Surefire Report

Summary

[Summary] [Package List] [Test Cases]


Tests Errors Failures Skipped Success Rate Time
740 2 1 3 99.189% 75.804

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.io 15 0 0 0 100% 0.049
ubic.basecode.math.linalg 5 0 0 0 100% 0.015
ubic.basecode.util 73 0 0 0 100% 5.505
ubic.basecode.dataStructure.params 2 0 0 0 100% 0.111
ubic.basecode.graphics 4 0 0 0 100% 0.369
ubic.basecode.ontology.search 13 2 0 0 84.615% 39.913
ubic.basecode.io.writer 4 0 0 0 100% 0.007
ubic.basecode.ontology.ncbo 3 0 0 3 0% 0.002
ubic.basecode.math.distribution 9 0 0 0 100% 0.02
ubic.basecode.ontology.providers 5 0 1 0 80% 10.17
ubic.basecode.util.r 42 0 0 0 100% 7.139
ubic.basecode.math.linearmodels 36 0 0 0 100% 5.839
ubic.basecode.math.metaanalysis 19 0 0 0 100% 0.003
ubic.basecode.ontology.jena 2 0 0 0 100% 0.055
ubic.basecode.dataStructure.graph 11 0 0 0 100% 0.246
ubic.basecode.dataStructure.matrix 193 0 0 0 100% 0.277
ubic.basecode.math 192 0 0 0 100% 4.024
ubic.basecode.io.reader 29 0 0 0 100% 0.628
ubic.basecode.datafilter 50 0 0 0 100% 0.119
ubic.basecode.ontology 5 0 0 0 100% 1.173
ubic.basecode.dataStructure.tree 7 0 0 0 100% 0
ubic.basecode.dataStructure 18 0 0 0 100% 0.002
ubic.basecode.io.excel 3 0 0 0 100% 0.138

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 15 0 0 0 100% 0.049

ubic.basecode.math.linalg

Class Tests Errors Failures Skipped Success Rate Time
 QRDecompositionTest 5 0 0 0 100% 0.015

ubic.basecode.util

Class Tests Errors Failures Skipped Success Rate Time
 ConfigUtilsTest 13 0 0 0 100% 0.106
 FileToolsTest 32 0 0 0 100% 0.036
 PrettyPrinterTest 1 0 0 0 100% 0.001
 SQLUtilsTest 1 0 0 0 100% 0
 TestStringUtil 8 0 0 0 100% 0.006
 BatchIteratorTest 3 0 0 0 100% 0.001
 StringUtilTest 5 0 0 0 100% 0
 NetUtilsTest 4 0 0 0 100% 5.344
 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% 0.111

ubic.basecode.graphics

Class Tests Errors Failures Skipped Success Rate Time
 MatrixDisplayTest 4 0 0 0 100% 0.369

ubic.basecode.ontology.search

Class Tests Errors Failures Skipped Success Rate Time
 OntologySearchTest 13 2 0 0 84.615% 39.913

ubic.basecode.io.writer

Class Tests Errors Failures Skipped Success Rate Time
 TestHistogramWriter 1 0 0 0 100% 0.002
 MatrixWriterTest 3 0 0 0 100% 0.005

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
 UniformDensityComputerTest 1 0 0 0 100% 0
 TestWishart 1 0 0 0 100% 0.002
 HistogramSamplerTest 1 0 0 0 100% 0.016
 NormalProbabilityComputerTest 4 0 0 0 100% 0.001
 HistogramTest 2 0 0 0 100% 0.001

ubic.basecode.ontology.providers

Class Tests Errors Failures Skipped Success Rate Time
 ObiServiceTest 2 0 1 0 50% 8.176
 AbstractOntologyServiceTest 3 0 0 0 100% 1.994

ubic.basecode.util.r

Class Tests Errors Failures Skipped Success Rate Time
 JRIClientTest 21 0 0 0 100% 0.002
 RServeClientTest 21 0 0 0 100% 7.137

