CRAN Package Check Results for Package aroma.affymetrix

Last updated on 2015-07-05 22:47:17.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.13.2 9.62 148.05 157.67 NOTE
r-devel-linux-x86_64-debian-gcc 2.13.2 9.25 149.51 158.76 NOTE
r-devel-linux-x86_64-fedora-clang 2.13.2 295.66 NOTE
r-devel-linux-x86_64-fedora-gcc 2.13.2 262.46 NOTE
r-devel-osx-x86_64-clang 2.13.2 274.22 NOTE
r-devel-windows-ix86+x86_64 2.13.2 34.00 197.00 231.00 NOTE
r-patched-linux-x86_64 2.13.2 9.42 146.67 156.10 NOTE
r-patched-solaris-sparc 2.13.2 1677.80 NOTE
r-patched-solaris-x86 2.13.2 338.30 NOTE
r-release-linux-x86_64 2.13.2 10.95 145.45 156.40 NOTE
r-release-osx-x86_64-mavericks 2.13.2 NOTE
r-release-windows-ix86+x86_64 2.13.2 40.00 205.00 245.00 NOTE
r-oldrel-windows-ix86+x86_64 2.13.2 45.00 328.00 373.00 NOTE

Check Details

Version: 2.13.2
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-x86_64

Version: 2.13.2
Check: R code for possible problems
Result: NOTE
    addColorMap.SpatialReporter: no visible global function definition for
     ‘gray.colors’
    annotateMvsA.AffymetrixCelFile: no visible global function definition
     for ‘abline’
    applyAnyOrder.CopyNumberChromosomalModel: no visible global function
     definition for ‘str’
    applyCCF0.CopyNumberChromosomalModel: no visible global function
     definition for ‘str’
    applyCFC0.CopyNumberChromosomalModel: no visible global function
     definition for ‘str’
    as.character.AffymetrixCnChpFile: no visible global function definition
     for ‘capture.output’
    as.character.AffymetrixCnChpFile: no visible global function definition
     for ‘str’
    averageQuantile.AffymetrixCelSet: no visible global function definition
     for ‘approx’
    bgAdjustGcrma.AffymetrixCelFile: no visible global function definition
     for ‘str’
    bgAdjustRma.AffymetrixCelFile: no visible global function definition
     for ‘rnorm’
    bpmapCluster2Cdf.default: no visible global function definition for
     ‘str’
    byChipType.UflSnpInformation: no visible global function definition for
     ‘str’
    byChipType.UgpGenomeInformation: no visible global function definition
     for ‘str’
    byPath.AffymetrixCelSetTuple: no visible global function definition for
     ‘str’
    calcRawCnStats.CopyNumberChromosomalModel: no visible global function
     definition for ‘str’
    calcRawCnStats.default: no visible global function definition for
     ‘median’
    calcRawCnStats.default: no visible global function definition for ‘mad’
    calculateAffinities.GcRmaBackgroundCorrection: no visible global
     function definition for ‘object.size’
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for ‘str’
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for ‘median’
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for ‘mad’
    calculateBaseline.ChipEffectSet: no visible global function definition
     for ‘str’
    calculateBaseline.ChipEffectSet: no visible global function definition
     for ‘median’
    calculateConfidenceScores.CrlmmModel: no visible global function
     definition for ‘str’
    calculateFieldBoxplotStats.ChipEffectSet: no visible binding for global
     variable ‘boxplot.stats’
    calculateFieldBoxplotStats.ChipEffectSet: no visible global function
     definition for ‘str’
    calculateMargins.SpatialReporter: no visible global function definition
     for ‘median’
    calculateNuseBoxplotStats.ChipEffectSet: no visible global function
     definition for ‘str’
    calculateNuseBoxplotStats.ChipEffectSet: no visible global function
     definition for ‘boxplot.stats’
    calculateParametersGsb.AffymetrixCelSet: no visible global function
     definition for ‘str’
    calculateParametersGsb.AffymetrixCelSet: no visible global function
     definition for ‘lm’
    calculateResidualSet.ProbeLevelModel: no visible global function
     definition for ‘str’
    calculateRleBoxplotStats.ChipEffectSet: no visible binding for global
     variable ‘boxplot.stats’
    calculateRleBoxplotStats.ChipEffectSet: no visible global function
     definition for ‘str’
    calculateTargetDistribution.QuantileNormalization: no visible global
     function definition for ‘str’
    calculateWeights.ExonRmaPlm : resFcn: no visible global function
     definition for ‘median’
    calculateWeights.ExonRmaPlm : resFcn : <anonymous>: no visible global
     function definition for ‘median’
    calculateWeights.ProbeLevelModel : resFcn : <anonymous>: no visible
     global function definition for ‘median’
    computeAffinities.AffymetrixCdfFile: Error while checking: invalid
     ‘envir’ argument
    computeAffinitiesByACS.AffymetrixCdfFile: Error while checking: invalid
     ‘envir’ argument
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for ‘str’
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for ‘object.size’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘object.size’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    createOutputTuple.SmoothMultiarrayModel: no visible global function
     definition for ‘str’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘object.size’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    doCRMAv1.AffymetrixCelSet: no visible global function definition for
     ‘str’
    doCRMAv2.AffymetrixCelSet: no visible global function definition for
     ‘str’
    doFIRMA.AffymetrixCelSet: no visible global function definition for
     ‘str’
    doGCRMA.AffymetrixCelSet: no visible global function definition for
     ‘str’
    doRMA.AffymetrixCelSet: no visible global function definition for ‘str’
    exportTotalAndFracB.DChipDcpSet: no visible global function definition
     for ‘str’
    exportTotalAndFracB.SnpChipEffectFile: no visible global function
     definition for ‘str’
    exportTotalAndFracB.SnpChipEffectSet: no visible global function
     definition for ‘str’
    exportTotalCnRatioSet.AffymetrixCnChpSet: no visible global function
     definition for ‘str’
    extractAlleleSet.SnpChipEffectSet: no visible global function
     definition for ‘str’
    extractChromosomalDataFrame.ChipEffectFile: no visible global function
     definition for ‘str’
    extractChromosomalDataFrame.ChipEffectSet: no visible global function
     definition for ‘str’
    extractDataFrame.ParameterCelFile: no visible global function
     definition for ‘str’
    extractDataFrame.ParameterCelSet: no visible global function definition
     for ‘str’
    extractExpressionSet.ChipEffectSet: no visible global function
     definition for ‘str’
    extractLogRatios.AffymetrixCnChpSet: no visible global function
     definition for ‘str’
    extractMatrix.AffymetrixCelFile: no visible global function definition
     for ‘str’
    extractMatrix.AffymetrixCelFile: no visible global function definition
     for ‘object.size’
    extractMatrix.AffymetrixCelSet: no visible global function definition
     for ‘str’
    extractMatrix.AffymetrixCelSet: no visible global function definition
     for ‘object.size’
    extractSnpQSet.SnpChipEffectSet: no visible global function definition
     for ‘str’
    extractTheta.ChipEffectFile: no visible global function definition for
     ‘str’
    extractTheta.ChipEffectSet: no visible global function definition for
     ‘str’
    extractTheta.DChipDcpSet: no visible global function definition for
     ‘str’
    extractTheta.SnpQSet: no visible global function definition for
     ‘packageVersion’
    extractTotalAndFracB.SnpChipEffectFile: no visible global function
     definition for ‘str’
    extractTotalAndFreqB.CnChipEffectFile: no visible global function
     definition for ‘str’
    extractTotalAndFreqB.CnChipEffectSet: no visible global function
     definition for ‘str’
    extractTotalAndFreqB.SnpChipEffectSet: no visible global function
     definition for ‘str’
    findUnitsTodo.ChipEffectFile: no visible global function definition for
     ‘str’
    findUnitsTodo.CrlmmModel: no visible global function definition for
     ‘str’
    findUnitsTodo.FirmaFile: no visible global function definition for
     ‘str’
    findUnitsTodo.QualityAssessmentFile: no visible global function
     definition for ‘str’
    findUnitsTodo.ResidualFile: no visible global function definition for
     ‘str’
    findUnitsTodo.WeightsFile: no visible global function definition for
     ‘str’
    fit.CrlmmModel: no visible global function definition for ‘str’
    fit.FirmaModel: no visible global function definition for ‘str’
    fit.ProbeLevelModel: no visible global function definition for ‘str’
    fit.ProbeLevelModel: no visible global function definition for ‘tail’
    fitCnProbes.UnitModel: no visible global function definition for ‘str’
    fitOne.BaseCountNormalization : fitBaseCounts : fitFcn: no visible
