CRAN Package Check Results for Package aroma.affymetrix

Last updated on 2014-08-29 11:54:44.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.12.0 9.44 141.08 150.52 NOTE
r-devel-linux-x86_64-debian-gcc 2.12.0 9.59 136.70 146.29 NOTE
r-devel-linux-x86_64-fedora-clang 2.12.0 321.95 NOTE
r-devel-linux-x86_64-fedora-gcc 2.12.0 300.28 NOTE
r-devel-osx-x86_64-clang 2.12.0 246.13 NOTE
r-devel-windows-ix86+x86_64 2.12.0 23.00 190.00 213.00 NOTE
r-patched-linux-x86_64 2.12.0 10.21 154.15 164.36 NOTE
r-patched-solaris-sparc 2.12.0 1856.00 NOTE
r-patched-solaris-x86 2.12.0 380.50 NOTE
r-release-linux-ix86 2.12.0 12.77 194.98 207.75 NOTE
r-release-linux-x86_64 2.12.0 10.17 161.82 171.99 NOTE
r-release-osx-x86_64-mavericks 2.12.0 NOTE
r-release-osx-x86_64-snowleopard 2.12.0 NOTE
r-release-windows-ix86+x86_64 2.12.0 24.00 222.00 246.00 NOTE
r-oldrel-windows-ix86+x86_64 2.12.0 26.00 222.00 248.00 NOTE

Check Details

Version: 2.12.0
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-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.12.0
Check: R code for possible problems
Result: NOTE
    Env2Cdf: no visible global function definition for ‘readCelHeader’
    allocateFromCdf.AffymetrixCelFile: no visible global function
     definition for ‘cdfHeaderToCelHeader’
    allocateFromCdf.AffymetrixCelFile: no visible global function
     definition for ‘createCel’
    as.character.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    as.character.AffymetrixCelSet: no visible global function definition
     for ‘GenericSummary’
    as.character.AffymetrixCelSetReporter: no visible global function
     definition for ‘GenericSummary’
    as.character.AffymetrixCnChpSet: no visible global function definition
     for ‘GenericSummary’
    as.character.AromaChipTypeAnnotationFile: no visible global function
     definition for ‘GenericSummary’
    as.character.ArrayExplorer: no visible global function definition for
     ‘GenericSummary’
    as.character.CnagCfhSet: no visible global function definition for
     ‘GenericSummary’
    as.character.DChipDcpSet: no visible global function definition for
     ‘GenericSummary’
    as.character.FirmaModel: no visible global function definition for
     ‘GenericSummary’
    as.character.GenericReporter: no visible global function definition for
     ‘GenericSummary’
    as.character.Model: no visible global function definition for
     ‘GenericSummary’
    as.character.QualityAssessmentModel: no visible global function
     definition for ‘GenericSummary’
    as.character.SpatialReporter: no visible global function definition for
     ‘GenericSummary’
    as.character.TransformReport: no visible global function definition for
     ‘GenericSummary’
    assertAnnotationData.ASCRMAv2: no visible binding for global variable
     ‘AromaCellSequenceFile’
    bgAdjustGcrma.AffymetrixCelFile: no visible global function definition
     for ‘updateCel’
    bgAdjustOptical.AffymetrixCelFile: no visible global function
     definition for ‘updateCel’
    bgAdjustRma.AffymetrixCelFile: no visible global function definition
     for ‘bg.adjust’
    bgAdjustRma.AffymetrixCelFile: no visible global function definition
     for ‘updateCel’
    bpmapCluster2Cdf.default: no visible global function definition for
     ‘readBpmapHeader’
    bpmapCluster2Cdf.default: no visible global function definition for
     ‘readBpmap’
    byPath.AffymetrixCelSet : <anonymous>: no visible global function
     definition for ‘readCelHeader’
    byPath.AffymetrixCelSetTuple: no visible binding for global variable
     ‘Class’
    byPath.CnagCfhSet: no visible binding for global variable
     ‘SampleAnnotationSet’
    calculateBaseline.ChipEffectSet: no visible binding for global variable
     ‘getPloidy’
    calculateParametersGsb.AffymetrixCelSet: no visible global function
     definition for ‘readCel’
    calculateResidualSet.ProbeLevelModel: no visible global function
     definition for ‘applyCdfGroups’
    calculateResidualSet.ProbeLevelModel: no visible global function
     definition for ‘updateCel’
    calculateWeights.ExonRmaPlm: no visible binding for global variable
     ‘aromaSettings’
    calculateWeights.ExonRmaPlm: no visible global function definition for
     ‘updateCelUnits’
    calculateWeights.ProbeLevelModel: no visible binding for global
