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

Last updated on 2014-10-10 15:49:51.

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

Package ACNE

Current CRAN status: NOTE: 6, OK: 9

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

Package aroma.affymetrix

Current CRAN status: NOTE: 15

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-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’ ‘pdInfoBuilder’
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’ ‘pdInfoBuilder’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang

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

Package aroma.apd

Current CRAN status: NOTE: 8, OK: 7

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

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

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

Package aroma.cn

Current CRAN status: NOTE: 10, OK: 5

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

Version: 1.5.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Package aroma.core

Current CRAN status: NOTE: 15

Version: 2.12.1
Check: package namespace information
Result: NOTE
    R < 3.0.2 had a limit of 500 registered S3 methods: found 782
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 2.12.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.12.1
Check: R code for possible problems
Result: NOTE
    byName.AromaPlatform: no visible binding for global variable ‘Class’
    byPathnames.SampleAnnotationSet: no visible binding for global variable
     ‘Class’
    calculateAverageColumnAcrossFiles.GenericTabularFileSet: no visible
     binding for global variable ‘aromaSettings’
    countBasesInternal.AromaCellSequenceFile: no visible binding for global
     variable ‘aromaSettings’
    createImage.matrix: no visible binding for global variable
     ‘aromaSettings’
    findPngDevice.default: no visible binding for global variable ‘System’
    fit2d.matrix: no visible global function definition for
     ‘robustSmoothSpline’
    fromPath.SampleAnnotationSet: no visible binding for global variable
     ‘Class’
    getAverageFile.AromaUnitPscnBinarySet: no visible binding for global
     variable ‘rowSds’
    getAverageFile.AromaUnitPscnBinarySet: no visible binding for global
     variable ‘aromaSettings’
    getAverageFile.AromaUnitTotalCnBinarySet: no visible binding for global
     variable ‘rowSds’
    getAverageFile.AromaUnitTotalCnBinarySet: no visible binding for global
     variable ‘aromaSettings’
    getMaxLengthRepeats.AromaCellSequenceFile: no visible binding for
     global variable ‘aromaSettings’
    getOutputDataSet0.AromaTransform: no visible binding for global
     variable ‘Class’
    getSnpPositions.AromaCellSequenceFile: no visible binding for global
     variable ‘aromaSettings’
    getUnitAnnotationDataFile.AromaPlatformInterface: no visible binding
     for global variable ‘Class’
    writeDataFrame.AromaUnitSignalBinaryFile: no visible binding for global
     variable ‘nbrOfFiles’
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: 2.12.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-osx-x86_64-snowleopard

Version: 2.12.1
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GLAD’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 2.12.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘EBImage’ ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks

Version: 2.12.1
Check: R code for possible problems
Result: NOTE
    getAverageFile.AromaUnitPscnBinarySet: no visible binding for global
     variable ‘rowSds’
    getAverageFile.AromaUnitTotalCnBinarySet: no visible binding for global
     variable ‘rowSds’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Package calmate

Current CRAN status: NOTE: 6, OK: 9

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

Package matrixStats

Current CRAN status: OK: 15

Package PSCBS

Current CRAN status: OK: 15

Package R.cache

Current CRAN status: OK: 15

Package R.devices

Current CRAN status: OK: 15

Package R.filesets

Current CRAN status: NOTE: 2, OK: 13

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

Package R.huge

Current CRAN status: OK: 15

Package R.matlab

Current CRAN status: OK: 15

Package R.methodsS3

Current CRAN status: OK: 15

Package R.oo

Current CRAN status: OK: 15

Package R.rsp

Current CRAN status: NOTE: 7, OK: 8

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

Version: 0.19.0
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Error: processing vignette 'RSP-refcard.tex.rsp' failed with diagnostics:
    Running 'texi2dvi' on 'RSP-refcard.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `titlesec.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    est/R.rsp/vignettes/RSP-refcard.tex:34: ==> Fatal error occurred, no output PD
    F file produced!
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Package R.utils

Current CRAN status: OK: 15