CRAN Package Check Results for Maintainer ‘Henrik Bengtsson <henrikb at braju.com>’

Last updated on 2015-02-05 23:50:56.

Package ERROR WARN NOTE OK
ACNE 13 2
aroma.affymetrix 15
aroma.apd 14 1
aroma.cn 14 1
aroma.core 15
calmate 13 2
matrixStats 15
PSCBS 5 10
R.cache 15
R.devices 6 9
R.filesets 8 7
R.huge 5 10
R.matlab 6 9
R.methodsS3 15
R.oo 6 9
R.rsp 13 2
R.utils 6 9

Package ACNE

Current CRAN status: NOTE: 13, OK: 2

Version: 0.7.0
Check: R code for possible problems
Result: NOTE
    .onAttach: no visible global function definition for ‘startupMessage’
    NmfPlm: no visible binding for global variable ‘Arguments’
    doACNE.AffymetrixCelSet: no visible binding for global variable
     ‘Arguments’
    doACNE.AffymetrixCelSet: no visible global function definition for
     ‘process’
    doACNE.AffymetrixCelSet: no visible global function definition for
     ‘findUnitsTodo’
    doACNE.AffymetrixCelSet: no visible global function definition for
     ‘fit’
    doACNE.default: no visible binding for global variable ‘Arguments’
    doACNE.default: no visible binding for global variable
     ‘AffymetrixCelSet’
    plot.SnpNmfFit: no visible binding for global variable ‘fit’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Package aroma.affymetrix