     variable ‘aromaSettings’
    calculateWeights.ProbeLevelModel: no visible global function definition
     for ‘updateCelUnits’
    clearData.AffymetrixCelFile: no visible global function definition for
     ‘updateCel’
    compare.AffymetrixCdfFile: no visible global function definition for
     ‘compareCdfs’
    computeAffinities.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    computeAffinitiesByACS.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    convert.AffymetrixCdfFile: no visible global function definition for
     ‘convertCdf’
    convertToUnique.AffymetrixCelSet: no visible global function definition
     for ‘readCdf’
    convertToUnique.AffymetrixCelSet: no visible global function definition
     for ‘readCelUnits’
    convertToUnique.AffymetrixCelSet: no visible global function definition
     for ‘cdfHeaderToCelHeader’
    convertToUnique.AffymetrixCelSet: no visible global function definition
     for ‘createCel’
    convertToUnique.AffymetrixCelSet: no visible global function definition
     for ‘updateCelUnits’
    createExonByTranscriptCdf.AffymetrixCdfFile : getCdfUnits: no visible
     global function definition for ‘readCdf’
    createExonByTranscriptCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfQc’
    createExonByTranscriptCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfHeader’
    createFrom.AffymetrixCelFile: no visible global function definition for
     ‘cdfHeaderToCelHeader’
    createFrom.AffymetrixCelFile: no visible global function definition for
     ‘createCel’
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for ‘readCel’
    createFrom.AffymetrixCelFile : <anonymous>: no visible global function
     definition for ‘updateCel’
    createMonocellCdf.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfGroupNames’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfQc’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfHeader’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfUnitNames’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfHeader’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfQcUnits’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdf’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfUnits’
    createMonocellCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfCellIndices’
    createUniqueCdf.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfGroupNames’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdf’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfQc’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfHeader’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfUnitNames’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfHeader’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfQcUnits’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘writeCdfUnits’
    createUniqueCdf.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfCellIndices’
    doCRMAv1.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    doCRMAv2.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    doCRMAv2.AffymetrixCelSet: no visible binding for global variable
     ‘AromaUnitTotalCnBinarySet’
    doCRMAv2.AffymetrixCelSet: no visible binding for global variable
     ‘AromaUnitFracBCnBinarySet’
    doFIRMA.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    doGCRMA.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    doRMA.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    env2Cdf: no visible global function definition for ‘readCelHeader’
    exportTotalAndFracB.DChipDcpSet: no visible binding for global variable
     ‘AromaUnitTotalCnBinarySet’
    exportTotalAndFracB.SnpChipEffectFile: no visible binding for global
     variable ‘AromaUnitTotalCnBinaryFile’
    exportTotalAndFracB.SnpChipEffectFile: no visible binding for global
     variable ‘AromaUnitFracBCnBinaryFile’
    exportTotalAndFracB.SnpChipEffectSet: no visible binding for global
     variable ‘AromaUnitTotalCnBinarySet’
    exportTotalAndFracB.SnpChipEffectSet: no visible binding for global
     variable ‘AromaUnitFracBCnBinarySet’
    exportTotalCnRatioSet.AffymetrixCnChpSet: no visible binding for global
     variable ‘AromaUnitTotalCnBinarySet’
    extractAffyBatch.AffymetrixCelSet: no visible global function
     definition for ‘cleancdfname’