     global function definition for ‘median’
    fitOne.BaseCountNormalization : fitBaseCounts : fitFcn: no visible
     global function definition for ‘predict’
    fitOne.BaseCountNormalization : fitSubset: no visible global function
     definition for ‘str’
    fitOne.BaseCountNormalization: no visible global function definition
     for ‘str’
    fitOne.BaseCountNormalization: no visible global function definition
     for ‘predict’
    fitOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for ‘str’
    fitOne.MatNormalization: no visible global function definition for
     ‘str’
    fitOne.ScaleNormalization3: no visible global function definition for
     ‘str’
    fitOne.ScaleNormalization3: no visible global function definition for
     ‘median’
    fitOne.UnitTypeScaleNormalization: no visible global function
     definition for ‘str’
    fitOne.UnitTypeScaleNormalization: no visible global function
     definition for ‘median’
    fitOneArray.SingleArrayUnitModel: no visible global function definition
     for ‘str’
    fitOneChromosome.SmoothMultiarrayModel: no visible global function
     definition for ‘str’
    fitPlasqUnit.matrix: no visible global function definition for ‘t.test’
    fitPlasqUnit.matrix: no visible global function definition for ‘glm’
    fitPlasqUnit.matrix: no visible binding for global variable ‘na.omit’
    fitPlasqUnit.matrix: no visible global function definition for ‘coef’
    fitPlasqUnit.matrix: no visible global function definition for
     ‘residuals’
    fitPlasqUnit.matrix: no visible global function definition for ‘dnorm’
    fitQuantileNormFcn.AffymetrixCelFile: no visible global function
     definition for ‘smooth.spline’
    getAM.ChipEffectFile: no visible global function definition for ‘str’
    getAM.ChipEffectSet: no visible global function definition for ‘str’
    getAlleleCellPairs.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getAlleleProbePairs.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getAlleleProbePairs3.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getCellIndices.AffymetrixCdfFile: no visible global function definition
     for ‘str’
    getCellIndices.AffymetrixCdfFile: no visible global function definition
     for ‘object.size’
    getCellIndices.CnChipEffectFile: no visible global function definition
     for ‘object.size’
    getCellIndices.ExonChipEffectFile: no visible global function
     definition for ‘object.size’
    getCellIndices.SnpChipEffectFile: no visible global function definition
     for ‘object.size’
    getCellsToInternal.ProbeLevelTransform3: no visible global function
     definition for ‘str’
    getCovariates.GcContentNormalization2: no visible global function
     definition for ‘str’
    getCrlmmSNPs.CrlmmModel: no visible global function definition for
     ‘str’
    getCrlmmSNPsOnChrX.CrlmmModel: no visible global function definition
     for ‘str’
    getCrlmmSplineParameters.CrlmmModel: no visible global function
     definition for ‘str’
    getData.AffymetrixCnChpFile: no visible global function definition for
     ‘capture.output’
    getData.AffymetrixCnChpFile: no visible global function definition for
     ‘str’
    getData.GenomeInformation: no visible global function definition for
     ‘str’
    getData.GenomeInformation: no visible global function definition for
     ‘na.omit’
    getData.SnpInformation: no visible global function definition for
     ‘na.omit’
    getData.UflSnpInformation: no visible global function definition for
     ‘str’
    getData.UflSnpInformation: no visible global function definition for
     ‘na.omit’
    getData.UgpGenomeInformation: no visible global function definition for
     ‘str’
    getData.UgpGenomeInformation: no visible global function definition for
     ‘na.omit’
    getDataFlat.ChipEffectFile: no visible global function definition for
     ‘str’
    getDataFlat.FirmaFile: no visible global function definition for ‘str’
    getDataFlat.ResidualFile: no visible global function definition for
     ‘str’
    getDataFlat.WeightsFile: no visible global function definition for
     ‘str’
    getDesignMatrix.BaseCountNormalization: no visible global function
     definition for ‘str’
    getDesignMatrix.BaseCountNormalization: no visible global function
     definition for ‘object.size’
    getDesignMatrix.BasePositionNormalization: no visible global function
     definition for ‘str’
    getDesignMatrix.BasePositionNormalization: no visible global function
     definition for ‘object.size’
    getDesignMatrix.MatNormalization: no visible global function definition
     for ‘str’
    getDesignMatrix.MatNormalization: no visible global function definition
     for ‘object.size’
    getExclusiveUnitSubsets.FragmentEquivalentClassNormalization: no
     visible global function definition for ‘str’
    getExpandedCellMap.ChipEffectFile: no visible global function
     definition for ‘str’
    getExpectedOutputFullnames.MatSmoothing: no visible global function
     definition for ‘str’
    getFilteredFragmentLengths.FragmentLengthNormalization: no visible
     global function definition for ‘str’
    getFitUnitFunction.FirmaModel : fitUnit: no visible global function
     definition for ‘mad’
    getFitUnitGroupFunction.AvgPlm : avgPlmModel: no visible global
     function definition for ‘str’
    getFitUnitGroupFunction.ExonRmaPlm : exonRmaModel: no visible global
     function definition for ‘medpolish’
    getFitUnitGroupFunction.ExonRmaPlm : getRlmPkg: no visible global
     function definition for ‘packageDescription’
    getFitUnitGroupFunction.ExonRmaPlm : getRlmPkg: no visible global
     function definition for ‘compareVersion’
    getFitUnitGroupFunction.ExonRmaPlm: no visible global function
     definition for ‘str’
    getFitUnitGroupFunction.HetLogAddPlm: no visible global function
     definition for ‘str’
    getFitUnitGroupFunction.RmaPlm : rmaModelAffyPlm: no visible global
     function definition for ‘str’
    getFitUnitGroupFunction.RmaPlm : rmaModelAffyPlm: no visible global
     function definition for ‘medpolish’
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for ‘packageDescription’
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for ‘compareVersion’
    getFitUnitGroupFunction.RmaPlm : rmaModelOligo: no visible global
     function definition for ‘str’
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for ‘str’
    getGcContent.GcContentNormalization: no visible global function
     definition for ‘str’
    getImage.AffymetrixCdfFile: no visible global function definition for
     ‘str’
    getImage.AffymetrixCdfFile: no visible global function definition for
     ‘object.size’
    getImage.AffymetrixCelFile: no visible global function definition for
     ‘str’
    getImage.AffymetrixCelFile: no visible global function definition for
     ‘object.size’
    getImage.AromaUnitTabularBinaryFile: no visible global function
     definition for ‘str’
    getImage.AromaUnitTabularBinaryFile: no visible global function
     definition for ‘object.size’
    getImage.ResidualFile: no visible global function definition for
     ‘rainbow’
    getImage.WeightsFile: no visible global function definition for
     ‘rainbow’
    getNormalEquations.LinearModelProbeSequenceNormalization: no visible
     global function definition for ‘str’
    getNormalizeSignalsOne.ScaleNormalization3: no visible global function
     definition for ‘str’
    getNormalizeSignalsOne.ScaleNormalization3: no visible global function
     definition for ‘median’
    getNormalizeSignalsOne.UnitTypeScaleNormalization: no visible global
     function definition for ‘str’
    getNormalizeSignalsOne.UnitTypeScaleNormalization: no visible global
     function definition for ‘median’
    getNumberOfFilesAveraged.CnChipEffectFile: no visible global function
     definition for ‘str’
    getOutputDataSet.Transform: no visible global function definition for
     ‘str’
    getOutputDataSet00.AdditiveCovariatesNormalization: no visible global
     function definition for ‘str’
    getOutputDataSet00.FragmentEquivalentClassNormalization: no visible
     global function definition for ‘str’
    getOutputDataSet00.FragmentLengthNormalization: no visible global
     function definition for ‘str’
    getPcuTheta.ChromosomalModel: no visible global function definition for
     ‘str’
    getPositionChipTypeUnit.ChromosomalModel: no visible global function
     definition for ‘str’
    getPositionChipTypeUnit.CopyNumberSegmentationModel: no visible global
     function definition for ‘str’
    getProbeSequenceData.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getResiduals.QualityAssessmentModel: no visible global function
     definition for ‘str’