Current CRAN status: NOTE: 15

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘dChipIO’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.13.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     addColorMap.ArrayExplorer addColorMap.SpatialReporter
     addExclCells.DChipQuantileNormalization
     allocate.AromaCellMatchScoreFile allocate.CrlmmParametersFile
     allocateFromCdf.AffymetrixCelFile allocateFromCdf.AromaCellCpgFile
     allocateFromCdf.AromaCellMatchScoreFile
     allocateFromCdf.AromaCellPositionFile
     allocateFromCdf.AromaCellSequenceFile allocateFromCdf.AromaUfcFile
     allocateFromCdf.AromaUflFile allocateFromCdf.AromaUnitGcContentFile
     allocateFromCdf.AromaUnitTabularBinaryFile
     annotateMvsA.AffymetrixCelFile append.AffymetrixCelSet
     append.CnagCfhSet applyAnyOrder.CopyNumberChromosomalModel
     applyCCF0.CopyNumberChromosomalModel
     applyCFC0.CopyNumberChromosomalModel
     applyToUnitIntensities.AffymetrixCelSet
     as.AffymetrixCelSet.AffymetrixCelSet as.AffymetrixCelSet.default
     as.AffymetrixCelSet.list as.AffymetrixCnChpSet.AffymetrixCnChpSet
     as.AffymetrixCnChpSet.default as.AffymetrixCnChpSet.list
     as.AffymetrixFileSet.AffymetrixFileSet as.AffymetrixFileSet.default
     as.AffymetrixFileSet.list as.ChipEffectSetTuple.ChipEffectSetTuple
     as.ChipEffectSetTuple.default
     as.CnChipEffectSetTuple.CnChipEffectSetTuple
     as.CnChipEffectSetTuple.default as.CnagCfhSet.CnagCfhSet
     as.CnagCfhSet.default as.CnagCfhSet.list
     as.CopyNumberDataSetTuple.CnChipEffectSet as.DChipDcpSet.DChipDcpSet
     as.DChipDcpSet.default as.DChipDcpSet.list
     as.character.AffymetrixCdfFile as.character.AffymetrixCelFile
     as.character.AffymetrixCelSet as.character.AffymetrixCelSetReporter
     as.character.AffymetrixCnChpFile as.character.AffymetrixCnChpSet
     as.character.AffymetrixPgfFile as.character.AffymetrixProbeTabFile
     as.character.AromaChipTypeAnnotationFile as.character.ArrayExplorer
     as.character.ChipEffectFile as.character.ChipEffectSet
     as.character.CnagCfhFile as.character.CnagCfhSet
     as.character.DChipCdfBinFile as.character.DChipDcpFile
     as.character.DChipDcpSet as.character.DChipQuantileNormalization
     as.character.FirmaModel as.character.GenericReporter
     as.character.GenomeInformation as.character.Model
     as.character.ProbeAffinityFile as.character.QualityAssessmentModel
     as.character.ResidualFile as.character.ResidualSet
     as.character.SmoothMultiarrayModel as.character.SnpInformation
     as.character.SpatialReporter as.character.TransformReport
     as.character.WeightsFile as.character.WeightsSet
     assertAnnotationData.ASCRMAv2 averageQuantile.AffymetrixCelSet
     bgAdjustGcrma.AffymetrixCelFile bgAdjustGcrma.AffymetrixCelSet
     bgAdjustOptical.AffymetrixCelFile bgAdjustRma.AffymetrixCelFile
     boxplotStats.ChipEffectSet bpmapCluster2Cdf.default
     byChipType.AffymetrixCsvGenomeInformation
     byChipType.AffymetrixProbeTabFile byChipType.AffymetrixTabularFile
     byChipType.AffymetrixTsvFile byChipType.AromaCellMatchScoreFile
     byChipType.AromaChipTypeAnnotationFile byChipType.DChipCdfBinFile
     byChipType.DChipGenomeInformation byChipType.DChipSnpInformation
     byChipType.GenomeInformation byChipType.SnpInformation
     byChipType.UflSnpInformation byChipType.UgpGenomeInformation
     byName.AffymetrixCelSet byName.AffymetrixCnChpSet
     byName.AromaChipTypeAnnotationFile byName.CnagCfhSet
     byName.CrlmmParametersSet byName.DChipDcpSet byPath.AffymetrixCelSet
     byPath.AffymetrixCelSetTuple byPath.AffymetrixCnChpSet
     byPath.AffymetrixFileSet byPath.ChipEffectSet byPath.CnChipEffectSet
     byPath.CnagCfhSet byPath.CrlmmParametersSet byPath.DChipDcpSet
     byPath.ExonChipEffectSet byPath.FirmaSet byPath.ResidualSet
     byPath.SnpChipEffectSet byPath.WeightsSet
     calcRawCnStats.CopyNumberChromosomalModel calcRawCnStats.default
     calculateAffinities.GcRmaBackgroundCorrection
     calculateAverages.FragmentEquivalentClassNormalization
     calculateBaseline.ChipEffectSet calculateConfidenceScores.CrlmmModel
     calculateFieldBoxplotStats.ChipEffectSet
     calculateMargins.SpatialReporter
     calculateNuseBoxplotStats.ChipEffectSet
     calculateParametersGsb.AffymetrixCelSet
     calculateResidualSet.FirmaModel calculateResidualSet.ProbeLevelModel
     calculateResiduals.FirmaModel calculateResiduals.ProbeLevelModel
     calculateRleBoxplotStats.ChipEffectSet
     calculateTargetDistribution.QuantileNormalization
     calculateWeights.ExonRmaPlm calculateWeights.FirmaModel
     calculateWeights.ProbeLevelModel
     calibrateOne.ReseqCrosstalkCalibration clearCache.AffymetrixCelSet
     clearData.AffymetrixCelFile clone.AffymetrixCelFile
     clone.AffymetrixCelSet clone.AffymetrixCnChpFile clone.CnagCfhFile
     clone.CnagCfhSet compare.AffymetrixCdfFile
     computeAffinities.AffymetrixCdfFile
     computeAffinitiesByACS.AffymetrixCdfFile convert.AffymetrixCdfFile
     convertToUnique.AffymetrixCelSet convertUnits.AffymetrixCdfFile
     createExonByTranscriptCdf.AffymetrixCdfFile
     createFrom.AffymetrixCelFile createMonocellCdf.AffymetrixCdfFile
     createOutputTuple.SmoothMultiarrayModel createParamCdf.ChipEffectFile
     createParamCdf.FirmaFile createUniqueCdf.AffymetrixCdfFile
     decode.ParameterCelFile dim.DChipDcpFile encode.ParameterCelFile
     excludeChrXFromFit.DChipQuantileNormalization
     exportAromaSignalBinaryFileList.CnChipEffectFile
     exportTotalAndFracB.CnChipEffectFile
     exportTotalAndFracB.CnChipEffectSet exportTotalAndFracB.DChipDcpSet
     exportTotalAndFracB.SnpChipEffectFile
     exportTotalAndFracB.SnpChipEffectSet
     exportTotalCnRatioSet.AffymetrixCnChpSet
     extractAffyBatch.AffymetrixCelSet extractAffyBatch.ChipEffectSet
     extractAlleleSet.SnpChipEffectSet extractCNT.SnpChipEffectFile
     extractCNT.SnpChipEffectSet
     extractChromosomalDataFrame.ChipEffectFile
     extractChromosomalDataFrame.ChipEffectSet
     extractDataFrame.ParameterCelFile extractDataFrame.ParameterCelSet
     extractExpressionSet.ChipEffectSet extractFeatureSet.AffymetrixCelSet
     extractLogRatios.AffymetrixCnChpFile
     extractLogRatios.AffymetrixCnChpSet extractMatrix.AffymetrixCelFile
     extractMatrix.AffymetrixCelSet extractMatrix.ChipEffectFile
     extractMatrix.ChipEffectSet extractMatrix.FirmaFile
     extractMatrix.FirmaSet extractMatrix.ParameterCelFile
     extractMatrix.ParameterCelSet extractSnpCnvQSet.SnpChipEffectSet
     extractSnpFeatureSet.AffymetrixCelSet extractSnpQSet.SnpChipEffectSet
     extractTheta.ChipEffectFile extractTheta.ChipEffectSet
     extractTheta.CnChipEffectFile extractTheta.CnChipEffectSet
     extractTheta.DChipDcpFile extractTheta.DChipDcpSet
     extractTheta.SnpChipEffectFile extractTheta.SnpChipEffectSet
     extractTheta.SnpCnvQSet extractTheta.SnpQSet
     extractTotalAndFracB.SnpChipEffectFile
     extractTotalAndFreqB.CnChipEffectFile
     extractTotalAndFreqB.CnChipEffectSet
     extractTotalAndFreqB.SnpChipEffectSet extractTotalAndFreqB.default
     findByCdf2.default findByChipType.AffymetrixCdfFile
     findByChipType.AffymetrixCsvFile
     findByChipType.AffymetrixCsvGenomeInformation
     findByChipType.AffymetrixNetAffxCsvFile
     findByChipType.AffymetrixPgfFile
     findByChipType.AffymetrixProbeTabFile
     findByChipType.AffymetrixTabularFile findByChipType.AffymetrixTsvFile
     findByChipType.AromaChipTypeAnnotationFile
     findByChipType.DChipCdfBinFile findByChipType.DChipGenomeInformation
     findByChipType.DChipSnpInformation findByChipType.UflSnpInformation
     findByChipType.UgpGenomeInformation findByName.AffymetrixCelSet
     findByName.AffymetrixCnChpSet findByName.ChipEffectSet
     findByName.CnagCfhSet findByName.DChipDcpSet
     findTargetDistributionFile.QuantileNormalization
     findUnitsTodo.AlleleSummation findUnitsTodo.ChipEffectFile
     findUnitsTodo.ChipEffectSet findUnitsTodo.CrlmmModel
     findUnitsTodo.CrlmmParametersFile findUnitsTodo.CrlmmParametersSet
     findUnitsTodo.ExonChipEffectSet findUnitsTodo.FirmaFile
     findUnitsTodo.FirmaModel findUnitsTodo.FirmaSet
     findUnitsTodo.ProbeLevelModel findUnitsTodo.QualityAssessmentFile
     findUnitsTodo.ResidualFile findUnitsTodo.ResidualSet
     findUnitsTodo.UnitModel findUnitsTodo.WeightsFile
     findUnitsTodo.WeightsSet fit.CrlmmModel fit.FirmaModel fit.Model
     fit.ProbeLevelModel fit.SingleArrayUnitModel
     fit.SmoothMultiarrayModel fitCnProbes.UnitModel
     fitOne.AbstractProbeSequenceNormalization
     fitOne.BaseCountNormalization
     fitOne.LinearModelProbeSequenceNormalization fitOne.MatNormalization
     fitOne.ReseqCrosstalkCalibration fitOne.ScaleNormalization3
     fitOne.UnitTypeScaleNormalization fitOneArray.SingleArrayUnitModel
     fitOneChromosome.SmoothMultiarrayModel fitPlasqUnit.matrix
     fitQuantileNormFcn.AffymetrixCelFile fixSearchPath.AromaAffymetrix
     fromCdf.AffymetrixProbeTabFile fromCdf.GenomeInformation
     fromCdf.SnpInformation fromDataFile.ChipEffectFile
     fromDataFile.FirmaFile fromDataFile.ResidualFile
     fromDataFile.WeightsFile fromDataSet.ChipEffectSet
     fromDataSet.FirmaSet fromDataSet.GenomeInformation
     fromDataSet.ResidualSet fromDataSet.SnpInformation
     fromDataSet.WeightsSet fromFile.AffymetrixCdfFile
     fromFile.AffymetrixCelFile fromFile.AffymetrixCnChpFile
     fromFile.AffymetrixPgfFile fromFile.AromaChipTypeAnnotationFile
     fromFile.CnagCfhFile fromFile.DChipCdfBinFile fromFile.DChipDcpFile
     getACSFile.AffymetrixCdfFile getAM.ChipEffectFile getAM.ChipEffectSet
     getAlias.ArrayExplorer getAlias.GenericReporter getAlias.Model
     getAlias.TransformReport getAlleleCellPairs.AffymetrixCdfFile
     getAlleleProbePairs.AffymetrixCdfFile
     getAlleleProbePairs2.AffymetrixCdfFile
     getAlleleProbePairs3.AffymetrixCdfFile getAm.AffymetrixCelFile
     getAromaCellMatchScoreFile.MatNormalization
     getAromaCellPositionFile.MatSmoothing
     getAromaCellSequenceFile.AbstractProbeSequenceNormalization
     getAromaCellSequenceFile.AffymetrixCdfFile
     getAromaUfcFile.FragmentEquivalentClassNormalization
     getAromaUflFile.UflSnpInformation
     getAromaUgpFile.UgpGenomeInformation
     getAromaUnitFracBCnBinarySet.default
     getAromaUnitTotalCnBinarySet.default
     getArrayNames.AffymetrixAptSummaryFile getArraysOfInput.ArrayExplorer
     getAsFullCelFile.ChipEffectFile getAsFullCelSet.ChipEffectSet
     getAsteriskTags.AdditiveCovariatesNormalization
     getAsteriskTags.AffineCnPlm getAsteriskTags.AffinePlm
     getAsteriskTags.AffineSnpPlm getAsteriskTags.AlleleSummation
     getAsteriskTags.AllelicCrosstalkCalibration
     getAsteriskTags.ArrayExplorer getAsteriskTags.AvgCnPlm
     getAsteriskTags.AvgPlm getAsteriskTags.AvgSnpPlm
     getAsteriskTags.BaseCountNormalization
     getAsteriskTags.BasePositionNormalization getAsteriskTags.CrlmmModel
     getAsteriskTags.ExonRmaPlm getAsteriskTags.FirmaModel
     getAsteriskTags.FragmentEquivalentClassNormalization
     getAsteriskTags.FragmentLengthNormalization
     getAsteriskTags.GenericReporter getAsteriskTags.HetLogAddCnPlm
     getAsteriskTags.HetLogAddPlm getAsteriskTags.HetLogAddSnpPlm
     getAsteriskTags.LimmaBackgroundCorrection
     getAsteriskTags.MatNormalization getAsteriskTags.MbeiCnPlm
     getAsteriskTags.MbeiPlm getAsteriskTags.MbeiSnpPlm
     getAsteriskTags.Model getAsteriskTags.NormExpBackgroundCorrection
     getAsteriskTags.ProbeLevelModel getAsteriskTags.ProbeLevelTransform3
     getAsteriskTags.QualityAssessmentModel
     getAsteriskTags.ReseqCrosstalkCalibration getAsteriskTags.RmaCnPlm
     getAsteriskTags.RmaPlm getAsteriskTags.RmaSnpPlm
     getAsteriskTags.ScaleNormalization
     getAsteriskTags.SmoothMultiarrayModel getAsteriskTags.SmoothRmaModel
     getAsteriskTags.SmoothSaModel getAsteriskTags.SnpChipEffectGroupMerge
     getAsteriskTags.UnitModel getAverage.AffymetrixCelSet
     getAverage.CnagCfhSet getAverageAsinh.AffymetrixCelSet
     getAverageAsinh.CnagCfhSet getAverageFile.AffymetrixCelSet
     getAverageFile.ChipEffectSet getAverageFile.CnChipEffectSet
     getAverageFile.CnagCfhSet getAverageFile.ExonChipEffectSet
     getAverageFile.ResidualSet getAverageFile.SnpChipEffectSet
     getAverageFile.WeightsSet getAverageLog.AffymetrixCelSet
     getAverageLog.CnagCfhSet getBandwidth.SmoothMultiarrayModel
     getBaseline.ChipEffectSet getBaseline.CnChipEffectSet
     getBaseline.SnpChipEffectSet
     getBlockSizes.SpatialRowColumnNormalization
     getCalculateResidualsFunction.AvgPlm
     getCalculateResidualsFunction.ProbeLevelModel
     getCalculateResidualsFunction.RmaPlm getCallSet.CrlmmModel
     getCalls.DChipDcpFile getCdf.AdditiveCovariatesNormalization
     getCdf.AffymetrixCelFile getCdf.AffymetrixCelSet
     getCdf.AffymetrixCnChpFile getCdf.AffymetrixCnChpSet
     getCdf.AffymetrixProbeTabFile getCdf.AffymetrixTsvFile
     getCdf.AromaUnitTabularBinaryFile getCdf.ChipEffectGroupMerge
     getCdf.CnagCfhFile getCdf.CnagCfhSet getCdf.FirmaModel
     getCdf.FragmentEquivalentClassNormalization
     getCdf.FragmentLengthNormalization getCdf.GcContentNormalization
     getCdf.Model getCdf.QualityAssessmentModel getCdf.TransformReport
     getCdfBin.DChipDcpSet getCellDim.DChipCdfBinFile
     getCellIndices.AffymetrixCdfFile getCellIndices.ChipEffectFile
     getCellIndices.ChipEffectSet getCellIndices.CnChipEffectFile
     getCellIndices.CnPlm getCellIndices.CnProbeAffinityFile
     getCellIndices.ExonChipEffectFile
     getCellIndices.ExonProbeAffinityFile getCellIndices.ExonRmaPlm
     getCellIndices.FirmaFile getCellIndices.FirmaSet
     getCellIndices.ProbeAffinityFile getCellIndices.ResidualFile