ubic.basecode.math.linearmodels

Class Tests Errors Failures Skipped Success Rate Time
 MeanVarianceEstimatorTest 5 0 0 0 100% 0.045
 LeastSquaresFitTest 20 0 0 0 100% 5.658
 ModeratedTstatTest 6 0 0 0 100% 0.131
 DesignMatrixTest 5 0 0 0 100% 0.005

ubic.basecode.math.metaanalysis

Class Tests Errors Failures Skipped Success Rate Time
 TestCorrelationEffectMetaAnalysis 9 0 0 0 100% 0.002
 MetaAnalysisTest 2 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% 0.055

ubic.basecode.dataStructure.graph

Class Tests Errors Failures Skipped Success Rate Time
 TestDirectedGraph 11 0 0 0 100% 0.246

ubic.basecode.dataStructure.matrix

Class Tests Errors Failures Skipped Success Rate Time
 CompressedSparseDoubleMatrixTest 38 0 0 0 100% 0.108
 DenseDoubleMatrixTest 39 0 0 0 100% 0.061
 CompressedNamedBitMatrixTest 9 0 0 0 100% 0.003
 FastRowAccessDoubleMatrixTest 39 0 0 0 100% 0.042
 DenseDouble3dMatrixTest 4 0 0 0 100% 0.003
 StringMatrixTest 4 0 0 0 100% 0.004
 MatrixUtilTest 7 0 0 0 100% 0.023
 SparseRaggedDoubleMatrixTest 10 0 0 0 100% 0.016
 RCDoubleMatrix1DTest 3 0 0 0 100% 0
 SparseDoubleMatrixTest 24 0 0 0 100% 0.011
 IntegerMatrixTest 16 0 0 0 100% 0.006

ubic.basecode.math

Class Tests Errors Failures Skipped Success Rate Time
 TestSpecFunc 7 0 0 0 100% 0.001
 TestDescriptiveWithMissing 44 0 0 0 100% 0.002
 TestRank 14 0 0 0 100% 0.003
 RandomChooserTest 7 0 0 0 100% 0.497
 TestMatrixStats 15 0 0 0 100% 0.02
 StringDistanceTest 16 0 0 0 100% 0.003
 TestKSTest 2 0 0 0 100% 0
 TestROC 3 0 0 0 100% 0.03
 TestWilcoxon 15 0 0 0 100% 3.256
 TestMatrixNormalizer 2 0 0 0 100% 0.001
 TestStats 14 0 0 0 100% 0
 TestMathUtil 5 0 0 0 100% 0
 KruskalWallisTest 1 0 0 0 100% 0.001
 TestMatrixRowStats 6 0 0 0 100% 0.001
 SingularValueDecompositionTest 1 0 0 0 100% 0.102
 CorrelationStatsTest 18 0 0 0 100% 0.059
 PrecisionRecallTest 5 0 0 0 100% 0
 MultipleTestCorrectionTest 5 0 0 0 100% 0.048
 DistanceTest 12 0 0 0 100% 0

ubic.basecode.io.reader

Class Tests Errors Failures Skipped Success Rate Time
 TestSparseRaggedDouble2DNamedMatrixReader 3 0 0 0 100% 0.577
 TestDoubleMatrixReader 15 0 0 0 100% 0.042
 TestSparseDoubleMatrixReader 2 0 0 0 100% 0.005
 TestMapReader 3 0 0 0 100% 0
 TestStringMatrixReader 4 0 0 0 100% 0.001
 HistogramReaderTest 2 0 0 0 100% 0.003

ubic.basecode.datafilter

Class Tests Errors Failures Skipped Success Rate Time
 TestRowNameFilter 4 0 0 0 100% 0.012
 TestRowAffyNameFilter 2 0 0 0 100% 0.005
 TestRowAbsentFilter 9 0 0 0 100% 0.016
 TestRowMissingFilter 11 0 0 0 100% 0.012
 TestRowLevelFilter 23 0 0 0 100% 0.074
 TestItemLevelFilter 1 0 0 0 100% 0

ubic.basecode.ontology

Class Tests Errors Failures Skipped Success Rate Time
 OntologyTermTest 5 0 0 0 100% 1.173