    getRlmFitFunctions.RmaPlm: no visible global function definition for
     ‘packageDescription’
    getRlmFitFunctions.RmaPlm: no visible global function definition for
     ‘compareVersion’
    getSetsOfProbes.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    getSteps.ASCRMAv2 : <anonymous>: no visible global function definition
     for ‘str’
    getSubsetOfCellIndices.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getSubsetOfUnits.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getSubsetToAvg.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    getSubsetToAvg.QuantileNormalization: no visible global function
     definition for ‘str’
    getSubsetToAvg.ReseqCrosstalkCalibration: no visible global function
     definition for ‘str’
    getSubsetToAvg.ScaleNormalization: no visible global function
     definition for ‘str’
    getSubsetToFit.AdditiveCovariatesNormalization: no visible global
     function definition for ‘str’
    getSubsetToFit.FragmentEquivalentClassNormalization: no visible global
     function definition for ‘str’
    getSubsetToFit.FragmentLengthNormalization: no visible global function
     definition for ‘str’
    getSubsetToUpdate.QuantileNormalization: no visible global function
     definition for ‘str’
    getSubsetToUpdate.ScaleNormalization: no visible global function
     definition for ‘str’
    getTargetAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for ‘str’
    getTargetDistribution.QuantileNormalization: no visible global function
     definition for ‘str’
    getTargetFunction.GcContentNormalization: no visible global function
     definition for ‘str’
    getTargetFunction.GcContentNormalization: no visible global function
     definition for ‘lowess’
    getTargetFunction.GcContentNormalization : fcn: no visible global
     function definition for ‘predict’
    getTargetFunctions.AdditiveCovariatesNormalization: no visible global
     function definition for ‘str’
    getTargetFunctions.AdditiveCovariatesNormalization: no visible global
     function definition for ‘lowess’
    getTargetFunctions.AdditiveCovariatesNormalization : <anonymous>: no
     visible global function definition for ‘predict’
    getTargetFunctions.FragmentLengthNormalization: no visible global
     function definition for ‘str’
    getTargetFunctions.FragmentLengthNormalization: no visible global
     function definition for ‘lowess’
    getTargetFunctions.FragmentLengthNormalization : <anonymous>: no
     visible global function definition for ‘predict’
    getUnitGroupCellArrayMap.ChipEffectFile: no visible global function
     definition for ‘str’
    getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile: no visible
     global function definition for ‘str’
    getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile: no visible
     global function definition for ‘object.size’
    getUnitGroupCellChromosomePositionMap.ChipEffectFile: no visible global
     function definition for ‘str’
    getUnitGroupCellChromosomePositionMap.ChipEffectFile: no visible global
     function definition for ‘object.size’
    getUnitGroupCellMap.AffymetrixCdfFile: no visible global function
     definition for ‘object.size’
    getUnitGroupCellMap.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    getUnitGroupCellMatrixMap.ChipEffectFile: no visible global function
     definition for ‘str’
    getUnitGroupNamesFromUgcMap.AffymetrixCdfFile: no visible global
     function definition for ‘str’
    getWeights.QualityAssessmentModel : resFcn : <anonymous>: no visible
     global function definition for ‘median’
    getXAM.ChipEffectFile: no visible global function definition for ‘str’
    getXAM.ChipEffectSet: no visible global function definition for ‘str’
    groupUnitsByDimension.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    highlight.AffymetrixCelFile: no visible global function definition for
     ‘points’
    identifyCells.AffymetrixCdfFile: no visible global function definition
     for ‘str’
    image270.AffymetrixCelFile: no visible global function definition for
     ‘gray.colors’
    image270.AffymetrixCelFile: no visible global function definition for
     ‘image’
    image270.AffymetrixCelFile: no visible global function definition for
     ‘text’
    importFromAffymetrixNetAffxCsvFile.AromaUflFile: no visible global
     function definition for ‘str’
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible binding for
     global variable ‘median’
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible global
     function definition for ‘median’
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible global
     function definition for ‘str’
    importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile: no visible
     global function definition for ‘str’
    importFromAffymetrixProbeTabFile.AromaCellSequenceFile: no visible
     global function definition for ‘str’
    importFromAffymetrixProbeTabFile.AromaCellSequenceFile: no visible
     global function definition for ‘head’
    importFromAffymetrixTabularFile.AromaUfcFile: no visible global
     function definition for ‘str’
    importFromApt.CnChipEffectSet: no visible global function definition
     for ‘str’
    importFromApt.CnChipEffectSet : <anonymous>: no visible global function
     definition for ‘str’
    importFromDChip.CnChipEffectSet : importUnits: no visible global
     function definition for ‘read.table’
    importFromDChip.CnChipEffectSet : importUnits: no visible global
     function definition for ‘str’
    importFromDChip.CnChipEffectSet: no visible global function definition
     for ‘str’
    importFromDChip.CnChipEffectSet : <anonymous>: no visible global
     function definition for ‘str’
    importFromDChip.CnChipEffectSet: no visible global function definition
     for ‘read.table’
    indexOfMissingSequences.AbstractProbeSequenceNormalization: no visible
     global function definition for ‘str’
    inferMmFromPm.AromaCellSequenceFile: no visible global function
     definition for ‘str’
    inferParameters.CnChipEffectSet: no visible global function definition
     for ‘str’
    inferParameters.SnpChipEffectSet: no visible global function definition
     for ‘str’
    justRMA.AffymetrixCelSet: no visible global function definition for
     ‘as’
    justSNPRMA.AffymetrixCelSet: no visible global function definition for
     ‘str’
    mapToUnitNamesFile.DChipCdfBinFile: no visible global function
     definition for ‘str’
    mergeGroups.ChipEffectFile: no visible global function definition for
     ‘str’
    migrateTool.CopyNumberSegmentationModel: no visible global function
     definition for ‘na.omit’
    normalizeOneArrayVector.FragmentEquivalentClassNormalization: no
     visible global function definition for ‘str’
    pdInfo2Cdf: no visible global function definition for ‘str’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘layout’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘par’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘plot’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘mtext’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘lines’
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for ‘points’
    plotBasepair.AllelicCrosstalkCalibration : linesAllelicCrosstalk: no
     visible global function definition for ‘lines’
    plotBasepair.AllelicCrosstalkCalibration : plotFcn: no visible global
     function definition for ‘smoothScatter’
    plotBasepair.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    plotBoxplotStats.list: no visible global function definition for ‘bxp’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘str’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘par’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘smoothScatter’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘abline’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘smooth.spline’
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for ‘lines’
    plotDensity.AffymetrixCelSet: no visible global function definition for
     ‘str’
    plotDensity.GenomeInformation: no visible global function definition
     for ‘density’
    plotDensity.GenomeInformation: no visible global function definition
     for ‘plot’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘layout’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘plot’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘abline’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘par’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘axis’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘box’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘lines’
    plotMvsA.AffymetrixCelFile: no visible global function definition for
     ‘plot’