     getCellIndices.ResidualSet getCellIndices.SnpChipEffectFile
     getCellIndices.SnpPlm getCellIndices.SnpProbeAffinityFile
     getCellIndices.UnitModel getCellIndices.WeightsFile
     getCellIndices.WeightsSet getCellMapForMainCdf.ChipEffectFile
     getCellQuartets.AffymetrixCdfFile getCellsTo.ProbeLevelTransform3
     getCellsToFit.ProbeLevelTransform3
     getCellsToInternal.ProbeLevelTransform3
     getCellsToUpdate.ProbeLevelTransform3
     getChipEffectFileClass.ChipEffectSet
     getChipEffectFileClass.CnChipEffectSet
     getChipEffectFileClass.ExonChipEffectSet
     getChipEffectFileClass.SnpChipEffectSet
     getChipEffectSet.AlleleSummation getChipEffectSet.CnPlm
     getChipEffectSet.ExonRmaPlm getChipEffectSet.ProbeLevelModel
     getChipEffectSet.QualityAssessmentModel getChipEffectSet.SnpPlm
     getChipEffectSetClass.AlleleSummation getChipEffectSetClass.CnPlm
     getChipEffectSetClass.ExonRmaPlm
     getChipEffectSetClass.ProbeLevelModel getChipEffectSetClass.SnpPlm
     getChipType.AffymetrixAptSummaryFile getChipType.AffymetrixCdfFile
     getChipType.AffymetrixCelFile getChipType.AffymetrixCelSet
     getChipType.AffymetrixCelSetReporter getChipType.AffymetrixCnChpFile
     getChipType.AffymetrixPgfFile getChipType.AffymetrixProbeTabFile
     getChipType.AffymetrixTsvFile getChipType.AromaChipTypeAnnotationFile
     getChipType.CnagCfhFile getChipType.CrlmmModel
     getChipType.DChipCdfBinFile getChipType.DChipDcpSet
     getChipType.GenomeInformation getChipType.SnpInformation
     getChipType.UflSnpInformation getChipType.UgpGenomeInformation
     getChromosomeStats.GenomeInformation getChromosomes.GenomeInformation
     getChromosomes.UgpGenomeInformation getCnNames.AffymetrixCdfFile
     getColorMaps.ArrayExplorer getColorMaps.SpatialReporter
     getColumnNames.AffymetrixProbeTabFile
     getCombineAlleles.CnChipEffectSet getCombineAlleles.CnPlm
     getConfidenceScoreSet.CrlmmModel
     getCovariates.AdditiveCovariatesNormalization
     getCovariates.GcContentNormalization2
     getCrlmmParametersSet.CrlmmModel getCrlmmPriors.CrlmmModel
     getCrlmmSNPs.CrlmmModel getCrlmmSNPsOnChrX.CrlmmModel
     getCrlmmSplineParameters.CrlmmModel getData.AffymetrixCelFile
     getData.AffymetrixCelSet getData.AffymetrixCnChpFile
     getData.AffymetrixProbeTabFile getData.AffymetrixTsvFile
     getData.CnagCfhSet getData.GenomeInformation getData.SnpInformation
     getData.UflSnpInformation getData.UgpGenomeInformation
     getDataColumns.GenomeInformation getDataColumns.UflSnpInformation
     getDataColumns.UgpGenomeInformation getDataFlat.ChipEffectFile
     getDataFlat.FirmaFile getDataFlat.ResidualFile
     getDataFlat.WeightsFile getDataPairs.AllelicCrosstalkCalibration
     getDataSet.AffymetrixCelSetReporter getDataSet.ArrayExplorer
     getDataSet.FirmaModel getDataSet.Model
     getDataSet.QualityAssessmentModel
     getDefaultColumnNames.AromaCellMatchScoreFile
     getDefaultColumnNames.AromaUfcFile
     getDefaultExtension.AffymetrixCdfFile
     getDefaultExtension.AffymetrixCsvFile
     getDefaultExtension.AffymetrixCsvGenomeInformation
     getDefaultExtension.AffymetrixNetAffxCsvFile
     getDefaultExtension.AffymetrixPgfFile
     getDefaultExtension.AffymetrixTsvFile
     getDefaultExtension.AromaCellMatchScoreFile
     getDefaultExtension.AromaChipTypeAnnotationFile
     getDefaultFullName.AffymetrixFileSet getDefaultFullName.CnagCfhSet
     getDefaultSettings.AromaAffymetrix getDefaultSettings.Package
     getDesignMatrix.BaseCountNormalization
     getDesignMatrix.BasePositionNormalization
     getDesignMatrix.LinearModelProbeSequenceNormalization
     getDesignMatrix.MatNormalization getDimension.AffymetrixCdfFile
     getDimension.AffymetrixPgfFile
     getExclCells.DChipQuantileNormalization
     getExclCells.QuantileNormalization getExcludes.DChipDcpFile
     getExclusiveUnitSubsets.FragmentEquivalentClassNormalization
     getExpandedCellMap.ChipEffectFile getExpandedCellMap.CnChipEffectFile
     getExpandedCellMap.SnpChipEffectFile
     getExpectedOutputFiles.MatSmoothing
     getExpectedOutputFullnames.MatSmoothing
     getExtensionPattern.AffymetrixCdfFile
     getExtensionPattern.AffymetrixCelFile
     getExtensionPattern.AffymetrixCnChpFile
     getExtensionPattern.AffymetrixCsvFile
     getExtensionPattern.AffymetrixPgfFile
     getExtensionPattern.AffymetrixTsvFile
     getExtensionPattern.AromaCellMatchScoreFile
     getExtensionPattern.AromaUfcFile getExtensionPattern.CnagCfhFile
     getExtensionPattern.DChipDcpFile getField.AffymetrixTsvFile
     getFields.SnpInformation getFields.UflSnpInformation
     getFileClass.FirmaSet getFileFormat.AffymetrixCdfFile
     getFileFormat.AffymetrixCelFile getFileFormat.AffymetrixCnChpFile
     getFileFormat.DChipCdfBinFile getFileFormat.DChipDcpFile
     getFileSet.AffymetrixFileSetReporter getFileSetClass.FirmaModel
     getFilenameExtension.AromaCellMatchScoreFile
     getFilenameExtension.AromaUfcFile
     getFilteredFragmentLengths.FragmentLengthNormalization
     getFirmaScores.FirmaModel getFirmaSet.FirmaModel
     getFirstCellIndices.AffymetrixCdfFile
     getFirstCellPerUnitIndices.ExonChipEffectSet
     getFit.BasePositionNormalization
     getFitSingleCellUnitFunction.UnitModel getFitUnitFunction.CnPlm
     getFitUnitFunction.FirmaModel getFitUnitFunction.MultiArrayUnitModel
     getFitUnitFunction.SingleArrayUnitModel getFitUnitFunction.UnitModel
     getFitUnitGroupFunction.AffinePlm getFitUnitGroupFunction.AvgPlm
     getFitUnitGroupFunction.ExonRmaPlm getFitUnitGroupFunction.FirmaModel
     getFitUnitGroupFunction.HetLogAddPlm getFitUnitGroupFunction.MbeiPlm
     getFitUnitGroupFunction.MultiArrayUnitModel
     getFitUnitGroupFunction.RmaPlm
     getFitUnitGroupFunction.SingleArrayUnitModel
     getFitUnitGroupFunction.SmoothMultiarrayModel
     getFitUnitGroupFunction.SmoothRmaModel
     getFitUnitGroupFunction.SmoothSaModel
     getFragmentLengths.AffymetrixTsvFile
     getFragmentLengths.SnpInformation
     getFragmentLengths.UflSnpInformation getFragmentStarts.SnpInformation
     getFragmentStarts.UflSnpInformation getFragmentStops.SnpInformation
     getFragmentStops.UflSnpInformation getFullName.GenericReporter
     getFullName.Model getFullName.QualityAssessmentModel
     getFullName.TransformReport getFullNames.ChipEffectSetTuple
     getGc.AffymetrixTsvFile getGcContent.GcContentNormalization
     getGenomeBuild.AffymetrixNetAffxCsvFile
     getGenomeInformation.AffymetrixCdfFile
     getGroupDirections.AffymetrixCdfFile getHeader.AffymetrixCdfFile
     getHeader.AffymetrixCelFile getHeader.AffymetrixCnChpFile
     getHeader.AffymetrixPgfFile getHeader.AromaChipTypeAnnotationFile
     getHeader.CnagCfhFile getHeader.DChipCdfBinFile
     getHeader.DChipDcpFile getHeaderAttributes.AffymetrixNetAffxCsvFile
     getHeaderLength.CnagCfhFile getHeaderV3.AffymetrixCelFile
     getIdentifier.AffymetrixCelFile getIdentifier.AffymetrixCelSet
     getIdentifier.AffymetrixFileSet getIdentifier.CnagCfhFile
     getIdentifier.CnagCfhSet getImage.AffymetrixCdfFile
     getImage.AffymetrixCelFile getImage.AromaUnitTabularBinaryFile
     getImage.ResidualFile getImage.WeightsFile
     getIndexToRowMap.AffymetrixProbeTabFile
     getInputDataSet.TransformReport
     getInputName.AffymetrixFileSetReporter getInputName.GenericReporter
     getInputTags.AffymetrixFileSetReporter getInputTags.GenericReporter
     getIntensities.AffymetrixCelSet getLabel.Model
     getListOfCdfs.AffymetrixCelSetTuple
     getListOfGenomeInformations.ChromosomalModel
     getListOfPriors.MultiArrayUnitModel getListOfReporters.ArrayExplorer
     getListOfUnitNamesFiles.AffymetrixCelSetTuple
     getListOfUnitNamesFiles.ArrayExplorer
     getListOfUnitTypesFiles.AffymetrixCelSetTuple
     getListOfUnitTypesFiles.ArrayExplorer getMainCdf.AffymetrixCdfFile
     getMainPath.GenericReporter
     getMatrixChipEffectFiles.CopyNumberChromosomalModel
     getMergeFunction.ChipEffectGroupMerge
     getMergeFunction.SnpChipEffectGroupMerge
     getMergeGroups.ExonChipEffectSet getMergeStrands.SnpChipEffectSet
     getMergeStrands.SnpPlm getMonoCell.AffymetrixCdfFile
     getMonocellCdf.AffymetrixCdfFile getName.AffymetrixPlatform
     getName.FirmaModel getName.GenericReporter getName.Model
     getName.QualityAssessmentModel getName.TransformReport
     getNameOfInput.ArrayExplorer getNetAffxBuild.AffymetrixNetAffxCsvFile
     getNetAffxDate.AffymetrixNetAffxCsvFile
     getNormalEquations.LinearModelProbeSequenceNormalization
     getNormalizeSignalsOne.ScaleNormalization3
     getNormalizeSignalsOne.UnitTypeScaleNormalization
     getNormalizedIntensities.DChipDcpFile
     getNumberOfFilesAveraged.CnChipEffectFile
     getOrderedFragmentPairMap.AromaUfcFile
     getOrderedFragmentPairs.AromaUfcFile getOutputDataSet.Transform
     getOutputDataSet.TransformReport
     getOutputDataSet00.AdditiveCovariatesNormalization
     getOutputDataSet00.FragmentEquivalentClassNormalization
     getOutputDataSet00.FragmentLengthNormalization
     getOutputDataSet00.GcContentNormalization getOutputFiles.Transform
     getOutputIdentifier.QuantileNormalization
     getOutputTuple.SmoothMultiarrayModel
     getParameter.AffymetrixAptSummaryFile getParameterSet.Model
     getParameters.AbstractProbeSequenceNormalization
     getParameters.AdditiveCovariatesNormalization
     getParameters.AllelicCrosstalkCalibration getParameters.AvgPlm
     getParameters.BackgroundCorrection
     getParameters.BaseCountNormalization
     getParameters.BasePositionNormalization getParameters.ChipEffectFile
     getParameters.ChipEffectGroupMerge getParameters.CnChipEffectFile
     getParameters.CnPlm getParameters.CrlmmModel
     getParameters.DChipQuantileNormalization
     getParameters.ExonChipEffectFile getParameters.ExonRmaPlm
     getParameters.FragmentEquivalentClassNormalization
     getParameters.FragmentLengthNormalization
     getParameters.GcContentNormalization
     getParameters.GcRmaBackgroundCorrection
     getParameters.LimmaBackgroundCorrection
     getParameters.MatNormalization getParameters.MatSmoothing
     getParameters.NormExpBackgroundCorrection
     getParameters.OpticalBackgroundCorrection
     getParameters.ProbeAffinityFile getParameters.ProbeLevelTransform3
     getParameters.QuantileNormalization
     getParameters.ReseqCrosstalkCalibration getParameters.ResidualFile
     getParameters.ResidualSet getParameters.RmaBackgroundCorrection
     getParameters.RmaPlm getParameters.ScaleNormalization
     getParameters.ScaleNormalization3 getParameters.SnpChipEffectFile
     getParameters.SnpChipEffectGroupMerge getParameters.SnpPlm
     getParameters.SpatialRowColumnNormalization getParameters.UnitModel
     getParameters.UnitTypeScaleNormalization getParameters.WeightsFile
     getParameters.WeightsSet getPath.AffymetrixCelSetReporter
     getPath.GenericReporter getPath.Model getPath.QualityAssessmentModel
     getPath.TransformReport getPcuTheta.ChromosomalModel
     getPlatform.AffymetrixCdfFile getPlatform.AffymetrixCelFile
     getPlatform.AffymetrixCelSet getPlatform.AffymetrixPgfFile
     getPlatform.AromaChipTypeAnnotationFile getPlatform.DChipCdfBinFile
     getPlatformDesignDB.CrlmmModel getPlm.FirmaModel
     getPlm.QualityAssessmentModel getPosition.AffymetrixTsvFile
     getPositionChipTypeUnit.ChromosomalModel
     getPositionChipTypeUnit.CopyNumberSegmentationModel
     getPositions.GenomeInformation getProbeAffinityFile.AffinePlm
     getProbeAffinityFile.AvgPlm getProbeAffinityFile.CnPlm
     getProbeAffinityFile.ExonRmaPlm getProbeAffinityFile.MbeiPlm
     getProbeAffinityFile.ProbeLevelModel getProbeAffinityFile.RmaPlm
     getProbeAffinityFile.SnpPlm getProbeSequenceData.AffymetrixCdfFile
     getProbesetIds.AffymetrixAptSummaryFile
     getQuantificationScale.AffymetrixAptSummaryFile
     getRawIntensities.DChipDcpFile
     getReadArguments.AffymetrixAptSummaryFile
     getRectangle.AffymetrixCelFile getReference.SpatialReporter
     getRegions.profileCGH getReportSet.GenericReporter
     getReportSet.SpatialReporter getResidualFileClass.ResidualSet
     getResidualSet.ProbeLevelModel getResidualSetClass.ProbeLevelModel
     getResiduals.QualityAssessmentModel getRestructor.AffymetrixCdfFile
     getRlmFitFunctions.RmaPlm getRootPath.AlleleSummation
     getRootPath.ChipEffectTransform getRootPath.CrlmmModel
     getRootPath.FirmaModel getRootPath.GenericReporter getRootPath.Model
     getRootPath.ProbeLevelModel getRootPath.ProbeLevelTransform
     getRootPath.QualityAssessmentModel getRootPath.SmoothMultiarrayModel
     getRootPath.SmoothRmaModel getRootPath.TransformReport
     getSetTuple.ArrayExplorer getSetsOfProbes.AllelicCrosstalkCalibration
     getSetsOfProbes.ReseqCrosstalkCalibration getSettings.Package
     getSignalTransform.BasePositionNormalization
     getSignalTransform.LinearModelProbeSequenceNormalization
     getSnpInformation.AffymetrixCdfFile getSnpNames.AffymetrixCdfFile
     getSpar.SpatialRowColumnNormalization getSteps.ASCRMAv2
     getSteps.AromaPipeline getSubsetOfCellIndices.AffymetrixCdfFile
     getSubsetOfUnits.AffymetrixCdfFile
     getSubsetToAvg.AllelicCrosstalkCalibration
     getSubsetToAvg.QuantileNormalization
     getSubsetToAvg.ReseqCrosstalkCalibration
     getSubsetToAvg.ScaleNormalization
     getSubsetToFit.AdditiveCovariatesNormalization
     getSubsetToFit.FragmentEquivalentClassNormalization
     getSubsetToFit.FragmentLengthNormalization
     getSubsetToFit.GcContentNormalization
     getSubsetToUpdate.BackgroundCorrection
     getSubsetToUpdate.DChipQuantileNormalization
     getSubsetToUpdate.QuantileNormalization
     getSubsetToUpdate.ScaleNormalization
     getSubsetToUpdate0.LimmaBackgroundCorrection getTags.FirmaModel