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
 DoubleAddingMapTest 1 0 0 0 100% 0
 CountingMapTest 6 0 0 0 100% 0.001
 BitUtilTest 5 0 0 0 100% 0

ubic.basecode.io.excel

Class Tests Errors Failures Skipped Success Rate Time
 ExcelUtilTest 3 0 0 0 100% 0.138

Test Cases

[Summary] [Package List] [Test Cases]

JRIClientTest

 testExec 0
 testListEvalA 0
 testListEvalB 0
 testExecError 0
 testDataFrameA 0
 testAssignAndRetrieveMatrix 0
 testAnovaA 0
 testAnovaB 0
 testAnovaC 0
 testAnovaD 0
 testAnovaE 0
 testAnovaF 0
 testLimmaA 0
 testExecDoubleArray 0.001
 testAssignAndRetrieveMatrixB 0
 testAssignAndRetrieveMatrixD 0
 testLinearModelA 0
 testLinearModelB 0
 testLinearModelC 0
 testLinearModelD 0
 testStringListEvalB 0

RServeClientTest

 testExec 0.93
 testListEvalA 0.306
 testListEvalB 0.313
 testExecError 0.316
 testDataFrameA 0.306
 testAssignAndRetrieveMatrix 0.303
 testAnovaA 0.309
 testAnovaB 0.31
 testAnovaC 0.31
 testAnovaD 0.31
 testAnovaE 0.306
 testAnovaF 0.309
 testLimmaA 0.309
 testExecDoubleArray 0.304
 testAssignAndRetrieveMatrixB 0.305
 testAssignAndRetrieveMatrixD 0.307
 testLinearModelA 0.308
 testLinearModelB 0.307
 testLinearModelC 0.308
 testLinearModelD 0.306
 testStringListEvalB 0.308

ConfigUtilsTest

 testLoadConfigURL 0.046
 testGetConfigBuilderFile 0.045
 testGetConfigBuilderString 0.001
 testGetConfigBuilderURLNew 0.001
 testGetConfigBuilderStringNew 0.001
 testLoadConfigString 0.001
 testLoadConfigURLNew 0.001
 testLoadConfigStringNewName 0.005
 testGetConfigBuilderURL 0.001
 testLoadConfigStringNew 0.001
 testLoadConfigFile 0.001
 testGetConfigBuilderFileNew 0.001
 testLoadConfigFileNew 0

FileToolsTest

 testHasImageExtension 0.002
 testTestDir 0
 testGetWithoutExtension 0.001
 testGetLines 0.001
 testTouch 0
 testListDirectoryFiles 0.002
 testAddImageExtension 0.001
 testChangeExtension 0
 testDeleteFilesAndDir 0.002
 testCleanFileName 0.001
 testgetStringListFromFile 0.001
 testGetWithoutExtensionB 0.001
 testGetWithoutExtensionC 0
 testResourcetoPath 0.001
 testCleanFileNameErr 0.001
 testIsGZipped 0.001
 testUnGzipFile 0.002
 testCopyFileFailOnDirectoryOutput 0
 testTestFileString 0.001
 testGetCompressedFile 0.001
 testCopyFile 0.001
 testGetExtension 0
 testCheckPathIsReadableFile 0.001
 testIsZipped 0
 testAddDataExtension 0.001
 testGetCompressedFileZip 0.002
 testTestFileFile 0
 testCheckPathIsReadableFileNot 0.001
 testCopyFileFailOnDirectoryInput 0.001
 testGetInputStreamFromPlainOrCompressedFile 0
 testHasXMLExtension 0.001
 testUnzipFile 0.008