    plotMvsX.AffymetrixCelFile: no visible global function definition for
     ‘points’
    plotMvsX.AffymetrixCelFile: no visible global function definition for
     ‘plot’
    plotXYCurve.TransformReport: no visible global function definition for
     ‘str’
    plotXYCurve.TransformReport: no visible global function definition for
     ‘box’
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for ‘coefficients’
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for ‘predict’
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for ‘str’
    predictOne.BaseCountNormalization: no visible global function
     definition for ‘str’
    predictOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for ‘str’
    predictOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for ‘predict’
    predictOne.MatNormalization: no visible global function definition for
     ‘str’
    process.AbstractProbeSequenceNormalization : readSeqs: no visible
     global function definition for ‘str’
    process.AbstractProbeSequenceNormalization: no visible global function
     definition for ‘str’
    process.AdditiveCovariatesNormalization: no visible global function
     definition for ‘str’
    process.AlleleSummation: no visible global function definition for
     ‘str’
    process.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    process.ChipEffectGroupMerge: no visible global function definition for
     ‘str’
    process.DChipQuantileNormalization: no visible global function
     definition for ‘str’
    process.FragmentEquivalentClassNormalization: no visible global
     function definition for ‘str’
    process.FragmentLengthNormalization: no visible global function
     definition for ‘str’
    process.GcContentNormalization: no visible global function definition
     for ‘str’
    process.LimmaBackgroundCorrection: no visible global function
     definition for ‘rnorm’
    process.LimmaBackgroundCorrection: no visible global function
     definition for ‘str’
    process.MatNormalization: no visible global function definition for
     ‘str’
    process.MatNormalization: no visible global function definition for
     ‘quantile’
    process.MatNormalization: no visible binding for global variable ‘var’
    process.MatSmoothing : calcNullDist0: no visible global function
     definition for ‘median’
    process.MatSmoothing : calcNullDist0: no visible global function
     definition for ‘sd’
    process.MatSmoothing : calcNullDist: no visible global function
     definition for ‘median’
    process.MatSmoothing : calcNullDist: no visible global function
     definition for ‘sd’
    process.MatSmoothing : calcNullDists: no visible global function
     definition for ‘median’
    process.MatSmoothing: no visible global function definition for ‘str’
    process.OpticalBackgroundCorrection: no visible global function
     definition for ‘str’
    process.QuantileNormalization: no visible global function definition
     for ‘str’
    process.ReseqCrosstalkCalibration: no visible global function
     definition for ‘str’
    process.ScaleNormalization: no visible global function definition for
     ‘str’
    process.ScaleNormalization: no visible global function definition for
     ‘median’
    process.ScaleNormalization3: no visible global function definition for
     ‘str’
    process.SpatialRowColumnNormalization: no visible global function
     definition for ‘str’
    process.SpatialRowColumnNormalization: no visible global function
     definition for ‘residuals’
    process.UnitTypeScaleNormalization: no visible global function
     definition for ‘str’
    readCfhUnits.default: no visible global function definition for ‘str’
    readCfnUnits.default: no visible global function definition for ‘str’
    readDataFrame.AffymetrixCdfFile: no visible global function definition
     for ‘str’
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for ‘na.omit’
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for ‘str’
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for ‘read.table’
    readDataFrame.UgpGenomeInformation: no visible global function
     definition for ‘str’
    readDataFrame2.AffymetrixProbeTabFile: no visible global function
     definition for ‘str’
    readDataUnitFragmentLength.AffymetrixNetAffxCsvFile: no visible global
     function definition for ‘str’
    readDataUnitFragmentLength.AffymetrixNetAffxCsvFile: no visible global
     function definition for ‘na.omit’
    readGeneAssignments.AffymetrixNetAffxCsvFile: no visible global
     function definition for ‘str’
    readPriorsByUnits.MultiArrayUnitModel: no visible global function
     definition for ‘str’
    readRawData.AffymetrixCnChpFile: no visible global function definition
     for ‘str’
    readSequenceDataFrame.AffymetrixProbeTabFile: no visible global
     function definition for ‘str’
    readUnits.AffymetrixCelSet: no visible global function definition for
     ‘str’
    readUnits.CnagCfhFile: no visible global function definition for
     ‘na.omit’
    readUnits.CnagCfhSet: no visible global function definition for ‘str’
    readUnits.MultiArrayUnitModel: no visible global function definition
     for ‘str’
    readUnits.ParameterCelFile: no visible global function definition for
     ‘object.size’
    readUnits.SingleArrayUnitModel: no visible global function definition
     for ‘str’
    rescaleByAll.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    rescaleByAll.AllelicCrosstalkCalibration: no visible global function
     definition for ‘median’
    rescaleByAll.ReseqCrosstalkCalibration: no visible global function
     definition for ‘str’
    rescaleByAll.ReseqCrosstalkCalibration: no visible global function
     definition for ‘median’
    rescaleByGroups.AllelicCrosstalkCalibration: no visible global function
     definition for ‘str’
    rescaleByGroups.AllelicCrosstalkCalibration: no visible global function
     definition for ‘median’
    restruct.AffymetrixCdfFile: no visible global function definition for
     ‘str’
    setUnitReadMap.AffymetrixCnChpFile: no visible global function
     definition for ‘str’
    smoothScatterMvsA.AffymetrixCelFile: no visible global function
     definition for ‘smoothScatter’
    updateParameter.CrlmmParametersFile: no visible global function
     definition for ‘str’
    updateUnits.ChipEffectSet: no visible global function definition for
     ‘str’
    updateUnits.FirmaSet: no visible global function definition for ‘str’
    updateUnits.ProbeAffinityFile: no visible global function definition
     for ‘str’
    updateUnits.ResidualSet: no visible global function definition for
     ‘str’
    updateUnits.WeightsSet: no visible global function definition for ‘str’
    writeAsFullCelFile.ChipEffectFile: no visible global function
     definition for ‘str’
    writeCNT.SnpChipEffectFile: no visible global function definition for
     ‘str’
    writeCNT.SnpChipEffectFile: no visible global function definition for
     ‘write.table’
    writeCNT.SnpChipEffectSet: no visible global function definition for
     ‘write.table’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘packageDescription’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘str’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘head’
    writeCdf.PDInfoList: no visible global function definition for ‘str’
    writeCdf.PDInfoList: no visible global function definition for ‘head’
    writeCdfByExcludingCells.AffymetrixCdfFile: no visible global function
     definition for ‘str’
    writeSgr.AffymetrixCelSet: no visible global function definition for
     ‘write.table’
    writeSignals.ProbeLevelTransform3: no visible global function
     definition for ‘str’
    writeWig.CnChipEffectSet: no visible global function definition for
     ‘col2rgb’
    writeWig.CnChipEffectSet: no visible global function definition for
     ‘write.table’
    Undefined global functions or variables:
     abline approx as axis box boxplot.stats bxp capture.output coef
     coefficients col2rgb compareVersion density dnorm glm gray.colors
     head image layout lines lm lowess mad median medpolish mtext na.omit
     object.size packageDescription packageVersion par plot points predict
     quantile rainbow read.table residuals rnorm sd smooth.spline
     smoothScatter str t.test tail text var write.table
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

Version: 2.13.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘pdInfoBuilder’ ‘dChipIO’
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-sparc

Version: 2.13.2
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

Version: 2.13.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘pdInfoBuilder’ ‘dChipIO’