     getTags.GenericReporter getTags.Model getTags.QualityAssessmentModel
     getTags.TransformReport getTagsOfInput.ArrayExplorer
     getTargetAverages.FragmentEquivalentClassNormalization
     getTargetDistribution.QuantileNormalization
     getTargetDistributionIdentifier.QuantileNormalization
     getTargetDistributionPathname.QuantileNormalization
     getTargetFile.AbstractProbeSequenceNormalization
     getTargetFunction.GcContentNormalization
     getTargetFunctions.AdditiveCovariatesNormalization
     getTargetFunctions.FragmentLengthNormalization
     getThetaStds.DChipDcpFile getThetas.DChipDcpFile
     getThetasAB.DChipDcpFile getTimeStamp.AffymetrixAptSummaryFile
     getTimestamp.AffymetrixCelFile getTimestamp.AffymetrixCnChpFile
     getTimestamp.CnagCfhFile getTimestamps.AffymetrixCelSet
     getTimestamps.CnagCfhSet getUniqueCdf.AffymetrixCdfFile
     getUnitGroupCellArrayMap.ChipEffectFile
     getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile
     getUnitGroupCellChromosomePositionMap.ChipEffectFile
     getUnitGroupCellMap.AffymetrixCdfFile
     getUnitGroupCellMap.AffymetrixCelSet
     getUnitGroupCellMap.ChipEffectFile getUnitGroupCellMap.FirmaFile
     getUnitGroupCellMap.ResidualFile getUnitGroupCellMap.WeightsFile
     getUnitGroupCellMapWithMonocell.AffymetrixCdfFile
     getUnitGroupCellMapWithUnique.AffymetrixCdfFile
     getUnitGroupCellMatrixMap.ChipEffectFile
     getUnitGroupNamesFromUgcMap.AffymetrixCdfFile
     getUnitIndices.GenomeInformation getUnitIntensities.AffymetrixCelSet
     getUnitNames.AffymetrixCdfFile getUnitNames.AffymetrixNetAffxCsvFile
     getUnitNames.AffymetrixPgfFile getUnitNames.DChipCdfBinFile
     getUnitNamesFile.AffymetrixCdfFile getUnitNamesFile.AffymetrixCelFile
     getUnitNamesFile.AffymetrixCelSet
     getUnitNamesFile.AffymetrixCnChpFile
     getUnitNamesFile.AffymetrixPgfFile
     getUnitNamesFile.AffymetrixPlatform getUnitNamesFile.TransformReport
     getUnitReadMap.AffymetrixCnChpFile getUnitSizes.AffymetrixCdfFile
     getUnitSizes.DChipCdfBinFile getUnitTypes.AffymetrixCdfFile
     getUnitTypesFile.AffymetrixCdfFile getUnitTypesFile.AffymetrixCelFile
     getUnitTypesFile.AffymetrixCelSet
     getUnitTypesFile.AffymetrixCnChpFile
     getUnitTypesFile.AffymetrixPlatform getUnitTypesFile.TransformReport
     getUnitsOnChromosome.GenomeInformation
     getUnitsOnChromosome.UgpGenomeInformation
     getUnitsOnChromosomes.GenomeInformation
     getUnitsTo.ProbeLevelTransform3 getUnitsToFit.CrlmmModel
     getUnitsToFit.ProbeLevelTransform3
     getUnitsToUpdate.ProbeLevelTransform3
     getWeights.QualityAssessmentModel getWeightsFileClass.WeightsSet
     getWeightsSet.ProbeLevelModel getWeightsSetClass.ProbeLevelModel
     getXAM.ChipEffectFile getXAM.ChipEffectSet getYY.TransformReport
     groupUnitsByDimension.AffymetrixCdfFile
     hasAlleleBFractions.CnChipEffectFile
     hasAlleleBFractions.CnChipEffectSet
     hasAlleleBFractions.CnChipEffectSetTuple
     hasColumnHeader.AffymetrixProbeTabFile hasMbeiData.DChipDcpFile
     hasNormalizedData.DChipDcpFile hasStrandiness.CnChipEffectFile
     hasStrandiness.CnChipEffectSet hasStrandiness.CnChipEffectSetTuple
     hasUnitReadMap.AffymetrixCnChpFile hasUnitTypes.AffymetrixCdfFile
     highlight.AffymetrixCelFile identifyCells.AffymetrixCdfFile
     image270.AffymetrixCelFile importFrom.AromaUnitTabularBinaryFile
     importFromAffymetrixNetAffxCsvFile.AromaUflFile
     importFromAffymetrixNetAffxCsvFile.AromaUgpFile
     importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile
     importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile
     importFromAffymetrixProbeTabFile.AromaCellSequenceFile
     importFromAffymetrixTabularFile.AromaUfcFile
     importFromAffymetrixTabularFile.AromaUgpFile
     importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile
     importFromApt.CnChipEffectSet importFromBpMap.AromaCellMatchScoreFile
     importFromBpMap.AromaCellSequenceFile
     importFromDChip.AffymetrixCelSet importFromDChip.CnChipEffectSet
     importFromDChipGenomeInformation.AromaUnitTabularBinaryFile
     importFromGenericTabularFile.AromaUnitTabularBinaryFile
     importFromGenomeInformation.AromaUgpFile
     importFromGenomeInformation.AromaUnitTabularBinaryFile
     indexOfMissingSequences.AbstractProbeSequenceNormalization
     inferMmFromPm.AromaCellSequenceFile inferParameters.CnChipEffectSet
     inferParameters.SnpChipEffectSet
     isCompatibleWithCdf.GenomeInformation
     isCompatibleWithCdf.SnpInformation
     isCompatibleWithCdf.UflSnpInformation
     isCompatibleWithCdf.UgpGenomeInformation
     isDuplicated.AffymetrixCelSet isDuplicated.CnagCfhSet
     isMissing.AromaCellMatchScoreFile isMonocellCdf.AffymetrixCdfFile
     isPm.AffymetrixCdfFile isResequenceChip.AffymetrixCdfFile
     isSnpChip.AffymetrixCdfFile isUniqueCdf.AffymetrixCdfFile
     isUnitGroupCellMap.data.frame isUnitGroupCellMap.default
     isUnitGroupCellMap.matrix justRMA.default justSNPRMA.AffymetrixCelSet
     justSNPRMA.character mapToUnitNamesFile.DChipCdfBinFile
     mergeGroups.ChipEffectFile mergeStrands.CnChipEffectFile
     mergeStrands.SnpChipEffectFile
     migrateTool.CopyNumberSegmentationModel
     nbrOfArrays.AffymetrixAptSummaryFile nbrOfArrays.AffymetrixCelSet
     nbrOfArrays.AffymetrixCelSetReporter nbrOfArrays.AffymetrixCnChpSet
     nbrOfArrays.CnagCfhSet nbrOfArrays.DChipDcpSet
     nbrOfArrays.QualityAssessmentModel nbrOfArrays.TransformReport
     nbrOfCells.AffymetrixCdfFile nbrOfCells.AffymetrixCelFile
     nbrOfCells.AffymetrixPgfFile nbrOfCells.CnagCfhFile
     nbrOfCells.DChipCdfBinFile nbrOfCells.DChipDcpFile
     nbrOfCellsPerUnit.AffymetrixCdfFile
     nbrOfCellsPerUnitGroup.AffymetrixCdfFile nbrOfChipTypes.ArrayExplorer
     nbrOfColumns.AffymetrixCdfFile nbrOfColumns.AffymetrixPgfFile
     nbrOfEnzymes.AromaUfcFile nbrOfEnzymes.SnpInformation
     nbrOfEnzymes.UflSnpInformation nbrOfGroupsPerUnit.AffymetrixCdfFile
     nbrOfQcUnits.AffymetrixCdfFile nbrOfRows.AffymetrixCdfFile
     nbrOfRows.AffymetrixPgfFile nbrOfSnps.AffymetrixCdfFile
     nbrOfSnps.CnagCfhFile nbrOfSteps.AromaPipeline
     nbrOfUnits.AffymetrixCdfFile nbrOfUnits.AffymetrixPgfFile
     nbrOfUnits.DChipCdfBinFile nbrOfUnits.DChipDcpFile
     nbrOfUnits.GenomeInformation nbrOfUnits.SnpInformation
     nbrOfUnits.UflSnpInformation nbrOfUnits.UgpGenomeInformation
     normalizeOneArrayVector.FragmentEquivalentClassNormalization
     normalizeQuantile.AffymetrixCelFile
     normalizeQuantile.AffymetrixCelSet patch.AromaAffymetrix
     plotAllelePairs.AllelicCrosstalkCalibration
     plotBasepair.AllelicCrosstalkCalibration plotBoxplot.ChipEffectSet
     plotBoxplotStats.list plotCovariateEffects.GcContentNormalization2
     plotDensity.AffymetrixCelFile plotDensity.AffymetrixCelSet
     plotDensity.GenomeInformation plotImage.AffymetrixCelFile
     plotMargins.SpatialReporter plotMvsA.AffymetrixCelFile
     plotMvsX.AffymetrixCelFile plotNuse.QualityAssessmentModel
     plotRle.QualityAssessmentModel plotXYCurve.TransformReport
     plotXYCurveLog2.TransformReport
     predictOne.AbstractProbeSequenceNormalization
     predictOne.BaseCountNormalization
     predictOne.LinearModelProbeSequenceNormalization
     predictOne.MatNormalization
     process.AbstractProbeSequenceNormalization
     process.AdditiveCovariatesNormalization process.AlleleSummation
     process.AllelicCrosstalkCalibration process.AromaPipeline
     process.ArrayExplorer process.BackgroundCorrection
     process.ChipEffectGroupMerge process.DChipQuantileNormalization
     process.FragmentEquivalentClassNormalization
     process.FragmentLengthNormalization process.GcContentNormalization
     process.GcRmaBackgroundCorrection process.GenericReporter
     process.LimmaBackgroundCorrection process.MatNormalization
     process.MatSmoothing process.OpticalBackgroundCorrection
     process.QuantileNormalization process.ReseqCrosstalkCalibration
     process.RmaBackgroundCorrection process.ScaleNormalization
     process.ScaleNormalization3 process.SpatialReporter
     process.SpatialRowColumnNormalization
     process.UnitTypeScaleNormalization range.AffymetrixCelFile
     range.AffymetrixCelSet range.CnagCfhFile range.CnagCfhSet
     read10K.DChipSnpInformation read250K.DChipSnpInformation
     read250KHg17.DChipGenomeInformation read50K.DChipSnpInformation
     read50KHg17.DChipGenomeInformation
     readArrays.AffymetrixAptSummaryFile readCfhHeader.default
     readCfhUnits.default readCfnHeader.default readCfnUnits.default
     readDataFrame.AffymetrixCdfFile
     readDataFrame.AffymetrixCsvGenomeInformation
     readDataFrame.AffymetrixTsvFile readDataFrame.AromaUfcFile
     readDataFrame.DChipCdfBinFile readDataFrame.DChipGenomeInformation
     readDataFrame.DChipSnpInformation readDataFrame.GenomeInformation
     readDataFrame.SnpInformation readDataFrame.UflSnpInformation
     readDataFrame.UgpGenomeInformation
     readDataFrame2.AffymetrixProbeTabFile
     readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile
     readDataUnitFragmentLength.AffymetrixNetAffxCsvFile
     readGeneAssignments.AffymetrixNetAffxCsvFile
     readGenomeWideSNP.DChipGenomeInformation
     readHeader.AffymetrixAptSummaryFile
     readMatchScores.AromaCellMatchScoreFile
     readMouse430.DChipGenomeInformation
     readMouse430KenHardwired.DChipGenomeInformation
     readParameter.CrlmmParametersFile readPlasqTypes.AffymetrixCdfFile
     readPriorsByUnits.MultiArrayUnitModel
     readProbesetIds.AffymetrixAptSummaryFile
     readRawData.AffymetrixCelFile readRawData.AffymetrixCnChpFile
     readRawData.AffymetrixPgfFile readRawDataRectangle.AffymetrixCelFile
     readRawDataRectangle.SpatialReporter
     readSequenceDataFrame.AffymetrixProbeTabFile
     readTableInternal.GenomeInformation readTableInternal.SnpInformation
     readUnitNames.AffymetrixNetAffxCsvFile readUnits.AffymetrixCdfFile
     readUnits.AffymetrixCelFile readUnits.AffymetrixCelSet
     readUnits.ChipEffectFile readUnits.ChipEffectSet
     readUnits.CnChipEffectFile readUnits.CnagCfhFile readUnits.CnagCfhSet
     readUnits.ExonChipEffectFile readUnits.FirmaFile readUnits.FirmaSet
     readUnits.MultiArrayUnitModel readUnits.ParameterCelFile
     readUnits.ProbeAffinityFile readUnits.ResidualFile
     readUnits.ResidualSet readUnits.SingleArrayUnitModel
     readUnits.SnpChipEffectFile readUnits.WeightsFile
     readUnits.WeightsSet readUnitsByQuartets.AffymetrixCdfFile
     rescale.AllelicCrosstalkCalibration
     rescaleByAll.AllelicCrosstalkCalibration
     rescaleByAll.ReseqCrosstalkCalibration
     rescaleByGroups.AllelicCrosstalkCalibration
     restruct.AffymetrixCdfFile seq.TransformReport setAlias.ArrayExplorer
     setAlias.GenericReporter setAlias.Model setAlias.TransformReport
     setArrays.ArrayExplorer setBandwidth.SmoothMultiarrayModel
     setCdf.AffymetrixCelFile setCdf.AffymetrixCelSet
     setCdf.AffymetrixCnChpFile setCdf.AffymetrixCnChpSet
     setCdf.CnagCfhFile setCdf.CnagCfhSet setColorMaps.ArrayExplorer
     setColorMaps.SpatialReporter setCombineAlleles.CnChipEffectSet
     setCombineAlleles.CnPlm setCombineAlleles.CnProbeAffinityFile
     setDecodeFunction.ParameterCelFile setEncodeFunction.ParameterCelFile
     setGenomeInformation.AffymetrixCdfFile setLabel.Model
     setListOfPriors.MultiArrayUnitModel
     setMergeFunction.ChipEffectGroupMerge
     setMergeGroups.ExonChipEffectSet setMergeGroups.ExonProbeAffinityFile
     setMergeGroups.ExonRmaPlm setMergeStrands.SnpChipEffectSet
     setMergeStrands.SnpPlm setMergeStrands.SnpProbeAffinityFile
     setReference.SpatialReporter setRestructor.AffymetrixCdfFile
     setSettings.Package setSnpInformation.AffymetrixCdfFile setTags.Model
     setUnitReadMap.AffymetrixCnChpFile setup.GenericReporter
     setupExampleData.AromaAffymetrix smoothScatterMvsA.AffymetrixCelFile
     stextChipType.AffymetrixCdfFile transformAffine.AffymetrixCelFile
     transformAffine.AffymetrixCelSet
     translateColumnNames.AffymetrixAptSummaryFile
     translateColumnNames.AffymetrixProbeTabFile
     translateColumnNames.AffymetrixTabularFile
     translateFullName.AffymetrixProbeTabFile update.AromaAffymetrix
     update2.AffymetrixCelSet updateDataFlat.ChipEffectFile
     updateDataFlat.FirmaFile updateDataFlat.ResidualFile
     updateDataFlat.WeightsFile updateMatchScores.AromaCellMatchScoreFile
     updateParameter.CrlmmParametersFile
     updateSampleAnnotationSet.AffymetrixCelSet updateSettings.Package
     updateSetupExplorerFile.ArrayExplorer updateUnits.AffymetrixCelFile
     updateUnits.ChipEffectFile updateUnits.ChipEffectSet
     updateUnits.FirmaFile updateUnits.FirmaSet
     updateUnits.ParameterCelFile updateUnits.ProbeAffinityFile
     updateUnits.ResidualFile updateUnits.ResidualSet
     updateUnits.WeightsFile updateUnits.WeightsSet
     validate.AffymetrixCdfFile validate.AvgPlm
     validate.MultiArrayUnitModel verify.AffymetrixCsvGenomeInformation
     verify.AffymetrixTsvFile verify.DChipGenomeInformation
     verify.DChipSnpInformation verify.GenomeInformation
     verify.SnpInformation verify.UflSnpInformation
     verify.UgpGenomeInformation writeAsFullCelFile.ChipEffectFile
     writeCNT.SnpChipEffectFile writeCNT.SnpChipEffectSet
     writeCdf.AffyGenePDInfo writeCdf.DBPDInfo writeCdf.PDInfoList
     writeCdf.default writeCdfByExcludingCells.AffymetrixCdfFile
     writeImage.AffymetrixCelFile writeImage.ResidualFile
     writeImage.WeightsFile writeImageCombined.TransformReport
     writeImages.SpatialReporter writeImages.TransformReport
     writeRegions.profileCGH writeSgr.AffymetrixCelSet
     writeSignals.ProbeLevelTransform3 writeWig.CnChipEffectSet