    extractAlleleSet.SnpChipEffectSet: no visible global function
     definition for ‘featureNames<-’
    extractAlleleSet.SnpChipEffectSet: no visible global function
     definition for ‘annotation<-’
    extractAlleleSet.SnpChipEffectSet: no visible global function
     definition for ‘sampleNames<-’
    extractExpressionSet.ChipEffectSet: no visible global function
     definition for ‘geometry’
    extractFeatureSet.AffymetrixCelSet: no visible global function
     definition for ‘read.celfiles’
    extractMatrix.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    extractMatrix.ParameterCelSet: no visible binding for global variable
     ‘aromaSettings’
    extractSnpCnvQSet.SnpChipEffectSet: no visible global function
     definition for ‘featureNames<-’
    extractSnpCnvQSet.SnpChipEffectSet: no visible global function
     definition for ‘annotation<-’
    extractSnpCnvQSet.SnpChipEffectSet: no visible global function
     definition for ‘sampleNames<-’
    extractSnpQSet.SnpChipEffectSet: no visible global function definition
     for ‘featureNames<-’
    extractSnpQSet.SnpChipEffectSet: no visible global function definition
     for ‘annotation<-’
    extractSnpQSet.SnpChipEffectSet: no visible global function definition
     for ‘sampleNames<-’
    extractTheta.SnpCnvQSet: no visible global function definition for
     ‘featureNames’
    extractTheta.SnpQSet: no visible global function definition for
     ‘featureNames’
    findTargetDistributionFile.QuantileNormalization: no visible binding
     for global variable ‘aromaSettings’
    findUnitsTodo.ChipEffectFile: no visible global function definition for
     ‘readCel’
    findUnitsTodo.QualityAssessmentFile: no visible global function
     definition for ‘readCelUnits’
    findUnitsTodo.ResidualFile: no visible global function definition for
     ‘applyCdfGroups’
    findUnitsTodo.ResidualFile: no visible global function definition for
     ‘readCel’
    findUnitsTodo.WeightsFile: no visible global function definition for
     ‘applyCdfGroups’
    findUnitsTodo.WeightsFile: no visible global function definition for
     ‘readCel’
    fit.CrlmmModel : extractLogRatios: no visible global function
     definition for ‘assayData’
    fit.CrlmmModel: no visible binding for global variable ‘aromaSettings’
    fit.CrlmmModel: no visible global function definition for ‘phenoData<-’
    fit.CrlmmModel: no visible global function definition for
     ‘featureNames’
    fit.CrlmmModel: no visible global function definition for ‘getM’
    fit.FirmaModel: no visible binding for global variable ‘aromaSettings’
    fit.ProbeLevelModel: no visible binding for global variable
     ‘aromaSettings’
    fitOne.BaseCountNormalization : fitBaseCounts : fitFcn: no visible
     global function definition for ‘robustSmoothSpline’
    fitOne.BaseCountNormalization: no visible global function definition
     for ‘robustSmoothSpline’
    fitOne.LinearModelProbeSequenceNormalization: no visible binding for
     global variable ‘aromaSettings’
    fitOne.MatNormalization: no visible binding for global variable
     ‘aromaSettings’
    fitOneChromosome.SmoothMultiarrayModel: no visible binding for global
     variable ‘getAttribute’
    fromDataFile.ChipEffectFile: no visible global function definition for
     ‘cdfHeaderToCelHeader’
    fromDataFile.ChipEffectFile: no visible global function definition for
     ‘createCel’
    fromDataFile.FirmaFile: no visible global function definition for
     ‘cdfHeaderToCelHeader’
    fromDataFile.FirmaFile: no visible global function definition for
     ‘createCel’
    fromFile.AffymetrixCdfFile: no visible global function definition for
     ‘readCdfHeader’
    fromFile.AffymetrixPgfFile: no visible global function definition for
     ‘readPgfHeader’
    fromFile.AromaChipTypeAnnotationFile: no visible binding for global
     variable ‘Class’
    getAlleleCellPairs.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getAlleleCellPairs.AffymetrixCdfFile: no visible global function
     definition for ‘cdfMergeAlleles’
    getAlleleProbePairs.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getAlleleProbePairs.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfGroupNames’
    getAlleleProbePairs.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfCellIndices’