Flavors: r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 2.13.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'AffymetrixDataTestFiles' 'dChipIO'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.13.2
Check: R code for possible problems
Result: NOTE
    addColorMap.SpatialReporter: no visible global function definition for
     'gray.colors'
    annotateMvsA.AffymetrixCelFile: no visible global function definition
     for 'abline'
    applyAnyOrder.CopyNumberChromosomalModel: no visible global function
     definition for 'str'
    applyCCF0.CopyNumberChromosomalModel: no visible global function
     definition for 'str'
    applyCFC0.CopyNumberChromosomalModel: no visible global function
     definition for 'str'
    as.character.AffymetrixCnChpFile: no visible global function definition
     for 'capture.output'
    as.character.AffymetrixCnChpFile: no visible global function definition
     for 'str'
    averageQuantile.AffymetrixCelSet: no visible global function definition
     for 'approx'
    bgAdjustGcrma.AffymetrixCelFile: no visible global function definition
     for 'str'
    bgAdjustRma.AffymetrixCelFile: no visible global function definition
     for 'rnorm'
    bpmapCluster2Cdf.default: no visible global function definition for
     'str'
    byChipType.UflSnpInformation: no visible global function definition for
     'str'
    byChipType.UgpGenomeInformation: no visible global function definition
     for 'str'
    byPath.AffymetrixCelSetTuple: no visible global function definition for
     'str'
    calcRawCnStats.CopyNumberChromosomalModel: no visible global function
     definition for 'str'
    calcRawCnStats.default: no visible global function definition for
     'median'
    calcRawCnStats.default: no visible global function definition for 'mad'
    calculateAffinities.GcRmaBackgroundCorrection: no visible global
     function definition for 'object.size'
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for 'str'
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for 'median'
    calculateAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for 'mad'
    calculateBaseline.ChipEffectSet: no visible global function definition
     for 'str'
    calculateBaseline.ChipEffectSet: no visible global function definition
     for 'median'
    calculateConfidenceScores.CrlmmModel: no visible global function
     definition for 'str'
    calculateFieldBoxplotStats.ChipEffectSet: no visible binding for global
     variable 'boxplot.stats'
    calculateFieldBoxplotStats.ChipEffectSet: no visible global function
     definition for 'str'
    calculateMargins.SpatialReporter: no visible global function definition
     for 'median'
    calculateNuseBoxplotStats.ChipEffectSet: no visible global function
     definition for 'str'
    calculateNuseBoxplotStats.ChipEffectSet: no visible global function
     definition for 'boxplot.stats'
    calculateParametersGsb.AffymetrixCelSet: no visible global function
     definition for 'str'
    calculateParametersGsb.AffymetrixCelSet: no visible global function
     definition for 'lm'
    calculateResidualSet.ProbeLevelModel: no visible global function
     definition for 'str'
    calculateRleBoxplotStats.ChipEffectSet: no visible binding for global
     variable 'boxplot.stats'
    calculateRleBoxplotStats.ChipEffectSet: no visible global function
     definition for 'str'
    calculateTargetDistribution.QuantileNormalization: no visible global
     function definition for 'str'
    calculateWeights.ExonRmaPlm : resFcn: no visible global function
     definition for 'median'
    calculateWeights.ExonRmaPlm : resFcn : <anonymous>: no visible global
     function definition for 'median'
    calculateWeights.ProbeLevelModel : resFcn : <anonymous>: no visible
     global function definition for 'median'
    computeAffinities.AffymetrixCdfFile : getGcrmaSplineCoefs: no visible
     global function definition for 'data'
    computeAffinities.AffymetrixCdfFile: no visible global function
     definition for 'str'
    computeAffinitiesByACS.AffymetrixCdfFile : getGcrmaSplineCoefs: no
     visible global function definition for 'data'
    computeAffinitiesByACS.AffymetrixCdfFile: no visible global function
     definition for 'str'
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for 'str'
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for 'object.size'
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for 'object.size'
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for 'str'
    createOutputTuple.SmoothMultiarrayModel: no visible global function
     definition for 'str'
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for 'object.size'
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for 'str'
    doCRMAv1.AffymetrixCelSet: no visible global function definition for
     'str'
    doCRMAv2.AffymetrixCelSet: no visible global function definition for
     'str'
    doFIRMA.AffymetrixCelSet: no visible global function definition for
     'str'
    doGCRMA.AffymetrixCelSet: no visible global function definition for
     'str'
    doRMA.AffymetrixCelSet: no visible global function definition for 'str'
    exportTotalAndFracB.DChipDcpSet: no visible global function definition
     for 'str'
    exportTotalAndFracB.SnpChipEffectFile: no visible global function
     definition for 'str'
    exportTotalAndFracB.SnpChipEffectSet: no visible global function
     definition for 'str'
    exportTotalCnRatioSet.AffymetrixCnChpSet: no visible global function
     definition for 'str'
    extractAlleleSet.SnpChipEffectSet: no visible global function
     definition for 'str'
    extractChromosomalDataFrame.ChipEffectFile: no visible global function
     definition for 'str'
    extractChromosomalDataFrame.ChipEffectSet: no visible global function
     definition for 'str'
    extractDataFrame.ParameterCelFile: no visible global function
     definition for 'str'
    extractDataFrame.ParameterCelSet: no visible global function definition
     for 'str'
    extractExpressionSet.ChipEffectSet: no visible global function
     definition for 'str'
    extractLogRatios.AffymetrixCnChpSet: no visible global function
     definition for 'str'
    extractMatrix.AffymetrixCelFile: no visible global function definition
     for 'str'
    extractMatrix.AffymetrixCelFile: no visible global function definition
     for 'object.size'
    extractMatrix.AffymetrixCelSet: no visible global function definition
     for 'str'
    extractMatrix.AffymetrixCelSet: no visible global function definition
     for 'object.size'
    extractSnpQSet.SnpChipEffectSet: no visible global function definition
     for 'str'
    extractTheta.ChipEffectFile: no visible global function definition for
     'str'
    extractTheta.ChipEffectSet: no visible global function definition for
     'str'
    extractTheta.DChipDcpSet: no visible global function definition for
     'str'
    extractTheta.SnpQSet: no visible global function definition for
     'packageVersion'
    extractTotalAndFracB.SnpChipEffectFile: no visible global function
     definition for 'str'
    extractTotalAndFreqB.CnChipEffectFile: no visible global function
     definition for 'str'
    extractTotalAndFreqB.CnChipEffectSet: no visible global function
     definition for 'str'
    extractTotalAndFreqB.SnpChipEffectSet: no visible global function
     definition for 'str'
    findUnitsTodo.ChipEffectFile: no visible global function definition for
     'str'
    findUnitsTodo.CrlmmModel: no visible global function definition for
     'str'
    findUnitsTodo.FirmaFile: no visible global function definition for
     'str'
    findUnitsTodo.QualityAssessmentFile: no visible global function
     definition for 'str'
    findUnitsTodo.ResidualFile: no visible global function definition for
     'str'
    findUnitsTodo.WeightsFile: no visible global function definition for
     'str'
    fit.CrlmmModel: no visible global function definition for 'str'
    fit.FirmaModel: no visible global function definition for 'str'
    fit.ProbeLevelModel: no visible global function definition for 'str'
    fit.ProbeLevelModel: no visible global function definition for 'tail'
    fitCnProbes.UnitModel: no visible global function definition for 'str'
    fitOne.BaseCountNormalization : fitBaseCounts : fitFcn: no visible
     global function definition for 'median'
    fitOne.BaseCountNormalization : fitBaseCounts : fitFcn: no visible
     global function definition for 'predict'
    fitOne.BaseCountNormalization : fitSubset: no visible global function
     definition for 'str'
    fitOne.BaseCountNormalization: no visible global function definition
     for 'str'
    fitOne.BaseCountNormalization: no visible global function definition
     for 'predict'
    fitOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for 'str'