PrettyPrinterTest

 testPrintBeans 0

SQLUtilsTest

 testBlobToString 0

TestStringUtil

 testTwoStringHashKey 0
 testCsvSplitA 0.004
 testCsvSplitB 0
 testCsvSplitC 0
 testCsvSplitD 0.001
 testCsvSplitE 0
 testCsvSplitF 0
 testTwoStringHashKeyB 0

BatchIteratorTest

 testBatches 0
 testBatchIterator 0
 testConcurrentModificationException 0

StringUtilTest

 testMakeRnames 0
 testCommonPrefixNone 0
 testCommonSuffixNone 0
 testCommonPrefix 0
 testCommonSuffix 0

NetUtilsTest

 testFtpFileSize 1.469
 testCheckForFile 0.906
 testFtpFileSizeDoesntExist 1.729
 testDownloadFile 1.24

DateUtilTest

 testgetRelative5yearsFromnow 0.004
 testRange 0.002
 testgetRelative5yearsago 0
 testgetRelativeTomorrow 0.001
 testgetRelativeDateDayago 0
 testRangeBad 0.001

TestDirectedGraph

 testDeleteLeaf1 0.002
 testDeleteLeafFail 0.001
 testGetChildren 0
 testToString 0
 testAddChild 0
 testTopoSort 0
 testAddParent 0.001
 testDeleteLeafNotLeaf 0
 testAddChildFail 0
 testAddParentFail 0
 testTreeView 0.24

CompressedSparseDoubleMatrixTest

 testSubsetRows 0.01
 testToArray 0.003
 testSortByColumnAbsoluteValue 0.021
 testGet 0.002
 testSet 0.003
 testRows2 0.002
 testCopy 0.003
 testGet2 0.002
 testRows 0.002
 testSet2 0.002
 testSize 0.002
 testToString 0.002
 testGetRowByNameFail 0.001
 testGetRowByNameNull 0.002
 testSetIntIntObject 0.002
 testGetRow2 0.002
 testSubsetColumns 0.004
 testViewRow 0.003
 testColumns 0.001
 testGetColRange 0.002
 testGetByKeys 0.001
 testGetColObj 0.002
 testGetColumn 0.001
 testIsMissing 0.004
 testViewColumn 0.002
 testGetColObj2 0.002
 testGetObject 0.002
 testGetRow 0.002
 testGetRowObj 0.001
 testGetRowRange 0.002
 testGetRowByName 0.002
 testIsMissing2 0.001
 testGetColByNameFail 0.002
 testGetColByNameNull 0.003
 testGetRowObj2 0.002
 testGetColByName 0.002
 testGetRowArrayList2 0.002
 testViewRow2 0.002

DenseDoubleMatrixTest

 testConstructFromArray 0.002
 testSubsetRows 0.002
 testToArray 0.001
 testSortByColumnAbsoluteValue 0.007
 testGet 0.002
 testSet 0.001
 testRows2 0.001
 testCopy 0.002
 testGet2 0.002
 testRows 0.001
 testSet2 0.001
 testSize 0.002
 testToString 0.002
 testGetRowByNameFail 0.001
 testGetRowByNameNull 0.002
 testSetIntIntObject 0.002
 testGetRow2 0.001
 testSubsetColumns 0.001
 testViewRow 0.001
 testColumns 0.002
 testGetColRange 0.001
 testGetByKeys 0.001
 testGetColObj 0.001
 testGetColumn 0.002
 testIsMissing 0.002
 testViewColumn 0.002
 testGetColObj2 0.001
 testGetObject 0.001
 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 0.002

CompressedNamedBitMatrixTest

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

FastRowAccessDoubleMatrixTest

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

DenseDouble3dMatrixTest

 testget 0.002
 testtostring 0.001
 testgetcolobj 0
 testgetrowobj 0

StringMatrixTest

 testToString 0.001
 testSubsetColumns 0.001
 testGetColObj 0.001
 testSubset 0.001