    getAlleleProbePairs2.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfGroupNames’
    getAlleleProbePairs2.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfCellIndices’
    getAlleleProbePairs2.AffymetrixCdfFile: no visible global function
     definition for ‘applyCdfGroups’
    getAlleleProbePairs2.AffymetrixCdfFile: no visible binding for global
     variable ‘cdfGetGroups’
    getAlleleProbePairs3.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getAlleleProbePairs3.AffymetrixCdfFile: no visible global function
     definition for ‘readCdf’
    getAromaCellPositionFile.MatSmoothing: no visible binding for global
     variable ‘AromaCellPositionFile’
    getAromaCellSequenceFile.AbstractProbeSequenceNormalization: no visible
     binding for global variable ‘AromaCellSequenceFile’
    getAromaCellSequenceFile.AffymetrixCdfFile: no visible binding for
     global variable ‘AromaCellSequenceFile’
    getAverageFile.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    getAverageFile.AffymetrixCelSet: no visible global function definition
     for ‘readCel’
    getAverageFile.AffymetrixCelSet: no visible global function definition
     for ‘updateCel’
    getAverageFile.CnagCfhSet: no visible binding for global variable
     ‘aromaSettings’
    getAverageFile.CnagCfhSet: no visible global function definition for
     ‘readCel’
    getAverageFile.CnagCfhSet: no visible global function definition for
     ‘updateCel’
    getBaseline.ChipEffectSet: no visible binding for global variable
     ‘aromaSettings’
    getCallSet.CrlmmModel: no visible binding for global variable
     ‘AromaUnitGenotypeCallSet’
    getCellIndices.AffymetrixCdfFile : getCellIndicesChunk: no visible
     global function definition for ‘readCdfCellIndices’
    getCellIndices.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getCellIndices.CnChipEffectFile: no visible binding for global variable
     ‘aromaSettings’
    getCellIndices.CnChipEffectFile : <anonymous>: no visible global
     function definition for ‘applyCdfGroups’
    getCellIndices.CnProbeAffinityFile: no visible global function
     definition for ‘applyCdfGroups’
    getCellIndices.ExonChipEffectFile: no visible binding for global
     variable ‘aromaSettings’
    getCellIndices.ExonChipEffectFile: no visible global function
     definition for ‘applyCdfGroups’
    getCellIndices.ExonProbeAffinityFile: no visible global function
     definition for ‘applyCdfGroups’
    getCellIndices.ExonRmaPlm: no visible global function definition for
     ‘applyCdfGroups’
    getCellIndices.SnpChipEffectFile: no visible binding for global
     variable ‘aromaSettings’
    getCellIndices.SnpChipEffectFile : <anonymous>: no visible global
     function definition for ‘applyCdfGroups’
    getCellIndices.SnpPlm: no visible global function definition for
     ‘applyCdfGroups’
    getCellIndices.SnpPlm: no visible binding for global variable
     ‘cdfMergeStrands’
    getCellIndices.SnpProbeAffinityFile: no visible global function
     definition for ‘applyCdfGroups’
    getCellIndices.SnpProbeAffinityFile: no visible binding for global
     variable ‘cdfMergeStrands’
    getCellQuartets.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getCellQuartets.AffymetrixCdfFile: no visible global function
     definition for ‘applyCdfGroups’
    getCellQuartets.AffymetrixCdfFile: no visible binding for global
     variable ‘cdfGetFields’
    getCovariates.GcContentNormalization2: no visible binding for global
     variable ‘AromaUgcFile’
    getCrlmmSNPsOnChrX.CrlmmModel: no visible global function definition
     for ‘dbGetQuery’
    getData.AffymetrixCnChpFile: no visible binding for global variable
     ‘aromaSettings’
    getData.SnpInformation: no visible global function definition for
     ‘readCdfUnitNames’
    getFirstCellIndices.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getFirstCellIndices.AffymetrixCdfFile: no visible global function
     definition for ‘applyCdfGroups’
    getFitUnitGroupFunction.AffinePlm : affineFit: no visible global
     function definition for ‘calibrateMultiscan’
    getFitUnitGroupFunction.ExonRmaPlm: no visible binding for global
     variable ‘aromaSettings’
    getFitUnitGroupFunction.MbeiPlm : liWong: no visible global function
     definition for ‘fit.li.wong’
    getFitUnitGroupFunction.RmaPlm: no visible binding for global variable
