0.003
 testGetWithoutExtensionB 0.002
 testGetWithoutExtensionC 0.001
 testResourcetoPath 0.002
 testCleanFileNameErr 0.002
 testIsGZipped 0.001
 testUnGzipFile 0.004
 testCopyFileFailOnDirectoryOutput 0.002
 testTestFileString 0.001
 testGetCompressedFile 0.003
 testCopyFile 0.002
 testGetExtension 0.002
 testCheckPathIsReadableFile 0.002
 testIsZipped 0.001
 testAddDataExtension 0.001
 testGetCompressedFileZip 0.003
 testTestFileFile 0.002
 testCheckPathIsReadableFileNot 0.001
 testCopyFileFailOnDirectoryInput 0.002
 testGetInputStreamFromPlainOrCompressedFile 0.002
 testHasXMLExtension 0.001
 testUnzipFile 0.012

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

PrettyPrinterTest

 testPrintBeans 0.018

LeastSquaresFitTest

 testTwoWayAnovaUnfittable 0.001
 testThreeWaySingular 0.084
 testEstrogen 3.729
 testVectorWeightedRegress 0.001
 testNHBE 4.607
 testLSFTwoLevels2 0.03
 testLSFTwoLevels3 0.025
 testSingular2 0.005
 testVectorWeightedRegressWithMissing 0.003
 testVectorRegress 0
 testLSFThreeLevelsOneContinuousWithMissing3 0.003
 testTwoWayAnovaWithInteractions 0.006
 testLSFTwoLevels 0.004
 testOneWayAnova 0.016
 testTwoWayTwoLevelsOneContinousInteractionC 0.006
 testLSFThreeLevelsOnecontinous2 0.002
 testMatrixWeightedRegress 0.001
 testSingular 0.013
 testLSFTwoLevelsOneContinuous 0.007
 testLSFOneContinuousWithMissing3 0.003

DoubleAddingMapTest

 test 0

CompressedNamedBitMatrixTest

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

TestMathUtil

 testMax 0.001
 testSumArray 0
 testFillRangeDown 0
 testFillRange 0
 testFillRangeNo 0

TestRowLevelFilter

 testFilterMinHigh 0.002
 testFilterFractionMaxRemoveHighAndLowBothFraction 0.004
 testFilterMaxTooHigh 0.004
 testFilterMedian 0.004
 testFilterNoFilter 0.004
 testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow 0.003
 testFilterFractionMaxRemoveNegHigh 0.004
 testFilterMax 0.003
 testFilterMin 0.003
 testFilterMaxFractionNoneRemoveNeg 0.005
 testFilterMedianHigh 0.003
 testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove 0.002
 testFilterFractionMaxRemoveNeg 0.003
 testFilterMaxFractionAll 0.004
 testFilterFractionMaxRemoveHighAndLowBothLevels 0.003
 testFilterMaxFraction 0.002
 testFilterBadFraction 0.002
 testFilterMaxFractionHigh 0.002
 testFilterMaxFractionNone 0.005
 testFilterFractionMaxRemoveHighAndLow 0.002
 testFilterMeanHigh 0.003
 testFilterMean 0.003
 testFilterMaxHigh 0.004

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.

PrecisionRecallTest

 testAveragePrecisionB 0.001
 testAveragePrecisionWithTie 0
 testAveragePrecisionNotInOrder 0
 testAveragePrecision 0
 testAveragePrecisionBNotInOrder 0

TestWilcoxon

 testWilxcoxonPExactB 0
 testWilxcoxonPExactC 0
 testWilxcoxonPExactD 1.959
 testWilxcoxonPGaussB 0
 testBGaussian 0
 testFVolume 0.002
 testWilxcoxonPVolume 0.004
 testBig 0
 testWilxcoxonPGauss 0.001
 testWilcoxonPExactA 0
 testCGaussian 0
 testDVolume 0.001
 testAExact 0.004
 testWilxcoxonPWithTies 0.001
 testEVolume 0.001