    fitOne.MatNormalization: no visible global function definition for
     'str'
    fitOne.ScaleNormalization3: no visible global function definition for
     'str'
    fitOne.ScaleNormalization3: no visible global function definition for
     'median'
    fitOne.UnitTypeScaleNormalization: no visible global function
     definition for 'str'
    fitOne.UnitTypeScaleNormalization: no visible global function
     definition for 'median'
    fitOneArray.SingleArrayUnitModel: no visible global function definition
     for 'str'
    fitOneChromosome.SmoothMultiarrayModel: no visible global function
     definition for 'str'
    fitPlasqUnit.matrix: no visible global function definition for 't.test'
    fitPlasqUnit.matrix: no visible global function definition for 'glm'
    fitPlasqUnit.matrix: no visible binding for global variable 'na.omit'
    fitPlasqUnit.matrix: no visible global function definition for 'coef'
    fitPlasqUnit.matrix: no visible global function definition for
     'residuals'
    fitPlasqUnit.matrix: no visible global function definition for 'dnorm'
    fitQuantileNormFcn.AffymetrixCelFile: no visible global function
     definition for 'smooth.spline'
    getAM.ChipEffectFile: no visible global function definition for 'str'
    getAM.ChipEffectSet: no visible global function definition for 'str'
    getAlleleCellPairs.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getAlleleProbePairs.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getAlleleProbePairs3.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getCellIndices.AffymetrixCdfFile: no visible global function definition
     for 'str'
    getCellIndices.AffymetrixCdfFile: no visible global function definition
     for 'object.size'
    getCellIndices.CnChipEffectFile: no visible global function definition
     for 'object.size'
    getCellIndices.ExonChipEffectFile: no visible global function
     definition for 'object.size'
    getCellIndices.SnpChipEffectFile: no visible global function definition
     for 'object.size'
    getCellsToInternal.ProbeLevelTransform3: no visible global function
     definition for 'str'
    getCovariates.GcContentNormalization2: no visible global function
     definition for 'str'
    getCrlmmSNPs.CrlmmModel: no visible global function definition for
     'str'
    getCrlmmSNPsOnChrX.CrlmmModel: no visible global function definition
     for 'str'
    getCrlmmSplineParameters.CrlmmModel: no visible global function
     definition for 'str'
    getData.AffymetrixCnChpFile: no visible global function definition for
     'capture.output'
    getData.AffymetrixCnChpFile: no visible global function definition for
     'str'
    getData.GenomeInformation: no visible global function definition for
     'str'
    getData.GenomeInformation: no visible global function definition for
     'na.omit'
    getData.SnpInformation: no visible global function definition for
     'na.omit'
    getData.UflSnpInformation: no visible global function definition for
     'str'
    getData.UflSnpInformation: no visible global function definition for
     'na.omit'
    getData.UgpGenomeInformation: no visible global function definition for
     'str'
    getData.UgpGenomeInformation: no visible global function definition for
     'na.omit'
    getDataFlat.ChipEffectFile: no visible global function definition for
     'str'
    getDataFlat.FirmaFile: no visible global function definition for 'str'
    getDataFlat.ResidualFile: no visible global function definition for
     'str'
    getDataFlat.WeightsFile: no visible global function definition for
     'str'
    getDesignMatrix.BaseCountNormalization: no visible global function
     definition for 'str'
    getDesignMatrix.BaseCountNormalization: no visible global function
     definition for 'object.size'
    getDesignMatrix.BasePositionNormalization: no visible global function
     definition for 'str'
    getDesignMatrix.BasePositionNormalization: no visible global function
     definition for 'object.size'
    getDesignMatrix.MatNormalization: no visible global function definition
     for 'str'
    getDesignMatrix.MatNormalization: no visible global function definition
     for 'object.size'
    getExclusiveUnitSubsets.FragmentEquivalentClassNormalization: no
     visible global function definition for 'str'
    getExpandedCellMap.ChipEffectFile: no visible global function
     definition for 'str'
    getExpectedOutputFullnames.MatSmoothing: no visible global function
     definition for 'str'
    getFilteredFragmentLengths.FragmentLengthNormalization: no visible
     global function definition for 'str'
    getFitUnitFunction.FirmaModel : fitUnit: no visible global function
     definition for 'mad'
    getFitUnitGroupFunction.AvgPlm : avgPlmModel: no visible global
     function definition for 'str'
    getFitUnitGroupFunction.ExonRmaPlm : exonRmaModel: no visible global
     function definition for 'medpolish'
    getFitUnitGroupFunction.ExonRmaPlm : getRlmPkg: no visible global
     function definition for 'packageDescription'
    getFitUnitGroupFunction.ExonRmaPlm : getRlmPkg: no visible global
     function definition for 'compareVersion'
    getFitUnitGroupFunction.ExonRmaPlm: no visible global function
     definition for 'str'
    getFitUnitGroupFunction.HetLogAddPlm: no visible global function
     definition for 'str'
    getFitUnitGroupFunction.RmaPlm : rmaModelAffyPlm: no visible global
     function definition for 'str'
    getFitUnitGroupFunction.RmaPlm : rmaModelAffyPlm: no visible global
     function definition for 'medpolish'
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for 'packageDescription'
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for 'compareVersion'
    getFitUnitGroupFunction.RmaPlm : rmaModelOligo: no visible global
     function definition for 'str'
    getFitUnitGroupFunction.RmaPlm: no visible global function definition
     for 'str'
    getGcContent.GcContentNormalization: no visible global function
     definition for 'str'
    getImage.AffymetrixCdfFile: no visible global function definition for
     'str'
    getImage.AffymetrixCdfFile: no visible global function definition for
     'object.size'
    getImage.AffymetrixCelFile: no visible global function definition for
     'str'
    getImage.AffymetrixCelFile: no visible global function definition for
     'object.size'
    getImage.AromaUnitTabularBinaryFile: no visible global function
     definition for 'str'
    getImage.AromaUnitTabularBinaryFile: no visible global function
     definition for 'object.size'
    getImage.ResidualFile: no visible global function definition for
     'rainbow'
    getImage.WeightsFile: no visible global function definition for
     'rainbow'
    getNormalEquations.LinearModelProbeSequenceNormalization: no visible
     global function definition for 'str'
    getNormalizeSignalsOne.ScaleNormalization3: no visible global function
     definition for 'str'
    getNormalizeSignalsOne.ScaleNormalization3: no visible global function
     definition for 'median'
    getNormalizeSignalsOne.UnitTypeScaleNormalization: no visible global
     function definition for 'str'
    getNormalizeSignalsOne.UnitTypeScaleNormalization: no visible global
     function definition for 'median'
    getNumberOfFilesAveraged.CnChipEffectFile: no visible global function
     definition for 'str'
    getOutputDataSet.Transform: no visible global function definition for
     'str'
    getOutputDataSet00.AdditiveCovariatesNormalization: no visible global
     function definition for 'str'
    getOutputDataSet00.FragmentEquivalentClassNormalization: no visible
     global function definition for 'str'
    getOutputDataSet00.FragmentLengthNormalization: no visible global
     function definition for 'str'
    getPcuTheta.ChromosomalModel: no visible global function definition for
     'str'
    getPositionChipTypeUnit.ChromosomalModel: no visible global function
     definition for 'str'
    getPositionChipTypeUnit.CopyNumberSegmentationModel: no visible global
     function definition for 'str'
    getProbeSequenceData.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getResiduals.QualityAssessmentModel: no visible global function
     definition for 'str'
    getRlmFitFunctions.RmaPlm: no visible global function definition for
     'packageDescription'
    getRlmFitFunctions.RmaPlm: no visible global function definition for
     'compareVersion'
    getSetsOfProbes.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    getSteps.ASCRMAv2 : <anonymous>: no visible global function definition
     for 'str'