     ‘aromaSettings’
    getFitUnitGroupFunction.SmoothRmaModel: no visible binding for global
     variable ‘smoothWRMA’
    getFitUnitGroupFunction.SmoothSaModel: no visible binding for global
     variable ‘smoothWSA’
    getGcContent.GcContentNormalization: no visible binding for global
     variable ‘AromaUgcFile’
    getGroupDirections.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getGroupDirections.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfUnits’
    getHeader.AffymetrixCdfFile: no visible global function definition for
     ‘readCdfHeader’
    getHeader.AffymetrixCelFile: no visible global function definition for
     ‘readCelHeader’
    getHeader.AffymetrixCnChpFile: no visible global function definition
     for ‘readCcgHeader’
    getHeader.AffymetrixPgfFile: no visible global function definition for
     ‘readPgfHeader’
    getNormalEquations.LinearModelProbeSequenceNormalization: no visible
     binding for global variable ‘aromaSettings’
    getNumberOfFilesAveraged.CnChipEffectFile: no visible global function
     definition for ‘readCel’
    getPlasqTypes: no visible global function definition for
     ‘applyCdfGroups’
    getPlasqTypes: no visible binding for global variable
     ‘cdfAddPlasqTypes’
    getPlasqTypes: no visible binding for global variable ‘cdfGetFields’
    getProbeSequenceData.AffymetrixCdfFile: no visible global function
     definition for ‘applyCdfGroups’
    getProbeSequenceData.AffymetrixCdfFile: no visible binding for global
     variable ‘cdfGetFields’
    getResiduals.QualityAssessmentModel: no visible binding for global
     variable ‘aromaSettings’
    getResiduals.QualityAssessmentModel: no visible global function
     definition for ‘cdfHeaderToCelHeader’
    getResiduals.QualityAssessmentModel: no visible global function
     definition for ‘createCel’
    getResiduals.QualityAssessmentModel: no visible global function
     definition for ‘updateCelUnits’
    getSetsOfProbes.AllelicCrosstalkCalibration: no visible binding for
     global variable ‘AromaCellSequenceFile’
    getSubsetOfCellIndices.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getTargetDistributionPathname.QuantileNormalization: no visible binding
     for global variable ‘aromaSettings’
    getTimestamp.AffymetrixCelFile: no visible global function definition
     for ‘readCcgHeader’
    getUnitGroupCellChromosomePositionMap.AffymetrixCdfFile: no visible
     binding for global variable ‘aromaSettings’
    getUnitGroupCellMap.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    getUnitGroupNamesFromUgcMap.AffymetrixCdfFile: no visible global
     function definition for ‘readCdfGroupNames’
    getUnitIntensities.AffymetrixCelSet: no visible global function
     definition for ‘readCelUnits’
    getUnitNames.AffymetrixCdfFile: no visible global function definition
     for ‘readCdfUnitNames’
    getUnitTypes.AffymetrixCdfFile: no visible binding for global variable
     ‘aromaSettings’
    getUnitTypes.AffymetrixCdfFile: no visible global function definition
     for ‘readCdf’
    getWeights.QualityAssessmentModel: no visible binding for global
     variable ‘aromaSettings’
    getWeights.QualityAssessmentModel: no visible global function
     definition for ‘cdfHeaderToCelHeader’
    getWeights.QualityAssessmentModel: no visible global function
     definition for ‘createCel’
    getWeights.QualityAssessmentModel: no visible global function
     definition for ‘updateCelUnits’
    identifyCells.AffymetrixCdfFile: no visible binding for global variable
     ‘aromaSettings’
    importFromAffymetrixProbeTabFile.AromaCellSequenceFile: no visible
     binding for global variable ‘aromaSettings’
    importFromApt.CnChipEffectSet: no visible global function definition
     for ‘updateCel’
    importFromBpMap.AromaCellMatchScoreFile: no visible global function
     definition for ‘readBpmap’
    importFromBpMap.AromaCellSequenceFile: no visible global function
     definition for ‘readBpmap’
    importFromDChip.AffymetrixCelSet: no visible global function definition
     for ‘invertMap’
    importFromDChip.AffymetrixCelSet: no visible global function definition
     for ‘convertCel’
    importFromDChip.CnChipEffectSet: no visible global function definition
     for ‘updateCel’
    inferMmFromPm.AromaCellSequenceFile: no visible binding for global
     variable ‘aromaSettings’
    inferParameters.CnChipEffectSet: no visible global function definition
     for ‘readCdfHeader’
    inferParameters.CnChipEffectSet: no visible global function definition
     for ‘readCdfGroupNames’
    inferParameters.CnChipEffectSet: no visible global function definition
     for ‘readCelUnits’
    inferParameters.SnpChipEffectSet: no visible global function definition
     for ‘readCdfHeader’
    inferParameters.SnpChipEffectSet: no visible global function definition
     for ‘readCdfGroupNames’
    inferParameters.SnpChipEffectSet: no visible global function definition
     for ‘readCelUnits’
    isPm.AffymetrixCdfFile: no visible global function definition for
     ‘readCdfIsPm’
    migrateTool.CopyNumberSegmentationModel: no visible binding for global
     variable ‘Class’
    nbrOfCellsPerUnit.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    nbrOfCellsPerUnitGroup.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    nbrOfCellsPerUnitGroup.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfNbrOfCellsPerUnitGroup’
    nbrOfGroupsPerUnit.AffymetrixCdfFile: no visible binding for global
     variable ‘aromaSettings’
    nbrOfGroupsPerUnit.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfGroupNames’
    normalizeQuantile.AffymetrixCelFile: no visible global function
     definition for ‘updateCel’
    pdInfo2Cdf: no visible global function definition for ‘readCelHeader’
    pdInfo2Cdf: no visible global function definition for ‘read.celfiles’
    pdInfo2Cdf: no visible global function definition for
     ‘getPlatformDesign’
    pdInfo2Cdf: no visible global function definition for ‘dbGetQuery’
    pdInfo2Cdf: no visible global function definition for ‘db’
    plotMargins.SpatialReporter: no visible global function definition for
     ‘robustSmoothSpline’
    predictOne.MatNormalization: no visible binding for global variable
     ‘aromaSettings’
    process.AbstractProbeSequenceNormalization: no visible binding for
     global variable ‘aromaSettings’
    process.AbstractProbeSequenceNormalization: no visible global function
     definition for ‘updateCel’
    process.AdditiveCovariatesNormalization: no visible global function
     definition for ‘normalizeFragmentLength’
    process.AdditiveCovariatesNormalization: no visible global function
     definition for ‘updateCel’
    process.AlleleSummation: no visible global function definition for
     ‘readCel’
    process.AllelicCrosstalkCalibration: no visible global function
     definition for ‘updateCel’
    process.DChipQuantileNormalization: no visible global function
     definition for ‘normalizeQuantileSpline’
    process.DChipQuantileNormalization: no visible global function
     definition for ‘updateCel’
    process.FragmentLengthNormalization: no visible global function
     definition for ‘normalizeFragmentLength’
    process.FragmentLengthNormalization: no visible global function
     definition for ‘updateCel’
    process.GcContentNormalization: no visible global function definition
     for ‘normalizeFragmentLength’
    process.LimmaBackgroundCorrection: no visible global function
     definition for ‘updateCel’
    process.MatNormalization: no visible binding for global variable
     ‘aromaSettings’
    process.MatNormalization: no visible global function definition for
     ‘updateCel’
    process.MatNormalization: no visible global function definition for
     ‘readCel’
    process.MatSmoothing: no visible global function definition for
     ‘updateCel’
    process.ReseqCrosstalkCalibration: no visible global function
     definition for ‘updateCel’
    process.ScaleNormalization: no visible global function definition for
     ‘updateCel’
    process.SpatialRowColumnNormalization: no visible global function
     definition for ‘updateCel’
    readCdfGroupStrands: no visible global function definition for
     ‘readCdf’
    readCfnHeader.default: no visible global function definition for
     ‘findCdf’
    readCfnHeader.default: no visible global function definition for
     ‘readCdfUnitNames’
    readDataFrame.AffymetrixCdfFile: no visible binding for global variable
     ‘readCdfDataFrame’
    readDataFrame.AffymetrixCdfFile: no visible binding for global variable
     ‘aromaSettings’
    readPlasqTypes.AffymetrixCdfFile: no visible global function definition
     for ‘readCdf’
    readRawData.AffymetrixCnChpFile: no visible global function definition
     for ‘readCcg’
    readRawData.AffymetrixPgfFile: no visible global function definition
     for ‘readPgfEnv’
    readRawDataRectangle.AffymetrixCelFile: no visible global function
     definition for ‘readCelRectangle’
    readUnits.AffymetrixCelFile: no visible global function definition for
     ‘readCelUnits’
    readUnits.AffymetrixCelSet: no visible global function definition for
     ‘readCelUnits’
    readUnits.ChipEffectFile: no visible binding for global variable
     ‘aromaSettings’
    readUnits.CnagCfhSet: no visible global function definition for
     ‘readCelUnits’
    readUnits.FirmaFile: no visible binding for global variable
     ‘aromaSettings’
    readUnits.ResidualFile: no visible binding for global variable
     ‘aromaSettings’
    readUnits.WeightsFile: no visible binding for global variable
     ‘aromaSettings’
    setCdf.AffymetrixCelSet: no visible binding for global variable
     ‘aromaSettings’
    transformAffine.AffymetrixCelFile: no visible global function
     definition for ‘updateCel’
    updateDataFlat.ChipEffectFile: no visible global function definition
     for ‘updateCel’
    updateDataFlat.FirmaFile: no visible global function definition for
     ‘updateCel’
    updateDataFlat.ResidualFile: no visible global function definition for
     ‘updateCel’
    updateDataFlat.WeightsFile: no visible global function definition for
     ‘updateCel’
    updateSampleAnnotationSet.AffymetrixCelSet: no visible binding for
     global variable ‘SampleAnnotationSet’
    updateSettings.Package: no visible binding for global variable
     ‘aromaSettings’
    updateUnits.AffymetrixCelFile: no visible global function definition
     for ‘updateCelUnits’
    writeAsFullCelFile.ChipEffectFile: no visible global function
     definition for ‘updateCel’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘cleanPlatformName’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘geometry’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘dbListTables’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘annotation’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘dbGetQuery’
    writeCdf.DBPDInfo: no visible global function definition for
     ‘annotation’
    writeCdfByExcludingCells.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfHeader’
    writeCdfByExcludingCells.AffymetrixCdfFile: no visible global function
     definition for ‘readCdfQc’
    writeCdfByExcludingCells.AffymetrixCdfFile: no visible global function
     definition for ‘readCdf’
    writeImageCombined.TransformReport: no visible global function
     definition for ‘devDone’
    writeImages.TransformReport: no visible global function definition for
     ‘devDone’
    writeRegions.profileCGH: no visible global function definition for
     ‘readCdfUnitNames’
    writeSgr.AffymetrixCelSet: no visible binding for global variable
     ‘AromaCellPositionFile’
    writeSignals.ProbeLevelTransform3: no visible global function
     definition for ‘updateCel’
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: 2.12.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘affyPLM’ ‘dChipIO’
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.12.0
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-patched-solaris-x86, r-release-osx-x86_64-snowleopard

Version: 2.12.0
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: 2.12.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘affyPLM’ ‘dChipIO’ ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-snowleopard

Version: 2.12.0
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: 2.12.0
Check: R code for possible problems
Result: NOTE
    extractFeatureSet.AffymetrixCelSet: no visible global function
     definition for ‘read.celfiles’
    pdInfo2Cdf: no visible global function definition for ‘read.celfiles’
    pdInfo2Cdf: no visible global function definition for
     ‘getPlatformDesign’
    writeCdf.AffyGenePDInfo: no visible global function definition for
     ‘cleanPlatformName’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.12.0
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘affyPLM’, ‘oligo’
Flavor: r-release-osx-x86_64-mavericks