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 2.13.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     addColorMap.ArrayExplorer addColorMap.SpatialReporter
     addExclCells.DChipQuantileNormalization
     allocateFromCdf.AffymetrixCelFile allocateFromCdf.AromaCellCpgFile
     allocateFromCdf.AromaCellMatchScoreFile
     allocateFromCdf.AromaCellPositionFile
     allocateFromCdf.AromaCellSequenceFile allocateFromCdf.AromaUfcFile
     allocateFromCdf.AromaUflFile allocateFromCdf.AromaUnitGcContentFile
     allocateFromCdf.AromaUnitTabularBinaryFile
     annotateMvsA.AffymetrixCelFile
     applyAnyOrder.CopyNumberChromosomalModel
     applyCCF0.CopyNumberChromosomalModel
     applyCFC0.CopyNumberChromosomalModel
     applyToUnitIntensities.AffymetrixCelSet
     as.AffymetrixCelSet.AffymetrixCelSet as.AffymetrixCelSet.default
     as.AffymetrixCelSet.list as.AffymetrixCnChpSet.AffymetrixCnChpSet
     as.AffymetrixCnChpSet.default as.AffymetrixCnChpSet.list
     as.AffymetrixFileSet.AffymetrixFileSet as.AffymetrixFileSet.default
     as.AffymetrixFileSet.list as.ChipEffectSetTuple.ChipEffectSetTuple
     as.ChipEffectSetTuple.default
     as.CnChipEffectSetTuple.CnChipEffectSetTuple
     as.CnChipEffectSetTuple.default as.CnagCfhSet.CnagCfhSet
     as.CnagCfhSet.default as.CnagCfhSet.list as.DChipDcpSet.DChipDcpSet
     as.DChipDcpSet.default as.DChipDcpSet.list
     assertAnnotationData.ASCRMAv2 averageQuantile.AffymetrixCelSet
     bgAdjustGcrma.AffymetrixCelFile bgAdjustGcrma.AffymetrixCelSet
     bgAdjustOptical.AffymetrixCelFile bgAdjustRma.AffymetrixCelFile
     boxplotStats.ChipEffectSet bpmapCluster2Cdf.default
     calcRawCnStats.CopyNumberChromosomalModel calcRawCnStats.default
     calculateAffinities.GcRmaBackgroundCorrection
     calculateAverages.FragmentEquivalentClassNormalization
     calculateBaseline.ChipEffectSet calculateConfidenceScores.CrlmmModel
     calculateFieldBoxplotStats.ChipEffectSet
     calculateMargins.SpatialReporter
     calculateNuseBoxplotStats.ChipEffectSet
     calculateParametersGsb.AffymetrixCelSet
     calculateResidualSet.FirmaModel calculateResidualSet.ProbeLevelModel
     calculateResiduals.FirmaModel calculateResiduals.ProbeLevelModel
     calculateRleBoxplotStats.ChipEffectSet
     calculateTargetDistribution.QuantileNormalization
     calculateWeights.ExonRmaPlm calculateWeights.FirmaModel
     calculateWeights.ProbeLevelModel
     calibrateOne.ReseqCrosstalkCalibration clearData.AffymetrixCelFile
     compare.AffymetrixCdfFile computeAffinities.AffymetrixCdfFile
     computeAffinitiesByACS.AffymetrixCdfFile convert.AffymetrixCdfFile
     convertToUnique.AffymetrixCelSet convertUnits.AffymetrixCdfFile
     createExonByTranscriptCdf.AffymetrixCdfFile
     createFrom.AffymetrixCelFile createMonocellCdf.AffymetrixCdfFile
     createOutputTuple.SmoothMultiarrayModel createParamCdf.ChipEffectFile
     createParamCdf.FirmaFile createUniqueCdf.AffymetrixCdfFile
     decode.ParameterCelFile encode.ParameterCelFile
     excludeChrXFromFit.DChipQuantileNormalization
     exportAromaSignalBinaryFileList.CnChipEffectFile
     exportTotalAndFracB.CnChipEffectFile
     exportTotalAndFracB.CnChipEffectSet exportTotalAndFracB.DChipDcpSet
     exportTotalAndFracB.SnpChipEffectFile
     exportTotalAndFracB.SnpChipEffectSet
     extractAffyBatch.AffymetrixCelSet extractAffyBatch.ChipEffectSet
     extractAlleleSet.SnpChipEffectSet extractCNT.SnpChipEffectFile
     extractCNT.SnpChipEffectSet
     extractChromosomalDataFrame.ChipEffectFile
     extractChromosomalDataFrame.ChipEffectSet
     extractDataFrame.ParameterCelFile extractDataFrame.ParameterCelSet
     extractExpressionSet.ChipEffectSet extractFeatureSet.AffymetrixCelSet
     extractLogRatios.AffymetrixCnChpFile
     extractLogRatios.AffymetrixCnChpSet
     extractSnpCnvQSet.SnpChipEffectSet
     extractSnpFeatureSet.AffymetrixCelSet extractSnpQSet.SnpChipEffectSet
     extractTheta.ChipEffectFile extractTheta.ChipEffectSet
     extractTheta.CnChipEffectFile extractTheta.CnChipEffectSet
     extractTheta.DChipDcpFile extractTheta.DChipDcpSet
     extractTheta.SnpChipEffectFile extractTheta.SnpChipEffectSet
     extractTheta.SnpCnvQSet extractTheta.SnpQSet
     extractTotalAndFracB.SnpChipEffectFile
     extractTotalAndFreqB.CnChipEffectFile
     extractTotalAndFreqB.CnChipEffectSet
     extractTotalAndFreqB.SnpChipEffectSet extractTotalAndFreqB.default
     findByCdf2.default findTargetDistributionFile.QuantileNormalization
     fitCnProbes.UnitModel fitOne.AbstractProbeSequenceNormalization
     fitOne.BaseCountNormalization
     fitOne.LinearModelProbeSequenceNormalization fitOne.MatNormalization
     fitOne.ReseqCrosstalkCalibration fitOne.ScaleNormalization3
     fitOne.UnitTypeScaleNormalization fitOneArray.SingleArrayUnitModel
     fitOneChromosome.SmoothMultiarrayModel fitPlasqUnit.matrix
     fitQuantileNormFcn.AffymetrixCelFile fromCdf.AffymetrixProbeTabFile
     fromCdf.GenomeInformation fromCdf.SnpInformation
     fromDataFile.ChipEffectFile fromDataFile.FirmaFile
     fromDataFile.ResidualFile fromDataFile.WeightsFile
     fromDataSet.ChipEffectSet fromDataSet.FirmaSet
     fromDataSet.GenomeInformation fromDataSet.ResidualSet
     fromDataSet.SnpInformation fromDataSet.WeightsSet
     getACSFile.AffymetrixCdfFile getAlleleCellPairs.AffymetrixCdfFile
     getAlleleProbePairs.AffymetrixCdfFile
     getAlleleProbePairs2.AffymetrixCdfFile
     getAlleleProbePairs3.AffymetrixCdfFile getAm.AffymetrixCelFile
     getAromaCellMatchScoreFile.MatNormalization
     getAromaCellPositionFile.MatSmoothing
     getAromaCellSequenceFile.AbstractProbeSequenceNormalization
     getAromaCellSequenceFile.AffymetrixCdfFile
     getAromaUfcFile.FragmentEquivalentClassNormalization
     getAromaUnitFracBCnBinarySet.default
     getAromaUnitTotalCnBinarySet.default
     getArrayNames.AffymetrixAptSummaryFile
     getAsFullCelFile.ChipEffectFile getAsFullCelSet.ChipEffectSet
     getAverage.AffymetrixCelSet getAverage.CnagCfhSet
     getAverageAsinh.AffymetrixCelSet getAverageAsinh.CnagCfhSet
     getAverageLog.AffymetrixCelSet getAverageLog.CnagCfhSet
     getBandwidth.SmoothMultiarrayModel getBaseline.ChipEffectSet
     getBaseline.CnChipEffectSet getBaseline.SnpChipEffectSet
     getBlockSizes.SpatialRowColumnNormalization
     getCalculateResidualsFunction.AvgPlm
     getCalculateResidualsFunction.ProbeLevelModel
     getCalculateResidualsFunction.RmaPlm getCallSet.CrlmmModel
     getCdf.AdditiveCovariatesNormalization getCdf.AffymetrixCelFile
     getCdf.AffymetrixCelSet getCdf.AffymetrixCnChpFile
     getCdf.AffymetrixCnChpSet getCdf.AffymetrixProbeTabFile
     getCdf.AffymetrixTsvFile getCdf.AromaUnitTabularBinaryFile
     getCdf.ChipEffectGroupMerge getCdf.CnagCfhFile getCdf.CnagCfhSet
     getCdf.FirmaModel getCdf.FragmentEquivalentClassNormalization
     getCdf.FragmentLengthNormalization getCdf.GcContentNormalization
     getCdf.Model getCdf.QualityAssessmentModel getCdf.TransformReport
     getCdfBin.DChipDcpSet getCellDim.DChipCdfBinFile
     getCellIndices.AffymetrixCdfFile getCellIndices.ChipEffectFile
     getCellIndices.ChipEffectSet getCellIndices.CnChipEffectFile
     getCellIndices.CnPlm getCellIndices.CnProbeAffinityFile
     getCellIndices.ExonChipEffectFile
     getCellIndices.ExonProbeAffinityFile getCellIndices.ExonRmaPlm
     getCellIndices.FirmaFile getCellIndices.FirmaSet
     getCellIndices.ProbeAffinityFile getCellIndices.ResidualFile
     getCellIndices.ResidualSet getCellIndices.SnpChipEffectFile
     getCellIndices.SnpPlm getCellIndices.SnpProbeAffinityFile
     getCellIndices.UnitModel getCellIndices.WeightsFile
     getCellIndices.WeightsSet getCellMapForMainCdf.ChipEffectFile
     getCellQuartets.AffymetrixCdfFile getCellsTo.ProbeLevelTransform3
     getCellsToFit.ProbeLevelTransform3
     getCellsToInternal.ProbeLevelTransform3
     getCellsToUpdate.ProbeLevelTransform3
     getChipEffectFileClass.ChipEffectSet
     getChipEffectFileClass.CnChipEffectSet
     getChipEffectFileClass.ExonChipEffectSet
     getChipEffectFileClass.SnpChipEffectSet
     getChipEffectSet.AlleleSummation getChipEffectSet.CnPlm
     getChipEffectSet.ExonRmaPlm getChipEffectSet.ProbeLevelModel
     getChipEffectSet.QualityAssessmentModel getChipEffectSet.SnpPlm
     getChipEffectSetClass.AlleleSummation getChipEffectSetClass.CnPlm
     getChipEffectSetClass.ExonRmaPlm
     getChipEffectSetClass.ProbeLevelModel getChipEffectSetClass.SnpPlm
     getChromosomeStats.GenomeInformation getCnNames.AffymetrixCdfFile
     getColorMaps.ArrayExplorer getColorMaps.SpatialReporter
     getCombineAlleles.CnChipEffectSet getCombineAlleles.CnPlm
     getConfidenceScoreSet.CrlmmModel
     getCovariates.AdditiveCovariatesNormalization
     getCovariates.GcContentNormalization2
     getCrlmmParametersSet.CrlmmModel getCrlmmPriors.CrlmmModel
     getCrlmmSNPs.CrlmmModel getCrlmmSNPsOnChrX.CrlmmModel
     getCrlmmSplineParameters.CrlmmModel getData.AffymetrixCelFile
     getData.AffymetrixCelSet getData.AffymetrixCnChpFile
     getData.AffymetrixProbeTabFile getData.AffymetrixTsvFile
     getData.CnagCfhSet getData.GenomeInformation getData.SnpInformation
     getData.UflSnpInformation getData.UgpGenomeInformation
     getDataColumns.GenomeInformation getDataColumns.UflSnpInformation
     getDataColumns.UgpGenomeInformation getDataFlat.ChipEffectFile
     getDataFlat.FirmaFile getDataFlat.ResidualFile
     getDataFlat.WeightsFile getDataPairs.AllelicCrosstalkCalibration
     getDataSet.AffymetrixCelSetReporter getDataSet.ArrayExplorer
     getDataSet.FirmaModel getDataSet.Model
     getDataSet.QualityAssessmentModel getDefaultSettings.AromaAffymetrix
     getDefaultSettings.Package getDesignMatrix.BaseCountNormalization
     getDesignMatrix.BasePositionNormalization
     getDesignMatrix.LinearModelProbeSequenceNormalization
     getDesignMatrix.MatNormalization getDimension.AffymetrixCdfFile
     getDimension.AffymetrixPgfFile
     getExclCells.DChipQuantileNormalization
     getExclCells.QuantileNormalization getExcludes.DChipDcpFile
     getExclusiveUnitSubsets.FragmentEquivalentClassNormalization
     getExpandedCellMap.ChipEffectFile getExpandedCellMap.CnChipEffectFile
     getExpandedCellMap.SnpChipEffectFile getField.AffymetrixTsvFile
     getFileFormat.AffymetrixCdfFile getFileFormat.AffymetrixCelFile
     getFileFormat.AffymetrixCnChpFile getFileFormat.DChipCdfBinFile
     getFileFormat.DChipDcpFile getFileSet.AffymetrixFileSetReporter
     getFileSetClass.FirmaModel
     getFilteredFragmentLengths.FragmentLengthNormalization
     getFirmaScores.FirmaModel getFirmaSet.FirmaModel
     getFirstCellIndices.AffymetrixCdfFile
     getFirstCellPerUnitIndices.ExonChipEffectSet
     getFit.BasePositionNormalization
     getFitSingleCellUnitFunction.UnitModel getFitUnitFunction.CnPlm
     getFitUnitFunction.FirmaModel getFitUnitFunction.MultiArrayUnitModel
     getFitUnitFunction.SingleArrayUnitModel getFitUnitFunction.UnitModel
     getFitUnitGroupFunction.AffinePlm getFitUnitGroupFunction.AvgPlm
     getFitUnitGroupFunction.ExonRmaPlm getFitUnitGroupFunction.FirmaModel
     getFitUnitGroupFunction.HetLogAddPlm getFitUnitGroupFunction.MbeiPlm
     getFitUnitGroupFunction.MultiArrayUnitModel
     getFitUnitGroupFunction.RmaPlm
     getFitUnitGroupFunction.SingleArrayUnitModel
     getFitUnitGroupFunction.SmoothMultiarrayModel
     getFitUnitGroupFunction.SmoothRmaModel
     getFitUnitGroupFunction.SmoothSaModel
     getFragmentLengths.AffymetrixTsvFile
     getFragmentLengths.SnpInformation
     getFragmentLengths.UflSnpInformation getFragmentStarts.SnpInformation
     getFragmentStarts.UflSnpInformation getFragmentStops.SnpInformation
     getFragmentStops.UflSnpInformation getGc.AffymetrixTsvFile
     getGcContent.GcContentNormalization
     getGenomeBuild.AffymetrixNetAffxCsvFile
     getGenomeInformation.AffymetrixCdfFile
     getGroupDirections.AffymetrixCdfFile
     getHeaderAttributes.AffymetrixNetAffxCsvFile
     getHeaderLength.CnagCfhFile getHeaderV3.AffymetrixCelFile
     getIdentifier.AffymetrixCelFile getIdentifier.AffymetrixCelSet
     getIdentifier.AffymetrixFileSet getIdentifier.CnagCfhFile
     getIdentifier.CnagCfhSet getIndexToRowMap.AffymetrixProbeTabFile
     getInputName.AffymetrixFileSetReporter getInputName.GenericReporter
     getInputTags.AffymetrixFileSetReporter getInputTags.GenericReporter
     getIntensities.AffymetrixCelSet getListOfCdfs.AffymetrixCelSetTuple
     getListOfGenomeInformations.ChromosomalModel
     getListOfPriors.MultiArrayUnitModel getListOfReporters.ArrayExplorer
     getMainCdf.AffymetrixCdfFile
     getMatrixChipEffectFiles.CopyNumberChromosomalModel
     getMergeFunction.ChipEffectGroupMerge
     getMergeFunction.SnpChipEffectGroupMerge
     getMergeGroups.ExonChipEffectSet getMergeStrands.SnpChipEffectSet
     getMergeStrands.SnpPlm getMonoCell.AffymetrixCdfFile
     getMonocellCdf.AffymetrixCdfFile
     getNetAffxBuild.AffymetrixNetAffxCsvFile
     getNetAffxDate.AffymetrixNetAffxCsvFile
     getNormalEquations.LinearModelProbeSequenceNormalization
     getNormalizeSignalsOne.ScaleNormalization3
     getNormalizeSignalsOne.UnitTypeScaleNormalization
     getNormalizedIntensities.DChipDcpFile
     getOrderedFragmentPairMap.AromaUfcFile
     getOrderedFragmentPairs.AromaUfcFile
     getOutputDataSet00.AdditiveCovariatesNormalization
     getOutputDataSet00.FragmentEquivalentClassNormalization
     getOutputDataSet00.FragmentLengthNormalization
     getOutputDataSet00.GcContentNormalization
     getOutputIdentifier.QuantileNormalization
     getOutputTuple.SmoothMultiarrayModel
     getParameter.AffymetrixAptSummaryFile getParameterSet.Model
     getPcuTheta.ChromosomalModel getPlatformDesignDB.CrlmmModel