    getSubsetOfCellIndices.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getSubsetOfUnits.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getSubsetToAvg.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    getSubsetToAvg.QuantileNormalization: no visible global function
     definition for 'str'
    getSubsetToAvg.ReseqCrosstalkCalibration: no visible global function
     definition for 'str'
    getSubsetToAvg.ScaleNormalization: no visible global function
     definition for 'str'
    getSubsetToFit.AdditiveCovariatesNormalization: no visible global
     function definition for 'str'
    getSubsetToFit.FragmentEquivalentClassNormalization: no visible global
     function definition for 'str'
    getSubsetToFit.FragmentLengthNormalization: no visible global function
     definition for 'str'
    getSubsetToUpdate.QuantileNormalization: no visible global function
     definition for 'str'
    getSubsetToUpdate.ScaleNormalization: no visible global function
     definition for 'str'
    getTargetAverages.FragmentEquivalentClassNormalization: no visible
     global function definition for 'str'
    getTargetDistribution.QuantileNormalization: no visible global function
     definition for 'str'
    getTargetFunction.GcContentNormalization: no visible global function
     definition for 'str'
    getTargetFunction.GcContentNormalization: no visible global function
     definition for 'lowess'
    getTargetFunction.GcContentNormalization : fcn: no visible global
     function definition for 'predict'
    getTargetFunctions.AdditiveCovariatesNormalization: no visible global
     function definition for 'str'
    getTargetFunctions.AdditiveCovariatesNormalization: no visible global
     function definition for 'lowess'
    getTargetFunctions.AdditiveCovariatesNormalization : <anonymous>: no
     visible global function definition for 'predict'
    getTargetFunctions.FragmentLengthNormalization: no visible global
     function definition for 'str'
    getTargetFunctions.FragmentLengthNormalization: no visible global
     function definition for 'lowess'
    getTargetFunctions.FragmentLengthNormalization : <anonymous>: no
     visible global function definition for 'predict'
    getUnitGroupCellArrayMap.ChipEffectFile: no visible global function
     definition for 'str'
    getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile: no visible
     global function definition for 'str'
    getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile: no visible
     global function definition for 'object.size'
    getUnitGroupCellChromosomePositionMap.ChipEffectFile: no visible global
     function definition for 'str'
    getUnitGroupCellChromosomePositionMap.ChipEffectFile: no visible global
     function definition for 'object.size'
    getUnitGroupCellMap.AffymetrixCdfFile: no visible global function
     definition for 'object.size'
    getUnitGroupCellMap.AffymetrixCdfFile: no visible global function
     definition for 'str'
    getUnitGroupCellMatrixMap.ChipEffectFile: no visible global function
     definition for 'str'
    getUnitGroupNamesFromUgcMap.AffymetrixCdfFile: no visible global
     function definition for 'str'
    getWeights.QualityAssessmentModel : resFcn : <anonymous>: no visible
     global function definition for 'median'
    getXAM.ChipEffectFile: no visible global function definition for 'str'
    getXAM.ChipEffectSet: no visible global function definition for 'str'
    groupUnitsByDimension.AffymetrixCdfFile: no visible global function
     definition for 'str'
    highlight.AffymetrixCelFile: no visible global function definition for
     'points'
    identifyCells.AffymetrixCdfFile: no visible global function definition
     for 'str'
    image270.AffymetrixCelFile: no visible global function definition for
     'gray.colors'
    image270.AffymetrixCelFile: no visible global function definition for
     'image'
    image270.AffymetrixCelFile: no visible global function definition for
     'text'
    importFromAffymetrixNetAffxCsvFile.AromaUflFile: no visible global
     function definition for 'str'
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible binding for
     global variable 'median'
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible global
     function definition for 'median'
    importFromAffymetrixNetAffxCsvFile.AromaUgpFile: no visible global
     function definition for 'str'
    importFromAffymetrixNetAffxCsvFile.AromaUnitGcContentFile: no visible
     global function definition for 'str'
    importFromAffymetrixProbeTabFile.AromaCellSequenceFile: no visible
     global function definition for 'str'
    importFromAffymetrixProbeTabFile.AromaCellSequenceFile: no visible
     global function definition for 'head'
    importFromAffymetrixTabularFile.AromaUfcFile: no visible global
     function definition for 'str'
    importFromApt.CnChipEffectSet: no visible global function definition
     for 'str'
    importFromApt.CnChipEffectSet : <anonymous>: no visible global function
     definition for 'str'
    importFromDChip.CnChipEffectSet : importUnits: no visible global
     function definition for 'read.table'
    importFromDChip.CnChipEffectSet : importUnits: no visible global
     function definition for 'str'
    importFromDChip.CnChipEffectSet: no visible global function definition
     for 'str'
    importFromDChip.CnChipEffectSet : <anonymous>: no visible global
     function definition for 'str'
    importFromDChip.CnChipEffectSet: no visible global function definition
     for 'read.table'
    indexOfMissingSequences.AbstractProbeSequenceNormalization: no visible
     global function definition for 'str'
    inferMmFromPm.AromaCellSequenceFile: no visible global function
     definition for 'str'
    inferParameters.CnChipEffectSet: no visible global function definition
     for 'str'
    inferParameters.SnpChipEffectSet: no visible global function definition
     for 'str'
    justRMA.AffymetrixCelSet: no visible global function definition for
     'as'
    justSNPRMA.AffymetrixCelSet: no visible global function definition for
     'str'
    mapToUnitNamesFile.DChipCdfBinFile: no visible global function
     definition for 'str'
    mergeGroups.ChipEffectFile: no visible global function definition for
     'str'
    migrateTool.CopyNumberSegmentationModel: no visible global function
     definition for 'na.omit'
    normalizeOneArrayVector.FragmentEquivalentClassNormalization: no
     visible global function definition for 'str'
    pdInfo2Cdf: no visible global function definition for 'str'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'layout'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'par'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'plot'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'mtext'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'lines'
    plotAllelePairs.AllelicCrosstalkCalibration: no visible global function
     definition for 'points'
    plotBasepair.AllelicCrosstalkCalibration : linesAllelicCrosstalk: no
     visible global function definition for 'lines'
    plotBasepair.AllelicCrosstalkCalibration : plotFcn: no visible global
     function definition for 'smoothScatter'
    plotBasepair.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    plotBoxplotStats.list: no visible global function definition for 'bxp'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'str'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'par'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'smoothScatter'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'abline'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'smooth.spline'
    plotCovariateEffects.GcContentNormalization2: no visible global
     function definition for 'lines'
    plotDensity.AffymetrixCelSet: no visible global function definition for
     'str'
    plotDensity.GenomeInformation: no visible global function definition
     for 'density'
    plotDensity.GenomeInformation: no visible global function definition
     for 'plot'
    plotMargins.SpatialReporter: no visible global function definition for
     'layout'
    plotMargins.SpatialReporter: no visible global function definition for
     'plot'
    plotMargins.SpatialReporter: no visible global function definition for
     'abline'
    plotMargins.SpatialReporter: no visible global function definition for
     'par'
    plotMargins.SpatialReporter: no visible global function definition for
     'axis'
    plotMargins.SpatialReporter: no visible global function definition for
     'box'
    plotMargins.SpatialReporter: no visible global function definition for
     'lines'
    plotMvsA.AffymetrixCelFile: no visible global function definition for
     'plot'
    plotMvsX.AffymetrixCelFile: no visible global function definition for
     'points'
    plotMvsX.AffymetrixCelFile: no visible global function definition for
     'plot'
    plotXYCurve.TransformReport: no visible global function definition for
     'str'
    plotXYCurve.TransformReport: no visible global function definition for
     'box'
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for 'coefficients'
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for 'predict'
    predictOne.BaseCountNormalization : predictBaseCounts : predictFcn: no
     visible global function definition for 'str'
    predictOne.BaseCountNormalization: no visible global function
     definition for 'str'
    predictOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for 'str'
    predictOne.LinearModelProbeSequenceNormalization: no visible global
     function definition for 'predict'
    predictOne.MatNormalization: no visible global function definition for
     'str'
    process.AbstractProbeSequenceNormalization : readSeqs: no visible
     global function definition for 'str'
    process.AbstractProbeSequenceNormalization: no visible global function
     definition for 'str'
    process.AdditiveCovariatesNormalization: no visible global function
     definition for 'str'
    process.AlleleSummation: no visible global function definition for
     'str'
    process.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    process.ChipEffectGroupMerge: no visible global function definition for
     'str'
    process.DChipQuantileNormalization: no visible global function
     definition for 'str'
    process.FragmentEquivalentClassNormalization: no visible global
     function definition for 'str'
    process.FragmentLengthNormalization: no visible global function
     definition for 'str'
    process.GcContentNormalization: no visible global function definition
     for 'str'
    process.LimmaBackgroundCorrection: no visible global function
     definition for 'rnorm'
    process.LimmaBackgroundCorrection: no visible global function
     definition for 'str'
    process.MatNormalization: no visible global function definition for
     'str'
    process.MatNormalization: no visible global function definition for
     'quantile'
    process.MatNormalization: no visible binding for global variable 'var'
    process.MatSmoothing : calcNullDist0: no visible global function
     definition for 'median'
    process.MatSmoothing : calcNullDist0: no visible global function
     definition for 'sd'
    process.MatSmoothing : calcNullDist: no visible global function
     definition for 'median'
    process.MatSmoothing : calcNullDist: no visible global function
     definition for 'sd'
    process.MatSmoothing : calcNullDists: no visible global function
     definition for 'median'
    process.MatSmoothing: no visible global function definition for 'str'
    process.OpticalBackgroundCorrection: no visible global function
     definition for 'str'
    process.QuantileNormalization: no visible global function definition
     for 'str'
    process.ReseqCrosstalkCalibration: no visible global function
     definition for 'str'
    process.ScaleNormalization: no visible global function definition for
     'str'
    process.ScaleNormalization: no visible global function definition for
     'median'
    process.ScaleNormalization3: no visible global function definition for
     'str'
    process.SpatialRowColumnNormalization: no visible global function
     definition for 'str'
    process.SpatialRowColumnNormalization: no visible global function
     definition for 'residuals'
    process.UnitTypeScaleNormalization: no visible global function
     definition for 'str'
    readCfhUnits.default: no visible global function definition for 'str'
    readCfnUnits.default: no visible global function definition for 'str'
    readDataFrame.AffymetrixCdfFile: no visible global function definition
     for 'str'
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for 'na.omit'
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for 'str'
    readDataFrame.AffymetrixCsvGenomeInformation: no visible global
     function definition for 'read.table'
    readDataFrame.UgpGenomeInformation: no visible global function
     definition for 'str'
    readDataFrame2.AffymetrixProbeTabFile: no visible global function
     definition for 'str'
    readDataUnitFragmentLength.AffymetrixNetAffxCsvFile: no visible global
     function definition for 'str'
    readDataUnitFragmentLength.AffymetrixNetAffxCsvFile: no visible global
     function definition for 'na.omit'
    readGeneAssignments.AffymetrixNetAffxCsvFile: no visible global
     function definition for 'str'
    readPriorsByUnits.MultiArrayUnitModel: no visible global function
     definition for 'str'
    readRawData.AffymetrixCnChpFile: no visible global function definition
     for 'str'
    readSequenceDataFrame.AffymetrixProbeTabFile: no visible global
     function definition for 'str'
    readUnits.AffymetrixCelSet: no visible global function definition for
     'str'
    readUnits.CnagCfhFile: no visible global function definition for
     'na.omit'
    readUnits.CnagCfhSet: no visible global function definition for 'str'
    readUnits.MultiArrayUnitModel: no visible global function definition
     for 'str'
    readUnits.ParameterCelFile: no visible global function definition for
     'object.size'
    readUnits.SingleArrayUnitModel: no visible global function definition
     for 'str'
    rescaleByAll.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    rescaleByAll.AllelicCrosstalkCalibration: no visible global function
     definition for 'median'
    rescaleByAll.ReseqCrosstalkCalibration: no visible global function
     definition for 'str'
    rescaleByAll.ReseqCrosstalkCalibration: no visible global function
     definition for 'median'
    rescaleByGroups.AllelicCrosstalkCalibration: no visible global function
     definition for 'str'
    rescaleByGroups.AllelicCrosstalkCalibration: no visible global function
     definition for 'median'
    restruct.AffymetrixCdfFile: no visible global function definition for
     'str'
    setUnitReadMap.AffymetrixCnChpFile: no visible global function
     definition for 'str'
    smoothScatterMvsA.AffymetrixCelFile: no visible global function
     definition for 'smoothScatter'
    updateParameter.CrlmmParametersFile: no visible global function
     definition for 'str'
    updateUnits.ChipEffectSet: no visible global function definition for
     'str'
    updateUnits.FirmaSet: no visible global function definition for 'str'
    updateUnits.ProbeAffinityFile: no visible global function definition
     for 'str'
    updateUnits.ResidualSet: no visible global function definition for
     'str'
    updateUnits.WeightsSet: no visible global function definition for 'str'
    writeAsFullCelFile.ChipEffectFile: no visible global function
     definition for 'str'
    writeCNT.SnpChipEffectFile: no visible global function definition for
     'str'
    writeCNT.SnpChipEffectFile: no visible global function definition for
     'write.table'
    writeCNT.SnpChipEffectSet: no visible global function definition for
     'write.table'
    writeCdf.AffyGenePDInfo: no visible global function definition for
     'packageDescription'
    writeCdf.AffyGenePDInfo: no visible global function definition for
     'str'
    writeCdf.AffyGenePDInfo: no visible global function definition for
     'head'
    writeCdf.PDInfoList: no visible global function definition for 'str'
    writeCdf.PDInfoList: no visible global function definition for 'head'
    writeCdfByExcludingCells.AffymetrixCdfFile: no visible global function
     definition for 'str'
    writeSgr.AffymetrixCelSet: no visible global function definition for
     'write.table'
    writeSignals.ProbeLevelTransform3: no visible global function
     definition for 'str'
    writeWig.CnChipEffectSet: no visible global function definition for
     'col2rgb'
    writeWig.CnChipEffectSet: no visible global function definition for
     'write.table'
    Undefined global functions or variables:
     abline approx as axis box boxplot.stats bxp capture.output coef
     coefficients col2rgb compareVersion data density dnorm glm
     gray.colors head image layout lines lm lowess mad median medpolish
     mtext na.omit object.size packageDescription packageVersion par plot
     points predict quantile rainbow read.table residuals rnorm sd
     smooth.spline smoothScatter str t.test tail text var write.table
Flavor: r-devel-windows-ix86+x86_64

Version: 2.13.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘oligo’ ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’ ‘dChipIO’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.13.2
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘affyPLM’, ‘oligo’
Flavor: r-release-osx-x86_64-mavericks