MatrixUtilTest

 testSelectColumnsAndRowsBad 0.003
 testSelectColumns 0.002
 testDropColumn 0.002
 testSelectColumnsAndRows 0.01
 testRemoveMissing1 0.002
 testRemoveMissing2 0.002
 testSelectRows 0.002

SparseRaggedDoubleMatrixTest

 testSubsetRows 0.011
 testSubsetRowsFail 0
 testRows 0.001
 testGetRowMatrix1D 0.001
 testGetRowArrayList 0
 testColumns 0.001
 testGetColRange 0
 testAddrow 0.001
 testGetRow 0
 testGetRowRange 0

RCDoubleMatrix1DTest

 testZSum 0
 testAssignAr 0
 testAssign 0

SparseDoubleMatrixTest

 testSubsetCols 0.003
 testSubsetRows 0.001
 testToArray 0.001
 testGet 0
 testSet 0
 testCopy 0.001
 testRows 0
 testSize 0
 testToString 0.001
 testGetRowArrayList 0
 testViewRow 0
 testColumns 0.001
 testGetColRange 0
 testGetByKeys 0
 testGetColObj 0.001
 testGetColumn 0.001
 testIsMissing 0
 testViewColumn 0
 testGetObject 0
 testGetRow 0
 testGetRowObj 0.001
 testGetRowRange 0
 testGetRowByName 0
 testGetColByName 0

IntegerMatrixTest

 testGetEntry 0.003
 testGet 0
 testSet 0
 testRows 0
 testSize 0
 testColumns 0.001
 testSetByKeys 0
 testToInteger 0
 testGetByKeys 0
 testGetColObj 0
 testGetColumn 0.001
 testIsMissing 0
 testGetObject 0
 testGetRow 0
 testGetRowObj 0
 testSetObj 0.001

ParamGrabberTest

 test 0

ParameterKeeperTest

 test 0.111

BinaryTreeTest

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

StringToStringSetMapTest

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

DoubleAddingMapTest

 test 0

CountingMapTest

 testSummation 0
 testCount 0
 testSeen 0
 testIncrement 0
 testSortedKeyList 0.001
 testSortedKeyListBoolean 0

BitUtilTest

 testGet 0
 testSet 0
 testClear 0
 testCount 0
 testToBool 0

TestRowNameFilter

 testFilterString 0.002
 testFilterExclude 0.004
 testFilter 0.003
 testFilterStringExclude 0.003

TestRowAffyNameFilter

 testStringFilter 0.002
 testFilter 0.003

TestRowAbsentFilter

 testFilterKeepMarginal 0.003
 testFilterPresentCountInvalid 0.001
 testFilterWithMissing 0.002
 testFilterNullFlags 0.001
 testFilterWithMissingLessStringent 0.002
 testFilterFractionInvalid 0.001
 testFilterStringMatrix 0.002
 testFilterFraction 0.002
 testFilter 0.002

TestRowMissingFilter

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

TestRowLevelFilter

 testFilterMinHigh 0.004
 testFilterFractionMaxRemoveHighAndLowBothFraction 0.003
 testFilterMaxTooHigh 0.004
 testFilterMedian 0.005
 testFilterNoFilter 0.002
 testFilterFractionMaxRemoveHighAndLowBothLevelsNegLow 0.003
 testFilterFractionMaxRemoveNegHigh 0.003
 testFilterMax 0.002
 testFilterMin 0.003
 testFilterMaxFractionNoneRemoveNeg 0.003
 testFilterMedianHigh 0.003
 testFilterFractionMaxRemoveHighAndLowBothLevelsNoNegRemove 0.002
 testFilterFractionMaxRemoveNeg 0.002
 testFilterMaxFractionAll 0.003
 testFilterFractionMaxRemoveHighAndLowBothLevels 0.002
 testFilterMaxFraction 0.002
 testFilterBadFraction 0.002
 testFilterMaxFractionHigh 0.002
 testFilterMaxFractionNone 0.003
 testFilterFractionMaxRemoveHighAndLow 0.002
 testFilterMeanHigh 0.013
 testFilterMean 0.002
 testFilterMaxHigh 0.002

TestItemLevelFilter

 testFilter 0

MatrixDisplayTest

 testWriteOutAsPNG2 0.348
 testWriteOutAsPNG 0.006
 testSaveImage 0.004
 testSaveImageStandardize 0.011

ExcelUtilTest

 testGetSheetFromFile 0.136
 testGetSet 0
 testSetFormula 0.002

TestSparseRaggedDouble2DNamedMatrixReader

 testReadStreamAdjList 0.001
 testReadInputStream 0.001
 testReadStreamAdjListBig 0.575

TestDoubleMatrixReader

 testReadChooseRowsBadfileName 0.001
 testReadInputStreamMissingBad 0
 testReadInputStreamGotColNameSkipColumn 0.001
 testReadInputStreamRowCount 0
 testReadInputStreamGotColName 0.001
 testReadInputStreamGotRowName 0
 testSmallNumbers 0.025
 testReadInputStreamMissingSpaces 0.008
 testReadBad 0.001
 testBadFileName 0
 testReadChooseRowsSkipcols 0
 testReadBlankCorner 0.002
 testReadInputStreamMissing 0.001
 testReadChooseRows 0
 testReadInputStreamColumnCount 0.001

TestSparseDoubleMatrixReader

 testReadStream 0
 testReadJW 0.005

TestMapReader

 testRead 0
 testReadNoHeader 0
 testReadNoHeaderFile 0

TestStringMatrixReader

 testReadInputStreamRowCount 0
 testReadInputStreamGotColName 0.001
 testReadInputStreamGotRowName 0
 testReadInputStreamColumnCount 0

HistogramReaderTest

 testHistogramReaderIs 0.003
 testHistogramReaderString 0

TestHistogramWriter

 testWriter 0.002

MatrixWriterTest

 testWriteMatrixB 0.003
 testWriteMatrix 0.001
 testWrite3DMatrix 0.001

TestByteArrayConverter

 testDoubleArrayToByteArrayConversionSpeed 0.004
 testByteArrayToBooleans 0.003
 testStringToDoubleArrayConversionSpeed 0.004
 testByteArrayToDoubleConversionSpeed 0.004
 testByteArrayToTabbedString 0.003
 testDoubleArrayToBytes 0.003
 testIntsToBytes 0.003
 testBooleansToLongArray 0.002
 testByteArrayToDoubles 0.002
 testStringToBytes 0.004
 testDoubleArrayToDelimitedStringConversionSpeed 0.004
 testObjectToBytes 0.003
 testBooleansToByteArray 0.005
 testByteArrayToLongs 0.002
 testByteArrayToDoubleMatrix 0.003

UniformDensityComputerTest

 testDensity 0

TestWishart

 testNextDoubleMatrix 0.002

HistogramSamplerTest

 testNextSample 0.016

NormalProbabilityComputerTest

 testProbabilityDoubleBoolean 0.001
 testProbabilityDoubleBooleanLower 0
 testInvalidVariance 0
 testProbabilityDouble 0

HistogramTest

 testGetBiggestBinSize 0.001
 testGetApproximateQuantile 0

QRDecompositionTest

 testScaledDesign 0.006
 testSingular2 0.002
 test1 0.004
 test3 0.002
 test2NoPivoting 0.001

MeanVarianceEstimatorTest

 testVoom 0.033
 testMeanVarianceNoDesignWithColsRowAllMissing 0
 testDuplicateRows 0.011
 testInterpolate 0
 testMeanVarianceNoDesignWithMissing 0.001