     getPlm.FirmaModel getPlm.QualityAssessmentModel
     getPositionChipTypeUnit.ChromosomalModel
     getPositionChipTypeUnit.CopyNumberSegmentationModel
     getProbeAffinityFile.AffinePlm getProbeAffinityFile.AvgPlm
     getProbeAffinityFile.CnPlm getProbeAffinityFile.ExonRmaPlm
     getProbeAffinityFile.MbeiPlm getProbeAffinityFile.ProbeLevelModel
     getProbeAffinityFile.RmaPlm getProbeAffinityFile.SnpPlm
     getProbeSequenceData.AffymetrixCdfFile
     getProbesetIds.AffymetrixAptSummaryFile
     getQuantificationScale.AffymetrixAptSummaryFile
     getRawIntensities.DChipDcpFile getRectangle.AffymetrixCelFile
     getReportSet.GenericReporter getReportSet.SpatialReporter
     getResidualFileClass.ResidualSet getResidualSet.ProbeLevelModel
     getResidualSetClass.ProbeLevelModel
     getResiduals.QualityAssessmentModel getRestructor.AffymetrixCdfFile
     getRlmFitFunctions.RmaPlm getSetsOfProbes.AllelicCrosstalkCalibration
     getSetsOfProbes.ReseqCrosstalkCalibration getSettings.Package
     getSignalTransform.BasePositionNormalization
     getSignalTransform.LinearModelProbeSequenceNormalization
     getSnpInformation.AffymetrixCdfFile getSnpNames.AffymetrixCdfFile
     getSpar.SpatialRowColumnNormalization getSteps.ASCRMAv2
     getSteps.AromaPipeline getSubsetOfCellIndices.AffymetrixCdfFile
     getSubsetOfUnits.AffymetrixCdfFile
     getSubsetToAvg.AllelicCrosstalkCalibration
     getSubsetToAvg.QuantileNormalization
     getSubsetToAvg.ReseqCrosstalkCalibration
     getSubsetToAvg.ScaleNormalization
     getSubsetToFit.AdditiveCovariatesNormalization
     getSubsetToFit.FragmentEquivalentClassNormalization
     getSubsetToFit.FragmentLengthNormalization
     getSubsetToFit.GcContentNormalization
     getSubsetToUpdate.BackgroundCorrection
     getSubsetToUpdate.DChipQuantileNormalization
     getSubsetToUpdate.QuantileNormalization
     getSubsetToUpdate.ScaleNormalization
     getSubsetToUpdate0.LimmaBackgroundCorrection
     getTargetAverages.FragmentEquivalentClassNormalization
     getTargetDistribution.QuantileNormalization
     getTargetDistributionIdentifier.QuantileNormalization
     getTargetDistributionPathname.QuantileNormalization
     getTargetFile.AbstractProbeSequenceNormalization
     getTargetFunction.GcContentNormalization
     getTargetFunctions.AdditiveCovariatesNormalization
     getTargetFunctions.FragmentLengthNormalization
     getThetaStds.DChipDcpFile getThetas.DChipDcpFile
     getThetasAB.DChipDcpFile getTimeStamp.AffymetrixAptSummaryFile
     getTimestamp.AffymetrixCelFile getTimestamp.AffymetrixCnChpFile
     getTimestamp.CnagCfhFile getTimestamps.AffymetrixCelSet
     getTimestamps.CnagCfhSet getUniqueCdf.AffymetrixCdfFile
     getUnitGroupCellArrayMap.ChipEffectFile
     getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile
     getUnitGroupCellChromosomePositionMap.ChipEffectFile
     getUnitGroupCellMap.AffymetrixCdfFile
     getUnitGroupCellMap.AffymetrixCelSet
     getUnitGroupCellMap.ChipEffectFile getUnitGroupCellMap.FirmaFile
     getUnitGroupCellMap.ResidualFile getUnitGroupCellMap.WeightsFile
     getUnitGroupCellMapWithMonocell.AffymetrixCdfFile
     getUnitGroupCellMapWithUnique.AffymetrixCdfFile
     getUnitGroupCellMatrixMap.ChipEffectFile
     getUnitGroupNamesFromUgcMap.AffymetrixCdfFile
     getUnitIndices.GenomeInformation getUnitIntensities.AffymetrixCelSet
     getUnitReadMap.AffymetrixCnChpFile getUnitSizes.AffymetrixCdfFile
     getUnitSizes.DChipCdfBinFile getUnitsTo.ProbeLevelTransform3
     getUnitsToFit.CrlmmModel getUnitsToFit.ProbeLevelTransform3
     getUnitsToUpdate.ProbeLevelTransform3 getWeightsFileClass.WeightsSet
     getWeightsSet.ProbeLevelModel getWeightsSetClass.ProbeLevelModel
     getYY.TransformReport groupUnitsByDimension.AffymetrixCdfFile
     hasMbeiData.DChipDcpFile hasNormalizedData.DChipDcpFile
     hasUnitReadMap.AffymetrixCnChpFile hasUnitTypes.AffymetrixCdfFile
     highlight.AffymetrixCelFile identifyCells.AffymetrixCdfFile
     image270.AffymetrixCelFile
     importFromAffymetrixNetAffxCsvFile.AromaUflFile
     importFromAffymetrixNetAffxCsvFile.AromaUgpFile
     importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile
     importFromAffymetrixNetAffxCsvFile.AromaUnitTabularBinaryFile
     importFromAffymetrixProbeTabFile.AromaCellSequenceFile
     importFromAffymetrixTabularFile.AromaUfcFile
     importFromAffymetrixTabularFile.AromaUgpFile
     importFromAffymetrixTabularFile.AromaUnitTabularBinaryFile
     importFromApt.CnChipEffectSet importFromBpMap.AromaCellMatchScoreFile
     importFromBpMap.AromaCellSequenceFile
     importFromDChip.AffymetrixCelSet importFromDChip.CnChipEffectSet
     importFromDChipGenomeInformation.AromaUnitTabularBinaryFile
     importFromGenomeInformation.AromaUgpFile
     importFromGenomeInformation.AromaUnitTabularBinaryFile
     indexOfMissingSequences.AbstractProbeSequenceNormalization
     inferMmFromPm.AromaCellSequenceFile inferParameters.CnChipEffectSet
     inferParameters.SnpChipEffectSet
     isCompatibleWithCdf.GenomeInformation
     isCompatibleWithCdf.SnpInformation
     isCompatibleWithCdf.UflSnpInformation
     isCompatibleWithCdf.UgpGenomeInformation
     isDuplicated.AffymetrixCelSet isDuplicated.CnagCfhSet
     isMonocellCdf.AffymetrixCdfFile isPm.AffymetrixCdfFile
     isResequenceChip.AffymetrixCdfFile isSnpChip.AffymetrixCdfFile
     isUniqueCdf.AffymetrixCdfFile isUnitGroupCellMap.data.frame
     isUnitGroupCellMap.default isUnitGroupCellMap.matrix justRMA.default
     justSNPRMA.AffymetrixCelSet justSNPRMA.character
     mapToUnitNamesFile.DChipCdfBinFile mergeGroups.ChipEffectFile
     mergeStrands.CnChipEffectFile mergeStrands.SnpChipEffectFile
     migrateTool.CopyNumberSegmentationModel
     nbrOfCellsPerUnit.AffymetrixCdfFile
     nbrOfCellsPerUnitGroup.AffymetrixCdfFile
     nbrOfGroupsPerUnit.AffymetrixCdfFile nbrOfQcUnits.AffymetrixCdfFile
     nbrOfSnps.AffymetrixCdfFile nbrOfSnps.CnagCfhFile
     nbrOfSteps.AromaPipeline
     normalizeOneArrayVector.FragmentEquivalentClassNormalization
     normalizeQuantile.AffymetrixCelFile
     normalizeQuantile.AffymetrixCelSet
     plotAllelePairs.AllelicCrosstalkCalibration
     plotBasepair.AllelicCrosstalkCalibration plotBoxplot.ChipEffectSet
     plotBoxplotStats.list plotCovariateEffects.GcContentNormalization2
     plotDensity.AffymetrixCelFile plotDensity.AffymetrixCelSet
     plotDensity.GenomeInformation plotImage.AffymetrixCelFile
     plotMargins.SpatialReporter plotMvsA.AffymetrixCelFile
     plotMvsX.AffymetrixCelFile plotNuse.QualityAssessmentModel
     plotRle.QualityAssessmentModel plotXYCurve.TransformReport
     plotXYCurveLog2.TransformReport
     predictOne.AbstractProbeSequenceNormalization
     predictOne.BaseCountNormalization
     predictOne.LinearModelProbeSequenceNormalization
     predictOne.MatNormalization read10K.DChipSnpInformation
     read250K.DChipSnpInformation read250KHg17.DChipGenomeInformation
     read50K.DChipSnpInformation read50KHg17.DChipGenomeInformation
     readArrays.AffymetrixAptSummaryFile readCfhHeader.default
     readCfhUnits.default readCfnHeader.default readCfnUnits.default
     readDataFrame2.AffymetrixProbeTabFile
     readDataUnitChromosomePosition.AffymetrixNetAffxCsvFile
     readDataUnitFragmentLength.AffymetrixNetAffxCsvFile
     readGeneAssignments.AffymetrixNetAffxCsvFile
     readGenomeWideSNP.DChipGenomeInformation
     readMatchScores.AromaCellMatchScoreFile
     readMouse430.DChipGenomeInformation
     readMouse430KenHardwired.DChipGenomeInformation
     readParameter.CrlmmParametersFile readPlasqTypes.AffymetrixCdfFile
     readPriorsByUnits.MultiArrayUnitModel
     readProbesetIds.AffymetrixAptSummaryFile
     readRawData.AffymetrixCelFile readRawData.AffymetrixCnChpFile
     readRawData.AffymetrixPgfFile readRawDataRectangle.AffymetrixCelFile
     readRawDataRectangle.SpatialReporter
     readSequenceDataFrame.AffymetrixProbeTabFile
     readTableInternal.GenomeInformation readTableInternal.SnpInformation
     readUnitNames.AffymetrixNetAffxCsvFile readUnits.AffymetrixCdfFile
     readUnits.AffymetrixCelFile readUnits.AffymetrixCelSet
     readUnits.ChipEffectFile readUnits.ChipEffectSet
     readUnits.CnChipEffectFile readUnits.CnagCfhFile readUnits.CnagCfhSet
     readUnits.ExonChipEffectFile readUnits.FirmaFile readUnits.FirmaSet
     readUnits.MultiArrayUnitModel readUnits.ParameterCelFile
     readUnits.ProbeAffinityFile readUnits.ResidualFile
     readUnits.ResidualSet readUnits.SingleArrayUnitModel
     readUnits.SnpChipEffectFile readUnits.WeightsFile
     readUnits.WeightsSet readUnitsByQuartets.AffymetrixCdfFile
     rescaleByAll.AllelicCrosstalkCalibration
     rescaleByAll.ReseqCrosstalkCalibration
     rescaleByGroups.AllelicCrosstalkCalibration
     restruct.AffymetrixCdfFile setBandwidth.SmoothMultiarrayModel
     setCdf.AffymetrixCelFile setCdf.AffymetrixCelSet
     setCdf.AffymetrixCnChpFile setCdf.AffymetrixCnChpSet
     setCdf.CnagCfhFile setCdf.CnagCfhSet setColorMaps.ArrayExplorer
     setColorMaps.SpatialReporter setCombineAlleles.CnChipEffectSet
     setCombineAlleles.CnPlm setCombineAlleles.CnProbeAffinityFile
     setDecodeFunction.ParameterCelFile setEncodeFunction.ParameterCelFile
     setGenomeInformation.AffymetrixCdfFile
     setListOfPriors.MultiArrayUnitModel
     setMergeFunction.ChipEffectGroupMerge
     setMergeGroups.ExonChipEffectSet setMergeGroups.ExonProbeAffinityFile
     setMergeGroups.ExonRmaPlm setMergeStrands.SnpChipEffectSet
     setMergeStrands.SnpPlm setMergeStrands.SnpProbeAffinityFile
     setRestructor.AffymetrixCdfFile setSettings.Package
     setSnpInformation.AffymetrixCdfFile
     setUnitReadMap.AffymetrixCnChpFile setupExampleData.AromaAffymetrix
     smoothScatterMvsA.AffymetrixCelFile transformAffine.AffymetrixCelFile
     transformAffine.AffymetrixCelSet updateDataFlat.ChipEffectFile
     updateDataFlat.FirmaFile updateDataFlat.ResidualFile
     updateDataFlat.WeightsFile updateMatchScores.AromaCellMatchScoreFile
     updateParameter.CrlmmParametersFile
     updateSampleAnnotationSet.AffymetrixCelSet updateSettings.Package
     updateUnits.AffymetrixCelFile updateUnits.ChipEffectFile
     updateUnits.ChipEffectSet updateUnits.FirmaFile updateUnits.FirmaSet
     updateUnits.ParameterCelFile updateUnits.ProbeAffinityFile
     updateUnits.ResidualFile updateUnits.ResidualSet
     updateUnits.WeightsFile updateUnits.WeightsSet
     writeAsFullCelFile.ChipEffectFile writeCNT.SnpChipEffectFile
     writeCNT.SnpChipEffectSet writeCdf.AffyGenePDInfo writeCdf.DBPDInfo
     writeCdf.PDInfoList writeCdf.default
     writeCdfByExcludingCells.AffymetrixCdfFile
     writeImageCombined.TransformReport writeImages.SpatialReporter
     writeImages.TransformReport writeSgr.AffymetrixCelSet
     writeSignals.ProbeLevelTransform3 writeWig.CnChipEffectSet
     seq.TransformReport update.AromaAffymetrix getLabel.Model
     setLabel.Model validate.AffymetrixCdfFile validate.AvgPlm
     validate.MultiArrayUnitModel allocate.AromaCellMatchScoreFile
     allocate.CrlmmParametersFile
     as.CopyNumberDataSetTuple.CnChipEffectSet
     byChipType.AffymetrixCsvGenomeInformation
     byChipType.AffymetrixProbeTabFile byChipType.AffymetrixTabularFile
     byChipType.AffymetrixTsvFile byChipType.AromaCellMatchScoreFile
     byChipType.AromaChipTypeAnnotationFile byChipType.DChipCdfBinFile
     byChipType.DChipGenomeInformation byChipType.DChipSnpInformation
     byChipType.GenomeInformation byChipType.SnpInformation
     byChipType.UflSnpInformation byChipType.UgpGenomeInformation
     exportTotalCnRatioSet.AffymetrixCnChpSet
     findByChipType.AffymetrixCdfFile findByChipType.AffymetrixCsvFile
     findByChipType.AffymetrixCsvGenomeInformation
     findByChipType.AffymetrixNetAffxCsvFile
     findByChipType.AffymetrixPgfFile
     findByChipType.AffymetrixProbeTabFile
     findByChipType.AffymetrixTabularFile findByChipType.AffymetrixTsvFile
     findByChipType.AromaChipTypeAnnotationFile
     findByChipType.DChipCdfBinFile findByChipType.DChipGenomeInformation
     findByChipType.DChipSnpInformation findByChipType.UflSnpInformation
     findByChipType.UgpGenomeInformation findUnitsTodo.AlleleSummation
     findUnitsTodo.ChipEffectFile findUnitsTodo.ChipEffectSet
     findUnitsTodo.CrlmmModel findUnitsTodo.CrlmmParametersFile
     findUnitsTodo.CrlmmParametersSet findUnitsTodo.ExonChipEffectSet
     findUnitsTodo.FirmaFile findUnitsTodo.FirmaModel
     findUnitsTodo.FirmaSet findUnitsTodo.ProbeLevelModel
     findUnitsTodo.QualityAssessmentFile findUnitsTodo.ResidualFile
     findUnitsTodo.ResidualSet findUnitsTodo.UnitModel
     findUnitsTodo.WeightsFile findUnitsTodo.WeightsSet fit.CrlmmModel
     fit.FirmaModel fit.Model fit.ProbeLevelModel fit.SingleArrayUnitModel
     fit.SmoothMultiarrayModel fixSearchPath.AromaAffymetrix
     getAM.ChipEffectFile getAM.ChipEffectSet getAlias.ArrayExplorer
     getAlias.GenericReporter getAlias.Model getAlias.TransformReport
     getAromaUflFile.UflSnpInformation
     getAromaUgpFile.UgpGenomeInformation getArraysOfInput.ArrayExplorer
     getAverageFile.AffymetrixCelSet getAverageFile.ChipEffectSet
     getAverageFile.CnChipEffectSet getAverageFile.CnagCfhSet
     getAverageFile.ExonChipEffectSet getAverageFile.ResidualSet
     getAverageFile.SnpChipEffectSet getAverageFile.WeightsSet
     getChipType.AffymetrixAptSummaryFile getChipType.AffymetrixCdfFile
     getChipType.AffymetrixCelFile getChipType.AffymetrixCelSet
     getChipType.AffymetrixCelSetReporter getChipType.AffymetrixCnChpFile
     getChipType.AffymetrixPgfFile getChipType.AffymetrixProbeTabFile
     getChipType.AffymetrixTsvFile getChipType.AromaChipTypeAnnotationFile
     getChipType.CnagCfhFile getChipType.CrlmmModel