TestStringMatrixReader

 testReadInputStreamRowCount 0
 testReadInputStreamGotColName 0
 testReadInputStreamGotRowName 0
 testReadInputStreamColumnCount 0

IntegerMatrixTest

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

DateUtilTest

 testgetRelative5yearsFromnow 0.006
 testRange 0.01
 testgetRelative5yearsago 0
 testgetRelativeTomorrow 0.001
 testgetRelativeDateDayago 0
 testRangeBad 0

StringMatrixTest

 testToString 0
 testSubsetColumns 0
 testGetColObj 0
 testSubset 0

TestSpecFunc

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

TestMeanDifferenceMetaAnalysis

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

ExcelUtilTest

 testGetSheetFromFile 0.516
 testGetSet 0.002
 testSetFormula 0.008

MatrixWriterTest

 testWriteMatrixB 0.036
 testWriteMatrix 0.002
 testWrite3DMatrix 0.006

NetUtilsTest

 testFtpFileSize 1.007
 testCheckForFile 0.852
 testFtpFileSizeDoesntExist 1.429
 testDownloadFile 1.066

BatchIteratorTest

 testBatches 0.001
 testBatchIterator 0
 testConcurrentModificationException 0

RCDoubleMatrix1DTest

 testZSum 0
 testAssignAr 0
 testAssign 0

TestKSTest

 testKSTestTwoSample 0
 testKSTestOneSample 0

BitUtilTest

 testGet 0
 testSet 0
 testClear 0
 testCount 0
 testToBool 0

TestHistogramWriter

 testWriter 0

DenseDoubleMatrixTest

 testConstructFromArray 0
 testSubsetRows 0
 testToArray 0
 testSortByColumnAbsoluteValue 0.005
 testGet 0.001
 testSet 0
 testRows2 0.001
 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 0.001
 testColumns 0.001
 testGetColRange 0
 testGetByKeys 0.001
 testGetColObj 0.001
 testGetColumn 0
 testIsMissing 0.002
 testViewColumn 0
 testGetColObj2 0.001
 testGetObject 0.001
 testGetRow 0
 testGetRowObj 0.001
 testGetRowRange 0.001
 testGetRowByName 0.001
 testIsMissing2 0.001
 testGetColByNameFail 0.001
 testGetColByNameNull 0
 testGetRowObj2 0.001
 testGetColByName 0.001
 testGetRowArrayList2 0.001
 testViewRow2 0

ParamGrabberTest

 test 0

TestRowMissingFilter

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

TestMatrixStats

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

JenaUtilsTest

 testInferenceCapabilities 0.109

MetaAnalysisTest

 testFisherCombinePvaluesB 0
 testFisherCombinePvalues 0

DenseDouble3dMatrixTest

 testget 0
 testtostring 0.001
 testgetcolobj 0
 testgetrowobj 0

TestRowAffyNameFilter

 testStringFilter 0.001
 testFilter 0

StringUtilTest

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

TestItemLevelFilter

 testFilter 0

TestSparseRaggedDouble2DNamedMatrixReader

 testReadStreamAdjList 0
 testReadInputStream 0
 testReadStreamAdjListBig 1.009

CorrelationStatsTest

 testSpearmanPvalueA 0
 testSpearmanPvalueB 0
 testSpearmanPvalueD 0
 testSpearmanPvalueE 0.054
 testSpearmanPvalueF 0.001
 testSpearmanPvalueG 0.057
 testCorrelationForPvalue 0.001
 testCorrelTooSmall 0
 testInverseFisherTransform 0
 testSpearmanPvalueTDist 0.001
 testCorrel 0
 testCorrelAsByte 0.001
 testPvalue 0
 testSpearmanPvalueA2 0
 testSpearmanPvalueD2 0
 testSpearmanPvalueEh 0.001
 testSpearmanPvalueEm 0.016
 testSpearmanPvalueG2 0.001

MeanVarianceEstimatorTest

 testVoom 0.032
 testMeanVarianceNoDesignWithColsRowAllMissing 0.001
 testDuplicateRows 0.016
 testInterpolate 0
 testMeanVarianceNoDesignWithMissing 0.002

TestDirectedGraph

 testDeleteLeaf1 0
 testDeleteLeafFail 0
 testGetChildren 0
 testToString 0
 testAddChild 0
 testTopoSort 0
 testAddParent 0
 testDeleteLeafNotLeaf 0
 testAddChildFail 0
 testAddParentFail 0
 testTreeView 0.341

UniformDensityComputerTest

 testDensity 0

UberonOntologySearchTest

 testScore 0.024
 testOmitDefinition 0.017

MatrixDisplayTest

 testWriteOutAsPNG2 0.153
 testWriteOutAsPNG 0.01
 testSaveImage 0.006
 testSaveImageStandardize 0.017

ConfigUtilsTest

 testLoadConfigURL 0.099
 testGetConfigBuilderFile 0.089
 testGetConfigBuilderString 0.002
 testGetConfigBuilderURLNew 0.001
 testGetConfigBuilderStringNew 0.001
 testLoadConfigString 0.001
 testLoadConfigURLNew 0.002
 testLoadConfigStringNewName 0.005
 testGetConfigBuilderURL 0
 testLoadConfigStringNew 0.001
 testLoadConfigFile 0.001
 testGetConfigBuilderFileNew 0.002
 testLoadConfigFileNew 0.001

MatrixUtilTest

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

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

ModeratedTstatTest

 testLimmaMissing 0.169
 testFdist 0.002
 testLimma 0.053
 testSqueezeVarB 0.216
 testSqueezeVar 0
 testSqueezeVarWMissing 0.001

TestByteArrayConverter

 testDoubleArrayToByteArrayConversionSpeed 0.012
 testByteArrayToBooleans 0.005
 testStringToDoubleArrayConversionSpeed 0.007
 testByteArrayToDoubleConversionSpeed 0.01
 testByteArrayToTabbedString 0.011
 testDoubleArrayToBytes 0.008
 testIntsToBytes 0.006
 testBooleansToLongArray 0.003
 testByteArrayToSquareDoubleMatrix 0.007
 testByteArrayToDoubles 0.003
 testStringArrayToBytes 0.003
 testDoubleArrayToDelimitedStringConversionSpeed 0.014
 testStringArrayToTabbedBytes 0.01
 testObjectToBytes 0.008
 testBooleansToByteArray 0.004
 testByteArrayToLongs 0.007
 testByteArrayToDoubleMatrix 0.007

RandomChooserTest

 testChooseRandomDeck 0.017
 testRepeatSubset 0.413
 testChooserandomInts 0.014
 testChooserandomWrep 0
 testRandomSubset 0
 testChooserandomInt 0.042
 testRepeat 0.313

HistogramTest

 testGetBiggestBinSize 0
 testGetApproximateQuantile 0

TestMatrixRowStats

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

TestRowNameFilter

 testFilterString 0.001
 testFilterExclude 0
 testFilter 0
 testFilterStringExclude 0

DistanceTest

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

TestRowAbsentFilter

 testFilterKeepMarginal 0.001
 testFilterPresentCountInvalid 0
 testFilterWithMissing 0
 testFilterNullFlags 0.002
 testFilterWithMissingLessStringent 0.005
 testFilterFractionInvalid 0.005
 testFilterStringMatrix 0.005
 testFilterFraction 0.005
 testFilter 0.005

OntologyTermTest

 testGetParentsHasProperPart 0.902
 testGetChildren 1.254
 testGetChildrenHasProperPart 0.052
 testGetParents 0.406
 testRejectNonEnglish 0.614

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
 testOmitBadPredicates
com.hp.hpl.jena.shared.CannotCreateException: Failed to resolve import for http://semantic-mediawiki.org/swivt/1.0.
 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.