LeastSquaresFitTest

 testTwoWayAnovaUnfittable 0.019
 testThreeWaySingular 0.092
 testEstrogen 2.426
 testVectorWeightedRegress 0
 testNHBE 3.031
 testLSFTwoLevels2 0.019
 testLSFTwoLevels3 0.014
 testSingular2 0.003
 testVectorWeightedRegressWithMissing 0.001
 testVectorRegress 0
 testLSFThreeLevelsOneContinuousWithMissing3 0.002
 testTwoWayAnovaWithInteractions 0.002
 testLSFTwoLevels 0.002
 testOneWayAnova 0.01
 testTwoWayTwoLevelsOneContinousInteractionC 0.003
 testLSFThreeLevelsOnecontinous2 0.001
 testMatrixWeightedRegress 0
 testSingular 0.007
 testLSFTwoLevelsOneContinuous 0.021
 testLSFOneContinuousWithMissing3 0.005

ModeratedTstatTest

 testLimmaMissing 0.021
 testFdist 0
 testLimma 0.015
 testSqueezeVarB 0.094
 testSqueezeVar 0.001
 testSqueezeVarWMissing 0

DesignMatrixTest

 testInteractionC 0.001
 test2 0.001
 testA 0
 testB 0.001
 testInteractionAndRelevel 0.002

TestCorrelationEffectMetaAnalysis

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

MetaAnalysisTest

 testFisherCombinePvaluesB 0.001
 testFisherCombinePvalues 0

TestMeanDifferenceMetaAnalysis

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

TestSpecFunc

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

TestDescriptiveWithMissing

 testRankInterpolated 0
 testKurtosis 0
 testCorrelationA 0
 testCorrelationB 0
 testQuantileInverse 0
 testStandardize 0
 testIncrementalWeightedUpdate 0
 testSumOfPowerDeviationsA 0
 testOptimizedCorrelation 0
 testMad 0
 testMax 0
 testMin 0
 testSum 0
 testMeanDoubleArB 0
 testSumOfInversions 0
 testLag1 0.001
 testMean 0
 testSkew 0
 testDurbinWatson 0
 testMeanAboveQuantile 0
 testSumOfSquares 0
 testProduct 0
 testGeometricMean 0
 testMeanDoubleAr 0
 testSampleSkew 0
 testQuantile 0
 testVariance 0
 testQuantiles 0
 testSampleKurtosis 0
 testDurbinWatsonTwo 0
 testKurtosisList 0.001
 testSumOfSquaredDeviations 0
 testSampleStandardDeviation 0
 testMeanEff 0
 testSumOfPowers 0
 testSampleVariance 0
 testWeightedMean 0
 testCovariance 0
 testIncrementalUpdate 0
 testMedian 0
 testTrimmedMean 0
 testIncrementalUpdateSums 0
 testDurbinWatsonShort 0
 testAutoCorrelation 0

TestRank

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

RandomChooserTest

 testChooseRandomDeck 0.021
 testRepeatSubset 0.238
 testChooserandomInts 0.008
 testChooserandomWrep 0.001
 testRandomSubset 0
 testChooserandomInt 0.03
 testRepeat 0.199

TestMatrixStats

 testRbfNormalize 0.001
 testSelfSquare 0
 testStandardize 0.002
 testCorrelationMatrix 0.002
 testMax 0
 testMin 0.001
 testNan 0
 testColSumsWithMissing 0
 testLogTransform 0.001
 testDoubleStandardize 0.005
 testCov2Cor 0.002
 testConvertToLog2Cpm 0.001
 testConvertLog 0.001
 testCountsPerMillionWithMissing 0
 testCorrelationMatrixThreshold 0.004

StringDistanceTest

 testWeightedHammingA 0
 testWeightedHammingB 0
 testWeightedHammingC 0
 testHammingDistance 0
 testBadMatch 0.002
 testEditDistanceA 0
 testEditDistanceB 0
 testEditDistanceC 0
 testEditDistanceD 0
 testEditDistanceE 0
 testEditDistanceF 0
 testEditDistanceG 0
 testEditDistanceH 0
 testWeightedSuffixHammingA 0
 testWeightedSuffixHammingB 0
 testWeightedSuffixHammingC 0.001