     getChipType.DChipCdfBinFile getChipType.DChipDcpSet
     getChipType.GenomeInformation getChipType.SnpInformation
     getChipType.UflSnpInformation getChipType.UgpGenomeInformation
     getChromosomes.GenomeInformation getChromosomes.UgpGenomeInformation
     getDefaultExtension.AffymetrixCdfFile
     getDefaultExtension.AffymetrixCsvFile
     getDefaultExtension.AffymetrixCsvGenomeInformation
     getDefaultExtension.AffymetrixNetAffxCsvFile
     getDefaultExtension.AffymetrixPgfFile
     getDefaultExtension.AffymetrixTsvFile
     getDefaultExtension.AromaCellMatchScoreFile
     getDefaultExtension.AromaChipTypeAnnotationFile
     getExpectedOutputFiles.MatSmoothing
     getExpectedOutputFullnames.MatSmoothing getImage.AffymetrixCdfFile
     getImage.AffymetrixCelFile getImage.AromaUnitTabularBinaryFile
     getImage.ResidualFile getImage.WeightsFile
     getInputDataSet.TransformReport
     getListOfUnitNamesFiles.AffymetrixCelSetTuple
     getListOfUnitNamesFiles.ArrayExplorer
     getListOfUnitTypesFiles.AffymetrixCelSetTuple
     getListOfUnitTypesFiles.ArrayExplorer getMainPath.GenericReporter
     getNameOfInput.ArrayExplorer
     getNumberOfFilesAveraged.CnChipEffectFile getOutputDataSet.Transform
     getOutputDataSet.TransformReport getOutputFiles.Transform
     getParameters.AbstractProbeSequenceNormalization
     getParameters.AdditiveCovariatesNormalization
     getParameters.AllelicCrosstalkCalibration getParameters.AvgPlm
     getParameters.BackgroundCorrection
     getParameters.BaseCountNormalization
     getParameters.BasePositionNormalization getParameters.ChipEffectFile
     getParameters.ChipEffectGroupMerge getParameters.CnChipEffectFile
     getParameters.CnPlm getParameters.CrlmmModel
     getParameters.DChipQuantileNormalization
     getParameters.ExonChipEffectFile getParameters.ExonRmaPlm
     getParameters.FragmentEquivalentClassNormalization
     getParameters.FragmentLengthNormalization
     getParameters.GcContentNormalization
     getParameters.GcRmaBackgroundCorrection
     getParameters.LimmaBackgroundCorrection
     getParameters.MatNormalization getParameters.MatSmoothing
     getParameters.NormExpBackgroundCorrection
     getParameters.OpticalBackgroundCorrection
     getParameters.ProbeAffinityFile getParameters.ProbeLevelTransform3
     getParameters.QuantileNormalization
     getParameters.ReseqCrosstalkCalibration getParameters.ResidualFile
     getParameters.ResidualSet getParameters.RmaBackgroundCorrection
     getParameters.RmaPlm getParameters.ScaleNormalization
     getParameters.ScaleNormalization3 getParameters.SnpChipEffectFile
     getParameters.SnpChipEffectGroupMerge getParameters.SnpPlm
     getParameters.SpatialRowColumnNormalization getParameters.UnitModel
     getParameters.UnitTypeScaleNormalization getParameters.WeightsFile
     getParameters.WeightsSet getPlatform.AffymetrixCdfFile
     getPlatform.AffymetrixCelFile getPlatform.AffymetrixCelSet
     getPlatform.AffymetrixPgfFile getPlatform.AromaChipTypeAnnotationFile
     getPlatform.DChipCdfBinFile getPositions.GenomeInformation
     getReference.SpatialReporter getRegions.profileCGH
     getRootPath.AlleleSummation getRootPath.ChipEffectTransform
     getRootPath.CrlmmModel getRootPath.FirmaModel
     getRootPath.GenericReporter getRootPath.Model
     getRootPath.ProbeLevelModel getRootPath.ProbeLevelTransform
     getRootPath.QualityAssessmentModel getRootPath.SmoothMultiarrayModel
     getRootPath.SmoothRmaModel getRootPath.TransformReport
     getSetTuple.ArrayExplorer getTagsOfInput.ArrayExplorer
     getUnitNames.AffymetrixCdfFile getUnitNames.AffymetrixNetAffxCsvFile
     getUnitNames.AffymetrixPgfFile getUnitNames.DChipCdfBinFile
     getUnitNamesFile.AffymetrixCdfFile getUnitNamesFile.AffymetrixCelFile
     getUnitNamesFile.AffymetrixCelSet
     getUnitNamesFile.AffymetrixCnChpFile
     getUnitNamesFile.AffymetrixPgfFile
     getUnitNamesFile.AffymetrixPlatform getUnitNamesFile.TransformReport
     getUnitTypes.AffymetrixCdfFile getUnitTypesFile.AffymetrixCdfFile
     getUnitTypesFile.AffymetrixCelFile getUnitTypesFile.AffymetrixCelSet
     getUnitTypesFile.AffymetrixCnChpFile
     getUnitTypesFile.AffymetrixPlatform getUnitTypesFile.TransformReport
     getUnitsOnChromosome.GenomeInformation
     getUnitsOnChromosome.UgpGenomeInformation
     getUnitsOnChromosomes.GenomeInformation
     getWeights.QualityAssessmentModel getXAM.ChipEffectFile
     getXAM.ChipEffectSet hasAlleleBFractions.CnChipEffectFile
     hasAlleleBFractions.CnChipEffectSet
     hasAlleleBFractions.CnChipEffectSetTuple
     hasStrandiness.CnChipEffectFile hasStrandiness.CnChipEffectSet
     hasStrandiness.CnChipEffectSetTuple
     importFrom.AromaUnitTabularBinaryFile
     importFromGenericTabularFile.AromaUnitTabularBinaryFile
     isMissing.AromaCellMatchScoreFile
     nbrOfArrays.AffymetrixAptSummaryFile nbrOfArrays.AffymetrixCelSet
     nbrOfArrays.AffymetrixCelSetReporter nbrOfArrays.AffymetrixCnChpSet
     nbrOfArrays.CnagCfhSet nbrOfArrays.DChipDcpSet
     nbrOfArrays.QualityAssessmentModel nbrOfArrays.TransformReport
     nbrOfCells.AffymetrixCdfFile nbrOfCells.AffymetrixCelFile
     nbrOfCells.AffymetrixPgfFile nbrOfCells.CnagCfhFile
     nbrOfCells.DChipCdfBinFile nbrOfCells.DChipDcpFile
     nbrOfChipTypes.ArrayExplorer nbrOfEnzymes.AromaUfcFile
     nbrOfEnzymes.SnpInformation nbrOfEnzymes.UflSnpInformation
     nbrOfUnits.AffymetrixCdfFile nbrOfUnits.AffymetrixPgfFile
     nbrOfUnits.DChipCdfBinFile nbrOfUnits.DChipDcpFile
     nbrOfUnits.GenomeInformation nbrOfUnits.SnpInformation
     nbrOfUnits.UflSnpInformation nbrOfUnits.UgpGenomeInformation
     patch.AromaAffymetrix process.AbstractProbeSequenceNormalization
     process.AdditiveCovariatesNormalization process.AlleleSummation
     process.AllelicCrosstalkCalibration process.AromaPipeline
     process.ArrayExplorer process.BackgroundCorrection
     process.ChipEffectGroupMerge process.DChipQuantileNormalization
     process.FragmentEquivalentClassNormalization
     process.FragmentLengthNormalization process.GcContentNormalization
     process.GcRmaBackgroundCorrection process.GenericReporter
     process.LimmaBackgroundCorrection process.MatNormalization
     process.MatSmoothing process.OpticalBackgroundCorrection
     process.QuantileNormalization process.ReseqCrosstalkCalibration
     process.RmaBackgroundCorrection process.ScaleNormalization
     process.ScaleNormalization3 process.SpatialReporter
     process.SpatialRowColumnNormalization
     process.UnitTypeScaleNormalization
     readHeader.AffymetrixAptSummaryFile
     rescale.AllelicCrosstalkCalibration setAlias.ArrayExplorer
     setAlias.GenericReporter setAlias.Model setAlias.TransformReport
     setArrays.ArrayExplorer setReference.SpatialReporter
     setup.GenericReporter stextChipType.AffymetrixCdfFile
     updateSetupExplorerFile.ArrayExplorer writeImage.AffymetrixCelFile
     writeImage.ResidualFile writeImage.WeightsFile
     writeRegions.profileCGH clearCache.AffymetrixCelSet
     clone.AffymetrixCelFile clone.AffymetrixCelSet
     clone.AffymetrixCnChpFile clone.CnagCfhFile clone.CnagCfhSet
     getCalls.DChipDcpFile getFields.SnpInformation
     getFields.UflSnpInformation getName.AffymetrixPlatform
     getName.FirmaModel getName.GenericReporter getName.Model
     getName.QualityAssessmentModel getName.TransformReport
     getPath.AffymetrixCelSetReporter getPath.GenericReporter
     getPath.Model getPath.QualityAssessmentModel getPath.TransformReport
     getPosition.AffymetrixTsvFile getTags.FirmaModel
     getTags.GenericReporter getTags.Model getTags.QualityAssessmentModel
     getTags.TransformReport append.AffymetrixCelSet append.CnagCfhSet
     byName.AffymetrixCelSet byName.AffymetrixCnChpSet
     byName.AromaChipTypeAnnotationFile byName.CnagCfhSet
     byName.CrlmmParametersSet byName.DChipDcpSet byPath.AffymetrixCelSet
     byPath.AffymetrixCelSetTuple byPath.AffymetrixCnChpSet
     byPath.AffymetrixFileSet byPath.ChipEffectSet byPath.CnChipEffectSet
     byPath.CnagCfhSet byPath.CrlmmParametersSet byPath.DChipDcpSet
     byPath.ExonChipEffectSet byPath.FirmaSet byPath.ResidualSet
     byPath.SnpChipEffectSet byPath.WeightsSet
     extractMatrix.AffymetrixCelFile extractMatrix.AffymetrixCelSet
     extractMatrix.ChipEffectFile extractMatrix.ChipEffectSet
     extractMatrix.FirmaFile extractMatrix.FirmaSet
     extractMatrix.ParameterCelFile extractMatrix.ParameterCelSet
     findByName.AffymetrixCelSet findByName.AffymetrixCnChpSet
     findByName.ChipEffectSet findByName.CnagCfhSet findByName.DChipDcpSet
     fromFile.AffymetrixCdfFile fromFile.AffymetrixCelFile
     fromFile.AffymetrixCnChpFile fromFile.AffymetrixPgfFile
     fromFile.AromaChipTypeAnnotationFile fromFile.CnagCfhFile
     fromFile.DChipCdfBinFile fromFile.DChipDcpFile
     getAsteriskTags.AdditiveCovariatesNormalization
     getAsteriskTags.AffineCnPlm getAsteriskTags.AffinePlm
     getAsteriskTags.AffineSnpPlm getAsteriskTags.AlleleSummation
     getAsteriskTags.AllelicCrosstalkCalibration
     getAsteriskTags.ArrayExplorer getAsteriskTags.AvgCnPlm
     getAsteriskTags.AvgPlm getAsteriskTags.AvgSnpPlm
     getAsteriskTags.BaseCountNormalization
     getAsteriskTags.BasePositionNormalization getAsteriskTags.CrlmmModel
     getAsteriskTags.ExonRmaPlm getAsteriskTags.FirmaModel
     getAsteriskTags.FragmentEquivalentClassNormalization
     getAsteriskTags.FragmentLengthNormalization
     getAsteriskTags.GenericReporter getAsteriskTags.HetLogAddCnPlm
     getAsteriskTags.HetLogAddPlm getAsteriskTags.HetLogAddSnpPlm
     getAsteriskTags.LimmaBackgroundCorrection
     getAsteriskTags.MatNormalization getAsteriskTags.MbeiCnPlm
     getAsteriskTags.MbeiPlm getAsteriskTags.MbeiSnpPlm
     getAsteriskTags.Model getAsteriskTags.NormExpBackgroundCorrection
     getAsteriskTags.ProbeLevelModel getAsteriskTags.ProbeLevelTransform3
     getAsteriskTags.QualityAssessmentModel
     getAsteriskTags.ReseqCrosstalkCalibration getAsteriskTags.RmaCnPlm
     getAsteriskTags.RmaPlm getAsteriskTags.RmaSnpPlm
     getAsteriskTags.ScaleNormalization
     getAsteriskTags.SmoothMultiarrayModel getAsteriskTags.SmoothRmaModel
     getAsteriskTags.SmoothSaModel getAsteriskTags.SnpChipEffectGroupMerge
     getAsteriskTags.UnitModel getColumnNames.AffymetrixProbeTabFile
     getDefaultColumnNames.AromaCellMatchScoreFile
     getDefaultColumnNames.AromaUfcFile
     getDefaultFullName.AffymetrixFileSet getDefaultFullName.CnagCfhSet
     getExtensionPattern.AffymetrixCdfFile
     getExtensionPattern.AffymetrixCelFile
     getExtensionPattern.AffymetrixCnChpFile
     getExtensionPattern.AffymetrixCsvFile
     getExtensionPattern.AffymetrixPgfFile
     getExtensionPattern.AffymetrixTsvFile
     getExtensionPattern.AromaCellMatchScoreFile
     getExtensionPattern.AromaUfcFile getExtensionPattern.CnagCfhFile
     getExtensionPattern.DChipDcpFile getFileClass.FirmaSet
     getFilenameExtension.AromaCellMatchScoreFile
     getFilenameExtension.AromaUfcFile getFullName.GenericReporter
     getFullName.Model getFullName.QualityAssessmentModel
     getFullName.TransformReport getFullNames.ChipEffectSetTuple
     getHeader.AffymetrixCdfFile getHeader.AffymetrixCelFile
     getHeader.AffymetrixCnChpFile getHeader.AffymetrixPgfFile
     getHeader.AromaChipTypeAnnotationFile getHeader.CnagCfhFile
     getHeader.DChipCdfBinFile getHeader.DChipDcpFile
     getReadArguments.AffymetrixAptSummaryFile
     hasColumnHeader.AffymetrixProbeTabFile nbrOfColumns.AffymetrixCdfFile
     nbrOfColumns.AffymetrixPgfFile nbrOfRows.AffymetrixCdfFile
     nbrOfRows.AffymetrixPgfFile readDataFrame.AffymetrixCdfFile
     readDataFrame.AffymetrixCsvGenomeInformation
     readDataFrame.AffymetrixTsvFile readDataFrame.AromaUfcFile
     readDataFrame.DChipCdfBinFile readDataFrame.DChipGenomeInformation
     readDataFrame.DChipSnpInformation readDataFrame.GenomeInformation
     readDataFrame.SnpInformation readDataFrame.UflSnpInformation
     readDataFrame.UgpGenomeInformation setTags.Model
     translateColumnNames.AffymetrixAptSummaryFile
     translateColumnNames.AffymetrixProbeTabFile
     translateColumnNames.AffymetrixTabularFile
     translateFullName.AffymetrixProbeTabFile update2.AffymetrixCelSet
     verify.AffymetrixCsvGenomeInformation verify.AffymetrixTsvFile
     verify.DChipGenomeInformation verify.DChipSnpInformation
     verify.GenomeInformation verify.SnpInformation
     verify.UflSnpInformation verify.UgpGenomeInformation
     as.character.AffymetrixCdfFile as.character.AffymetrixCelFile
     as.character.AffymetrixCelSet as.character.AffymetrixCelSetReporter
     as.character.AffymetrixCnChpFile as.character.AffymetrixCnChpSet
     as.character.AffymetrixPgfFile as.character.AffymetrixProbeTabFile
     as.character.AromaChipTypeAnnotationFile as.character.ArrayExplorer
     as.character.ChipEffectFile as.character.ChipEffectSet
     as.character.CnagCfhFile as.character.CnagCfhSet
     as.character.DChipCdfBinFile as.character.DChipDcpFile
     as.character.DChipDcpSet as.character.DChipQuantileNormalization
     as.character.FirmaModel as.character.GenericReporter
     as.character.GenomeInformation as.character.Model
     as.character.ProbeAffinityFile as.character.QualityAssessmentModel
     as.character.ResidualFile as.character.ResidualSet
     as.character.SmoothMultiarrayModel as.character.SnpInformation
     as.character.SpatialReporter as.character.TransformReport
     as.character.WeightsFile as.character.WeightsSet dim.DChipDcpFile
     range.AffymetrixCelFile range.AffymetrixCelSet range.CnagCfhFile
     range.CnagCfhSet
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘dChipIO’ ‘pdInfoBuilder’
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-sparc