TestKSTest

 testKSTestTwoSample 0
 testKSTestOneSample 0

TestROC

 testBig 0.028
 testAroc 0
 testArocPvalue 0.002

TestWilcoxon

 testWilxcoxonPExactB 0
 testWilxcoxonPExactC 0
 testWilxcoxonPExactD 3.246
 testWilxcoxonPGaussB 0
 testBGaussian 0
 testFVolume 0.001
 testWilxcoxonPVolume 0.003
 testBig 0
 testWilxcoxonPGauss 0
 testWilcoxonPExactA 0
 testCGaussian 0
 testDVolume 0.001
 testAExact 0.003
 testWilxcoxonPWithTies 0
 testEVolume 0

TestMatrixNormalizer

 testQuantileNormalize 0
 testQuantileNormalizeWithMissing 0.001

TestStats

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

TestMathUtil

 testMax 0
 testSumArray 0
 testFillRangeDown 0
 testFillRange 0
 testFillRangeNo 0

KruskalWallisTest

 testKW 0

TestMatrixRowStats

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

SingularValueDecompositionTest

 testSingularValueDecomposition 0.102

CorrelationStatsTest

 testSpearmanPvalueA 0
 testSpearmanPvalueB 0
 testSpearmanPvalueD 0
 testSpearmanPvalueE 0.035
 testSpearmanPvalueF 0
 testSpearmanPvalueG 0.018
 testCorrelationForPvalue 0
 testCorrelTooSmall 0
 testInverseFisherTransform 0
 testSpearmanPvalueTDist 0
 testCorrel 0
 testCorrelAsByte 0
 testPvalue 0
 testSpearmanPvalueA2 0
 testSpearmanPvalueD2 0
 testSpearmanPvalueEh 0.001
 testSpearmanPvalueEm 0.005
 testSpearmanPvalueG2 0

PrecisionRecallTest

 testAveragePrecisionB 0
 testAveragePrecisionWithTie 0
 testAveragePrecisionNotInOrder 0
 testAveragePrecision 0
 testAveragePrecisionBNotInOrder 0

MultipleTestCorrectionTest

 testBenjaminiYekuteliCut 0.008
 testBenjaminiHochbergCut 0.008
 testBenjaminiHochberg 0.011
 testBenjaminiHochbergM 0.011
 testBonferroniCut 0.01

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

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.

OntologySearchTest

 testPersistence
+ [ Detail ]
 0.49
org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.645
 testOmitDefinitions2 0.023
 testOmitDefinitions3 0.017
 testOmitDefinitions4 0.719
 testScore 0.015
 testOmitBadPredicates2 0.02
 testOmitBadPredicates 0.018
 testOmitDefinition 0.005
 testIndexing
+ [ Detail ]
 0.15
org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.002
 matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException 0.003
 testOmitDefinitions 0.019

OntologyLoaderTest

 testCacheOntologyToDisk 0.049
 testHasChanged 0.004

OntologyTermTest

 testGetParentsHasProperPart 0.034
 testGetChildren 0.578
 testGetChildrenHasProperPart 0.012
 testGetParents 0.219
 testRejectNonEnglish 0.325

ObiServiceTest

 testLoadAndSearch
+ [ Detail ]
 7.908
 testWithoutCache 0.229

AbstractOntologyServiceTest

 testInitializeInBackgroundThread 0.001
 testCacheOntologyToDisk 1.951
 testGenericOntologyServiceMem 0.036

Failure Details

[Summary] [Package List] [Test Cases]


 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.
 testPersistence
com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
 testIndexing
com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException; systemId: http://purl.org/dc/elements/1.1/; lineNumber: 9; columnNumber: 3; The element type "p" must be terminated by the matching end-tag "</p>".
 testLoadAndSearch
java.lang.AssertionError