Version: 2.13.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘affyPLM’
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-sparc, r-release-osx-x86_64-snowleopard

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘dChipIO’ ‘pdInfoBuilder’
Flavors: r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'dChipIO' 'AffymetrixDataTestFiles'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘dChipIO’ ‘oligo’ ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.13.0
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘affyPLM’, ‘oligo’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘dChipIO’ ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’
Flavor: r-release-osx-x86_64-snowleopard

Package aroma.apd

Current CRAN status: NOTE: 14, OK: 1

Version: 0.5.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘affxparser’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 0.5.0
Check: R code for possible problems
Result: NOTE
    cdfToApdMap.default: no visible global function definition for
     ‘readCdfHeader’
    cdfToApdMap.default: no visible global function definition for
     ‘readCdfUnitsWriteMap’
    cdfToApdMap.default: no visible global function definition for
     ‘invertMap’
    celToApd.default: no visible global function definition for ‘readCel’
    celToApd.default: no visible global function definition for ‘invertMap’
    gtypeCelToPQ.default: no visible global function definition for
     ‘readCelHeader’
    gtypeCelToPQ.default: no visible global function definition for
     ‘findCdf’
    gtypeCelToPQ.default: no visible global function definition for
     ‘readCdfUnits’
    gtypeCelToPQ.default: no visible global function definition for
     ‘applyCdfGroups’
    gtypeCelToPQ.default: no visible binding for global variable
     ‘cdfGtypeCelToPQ’
    gtypeCelToPQ.default: no visible global function definition for
     ‘readCelUnits’
    readApdRectangle.default: no visible global function definition for
     ‘findCdf’
    readApdRectangle.default: no visible global function definition for
     ‘readCdfHeader’
    readApdUnits.default: no visible global function definition for
     ‘findCdf’
    readApdUnits.default: no visible global function definition for
     ‘readCdfCellIndices’
    readApdUnits.default: no visible global function definition for
     ‘applyCdfGroups’
    readApdUnits.default: no visible binding for global variable
     ‘cdfGetFields’
    readApdUnits.default: no visible global function definition for
     ‘readCdfHeader’
    updateApdUnits.default: no visible global function definition for
     ‘findCdf’
    updateApdUnits.default: no visible global function definition for
     ‘readCdfCellIndices’
    updateApdUnits.default: no visible global function definition for
     ‘applyCdfGroups’
    updateApdUnits.default: no visible binding for global variable
     ‘cdfGetFields’
    updateApdUnits.default: no visible global function definition for
     ‘readCdfHeader’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 0.5.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘affxparser’
Flavor: r-release-osx-x86_64-snowleopard

Version: 0.5.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘affxparser’
Flavor: r-release-osx-x86_64-snowleopard

Package aroma.cn

Current CRAN status: NOTE: 14, OK: 1

Version: 1.5.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     callPeaks.data.frame makeSmoothSplinePredict.numeric
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 1.5.0
Check: R code for possible problems
Result: NOTE
    backtransformOne.PrincipalCurveNormalization: no visible global
     function definition for ‘backtransformPrincipalCurve’
    backtransformOne.XYCurveNormalization: no visible global function
     definition for ‘backtransformXYCurve’
    calibrateC1C2.PairedPSCBS: no visible global function definition for
     ‘devSet’
    callAllelicBalanceByBAFs.PairedPSCBS: no visible global function
     definition for ‘findPeaksAndValleys’
    callGenotypes.TotalFracBSnpData: no visible global function definition
     for ‘findPeaksAndValleys’
    callXXorXY.numeric: no visible global function definition for
     ‘findPeaksAndValleys’
    drawC1C2Density.PairedPSCBS: no visible global function definition for
     ‘findPeaksAndValleys’
    estimateDeshearingParameter.PSCBS: no visible global function
     definition for ‘findPeaksAndValleys’
    estimateDeshearingParameter_20130815.PSCBS: no visible global function
     definition for ‘findPeaksAndValleys’
    fitC1C2Densities.PairedPSCBS : <anonymous>: no visible global function
     definition for ‘findPeaksAndValleys’
    fitC1C2Peaks.PairedPSCBS: no visible global function definition for
     ‘devSet’
    fitDeltaXYShearModel.matrix: no visible global function definition for
     ‘findPeaksAndValleys’
    fitOne.MultiSourceCopyNumberNormalization: no visible global function
     definition for ‘backtransformPrincipalCurve’
    fitOne.MultiSourceCopyNumberNormalization: no visible global function
     definition for ‘normalizeDifferencesToAverage’
    fitOne.PrincipalCurveNormalization: no visible global function
     definition for ‘fitPrincipalCurve’
    fitOne.XYCurveNormalization: no visible global function definition for
     ‘fitXYCurve’
    getAllNames.MultiSourceCopyNumberNormalization: no visible binding for
     global variable ‘getNames’
    getBacktransforms.PrincipalCurve: no visible global function definition
     for ‘backtransformPrincipalCurve’
    getOutputDataSet0.TotalCnSmoothing: no visible binding for global
     variable ‘Class’
    getOutputFileClass.TotalCnSmoothing: no visible binding for global
     variable ‘Class’
    getOutputFileSetClass.TotalCnSmoothing: no visible binding for global
     variable ‘Class’
    getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization :
     robustSmoother: no visible global function definition for
     ‘robustSmoothSpline’
    getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization : fcn: no
     visible global function definition for ‘fitPrincipalCurve’
    normalizeMirroredBAFsByRegions.matrix: no visible global function
     definition for ‘fitXYCurve’
    normalizeMirroredBAFsByRegions.matrix: no visible global function
     definition for ‘devSet’
    normalizeOne.MultiSourceCopyNumberNormalization: no visible global
     function definition for ‘backtransformPrincipalCurve’
    normalizePrincipalCurve.matrix: no visible global function definition
     for ‘fitPrincipalCurve’
    process.NaiveFracBGenotyping: no visible binding for global variable
     ‘AromaUnitGenotypeCallSet’
    process.NaiveFracBGenotyping: no visible binding for global variable
     ‘AromaUnitSignalBinarySet’
    smoothRawCopyNumbers.TotalCnBinnedSmoothing: no visible binding for
     global variable ‘colBinnedSmoothing.matrix’
    smoothRawCopyNumbers.TotalCnKernelSmoothing: no visible binding for
     global variable ‘colKernelSmoothing.matrix’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.5.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Package aroma.core

Current CRAN status: NOTE: 15

Version: 2.13.0
Check: package namespace information
Result: NOTE
    R < 3.0.2 had a limit of 500 registered S3 methods: found 781
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.13.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     apply.default as.character.AromaMicroarrayDataSetTuple
     as.character.AromaPlatform byPathnames.SampleAnnotationSet
     calcMargins.matrix downloadPackagePatch.default
     drawCytoband.ChromosomalModel drawCytoband.profileCGH
     drawCytoband2.default equals.AromaPlatform
     findChangePointsByState.SegmentedGenomicSignalsInterface
     findSAFs.SampleAnnotationSet fit2d.matrix
     fitGenotypeConeByExpectile.matrix fitGenotypeConeBySfit.matrix
     fitMultiDimensionalCone.matrix fixSearchPath.AromaCore
     getAromaUflFile.AromaPlatformInterface
     getGenericSummary.RichDataFrame
     getListOfUnitNamesFiles.ChromosomalModel
     getListOfUnitTypesFiles.ChromosomalModel
     getLog2Ratios.CopyNumberSegmentationModel
     getOutputSet.ChromosomalModel getRawCnData.CopyNumberChromosomalModel
     getSampleLayerName.Explorer getSetTag.ChromosomalModel
     getVerbose.AromaRepository getVerbose.AromaSettings
     getVersion.Explorer getVirtualColumnFunctions.RichDataFrame
     isDone.AromaTransform listToXml.list norm2d.matrix
     normalizeGenotypeCone.matrix patchPackage.default
     plotProfile2.profileCGH processTime.default reorder.BinnedScatter
     requireWithMemory.default setVirtualColumnFunctions.RichDataFrame
     stextChipType.character stextLabel.AromaMicroarrayDataFile
     stextLabels.AromaMicroarrayDataFile stextSize.AromaMicroarrayDataFile
     stringTree.character whatDataType.default write.default
     writeAxesLayers.ChromosomeExplorer
     writeCopyNumberRegionLayers.ChromosomeExplorer
     writeCytobandLayers.ChromosomeExplorer
     writeDataFrame.AromaUnitFracBCnBinarySet
     writeDataFrame.AromaUnitPscnBinarySet
     writeDataFrame.AromaUnitSignalBinaryFile
     writeDataFrame.AromaUnitSignalBinarySet
     writeDataFrame.AromaUnitTabularBinaryFile
     writeDataFrame.AromaUnitTotalCnBinarySet
     writeGraphs.ChromosomeExplorer
     writeGridHorizontalLayers.ChromosomeExplorer
     writeRawCopyNumberLayers.ChromosomeExplorer
     writeRegions.ChromosomeExplorer
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 2.13.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     apply.default byPathnames.SampleAnnotationSet calcMargins.matrix
     downloadPackagePatch.default drawCytoband.ChromosomalModel
     drawCytoband.profileCGH drawCytoband2.default
     findChangePointsByState.SegmentedGenomicSignalsInterface
     findSAFs.SampleAnnotationSet fit2d.matrix
     fitGenotypeConeByExpectile.matrix fitGenotypeConeBySfit.matrix
     fitMultiDimensionalCone.matrix fixSearchPath.AromaCore
     getAromaUflFile.AromaPlatformInterface
     getGenericSummary.RichDataFrame
     getListOfUnitNamesFiles.ChromosomalModel
     getListOfUnitTypesFiles.ChromosomalModel
     getLog2Ratios.CopyNumberSegmentationModel
     getOutputSet.ChromosomalModel getRawCnData.CopyNumberChromosomalModel
     getSampleLayerName.Explorer getSetTag.ChromosomalModel
     getVirtualColumnFunctions.RichDataFrame listToXml.list norm2d.matrix
     normalizeGenotypeCone.matrix patchPackage.default
     plotProfile2.profileCGH processTime.default requireWithMemory.default
     setVirtualColumnFunctions.RichDataFrame stextChipType.character
     stextLabel.AromaMicroarrayDataFile
     stextLabels.AromaMicroarrayDataFile stextSize.AromaMicroarrayDataFile
     stringTree.character whatDataType.default write.default
     writeAxesLayers.ChromosomeExplorer
     writeCopyNumberRegionLayers.ChromosomeExplorer
     writeCytobandLayers.ChromosomeExplorer writeGraphs.ChromosomeExplorer
     writeGridHorizontalLayers.ChromosomeExplorer
     writeRawCopyNumberLayers.ChromosomeExplorer
     writeRegions.ChromosomeExplorer reorder.BinnedScatter
     getVerbose.AromaRepository getVerbose.AromaSettings
     isDone.AromaTransform writeDataFrame.AromaUnitFracBCnBinarySet
     writeDataFrame.AromaUnitPscnBinarySet
     writeDataFrame.AromaUnitSignalBinaryFile
     writeDataFrame.AromaUnitSignalBinarySet
     writeDataFrame.AromaUnitTabularBinaryFile
     writeDataFrame.AromaUnitTotalCnBinarySet equals.AromaPlatform
     getVersion.Explorer as.character.AromaMicroarrayDataSetTuple
     as.character.AromaPlatform
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-osx-x86_64-snowleopard

Version: 2.13.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GLAD’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 2.13.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘EBImage’ ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavor: r-release-osx-x86_64-mavericks

Package calmate

Current CRAN status: NOTE: 13, OK: 2

Version: 0.11.0
Check: R code for possible problems
Result: NOTE
    process.CalMaTeCalibration: no visible binding for global variable
     ‘aromaSettings’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Package matrixStats

Current CRAN status: OK: 15

Package PSCBS

Current CRAN status: NOTE: 5, OK: 10

Version: 0.43.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     callGLAO.CBS encodeCalls.data.frame unTumorBoost.PairedPSCBS
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Package R.cache

Current CRAN status: OK: 15

Package R.devices

Current CRAN status: NOTE: 6, OK: 9

Version: 2.12.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘digest’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Package R.filesets

Current CRAN status: NOTE: 8, OK: 7

Version: 2.6.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘BatchJobs’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 2.6.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     is.na.GenericDataFile is.na.GenericDataFileSet linkTo.GenericDataFile
     readChecksums.ChecksumFileSet rep.GenericDataFileSet
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 2.6.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     linkTo.GenericDataFile readChecksums.ChecksumFileSet
     is.na.GenericDataFile is.na.GenericDataFileSet rep.GenericDataFileSet
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.6.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘BiocParallel’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Package R.huge

Current CRAN status: NOTE: 5, OK: 10

Version: 0.8.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     colnames.default ncol.default nrow.default rownames.default
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Package R.matlab

Current CRAN status: NOTE: 6, OK: 9

Version: 3.1.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘Matrix’ ‘SparseM’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Package R.methodsS3

Current CRAN status: OK: 15

Package R.oo

Current CRAN status: NOTE: 6, OK: 9

Version: 1.18.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘pkg’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 1.18.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     getClasses.default getMethods.default
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Package R.rsp

Current CRAN status: NOTE: 13, OK: 2

Version: 0.19.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘tcltk’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 0.19.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     parse.default rcat.expression rfile.expression rsource.expression
     rspToHtml.default rsptex.default rstring.expression
     setMetadata.RspProduct setMetadata.RspString sourceRspV2.default
     write.default
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

Version: 0.19.0
Check: R code for possible problems
Result: NOTE
    compileAsciiDocNoweb.default: no visible global function definition for
     ‘Asciidoc’
    compileKnitr.default: no visible global function definition for ‘knit’
    epsDev: no visible global function definition for ‘devNew’
    epsDev: no visible binding for global variable ‘eps’
    parse.RspRSourceCode: no visible global function definition for
     ‘digest’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Package R.utils

Current CRAN status: NOTE: 6, OK: 9

Version: 1.34.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘digest’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 1.34.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     warnings.default
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang