CRAN Package Check Results for Package aroma.core

Last updated on 2015-08-29 10:46:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.13.1 4.73 80.78 85.51 NOTE
r-devel-linux-x86_64-debian-gcc 2.13.1 4.88 79.90 84.78 NOTE
r-devel-linux-x86_64-fedora-clang 2.13.1 166.97 NOTE
r-devel-linux-x86_64-fedora-gcc 2.13.1 155.14 NOTE
r-devel-osx-x86_64-clang 2.13.1 147.19 NOTE
r-devel-windows-ix86+x86_64 2.13.1 44.00 125.00 169.00 NOTE
r-patched-linux-x86_64 2.13.1 5.95 84.15 90.10 NOTE
r-patched-solaris-sparc 2.13.1 1055.90 NOTE
r-patched-solaris-x86 2.13.1 196.20 NOTE
r-release-linux-x86_64 2.13.1 5.13 82.13 87.26 NOTE
r-release-osx-x86_64-mavericks 2.13.1 NOTE
r-release-windows-ix86+x86_64 2.13.1 25.00 130.00 155.00 NOTE
r-oldrel-windows-ix86+x86_64 2.13.1 31.00 163.00 194.00 NOTE

Check Details

Version: 2.13.1
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-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.13.1
Check: R code for possible problems
Result: NOTE
    barSequence.ProbePositionEffects: no visible global function definition
     for ‘lines’
    calcMargins.matrix: no visible global function definition for ‘median’
    calculateChromosomeStatistics.CopyNumberChromosomalModel: no visible
     global function definition for ‘sd’
    calculateChromosomeStatistics.CopyNumberChromosomalModel: no visible
     global function definition for ‘median’
    calculateChromosomeStatistics.CopyNumberChromosomalModel: no visible
     global function definition for ‘mad’
    calculateChromosomeStatistics.CopyNumberChromosomalModel: no visible
     global function definition for ‘quantile’
    colGaussianSmoothing.matrix: no visible global function definition for
     ‘dnorm’
    colKernelSmoothing.matrix : kernel: no visible global function
     definition for ‘dnorm’
    colorize.Image: no visible global function definition for ‘gray.colors’
    colorize.Image: no visible global function definition for ‘col2rgb’
    colorize.RasterImage: no visible global function definition for
     ‘gray.colors’
    colorize.RasterImage: no visible global function definition for
     ‘col2rgb’
    display.RasterImage: no visible global function definition for
     ‘as.raster’
    display.RasterImage: no visible global function definition for ‘par’
    display.RasterImage: no visible global function definition for ‘plot’
    display.RasterImage: no visible global function definition for
     ‘rasterImage’
    drawCytoband.ChromosomalModel: no visible global function definition
     for ‘aggregate’
    drawCytoband.ChromosomalModel: no visible global function definition
     for ‘par’
    drawCytoband.profileCGH: no visible global function definition for
     ‘aggregate’
    drawCytoband.profileCGH: no visible global function definition for
     ‘par’
    drawCytoband2.default : seqPalette: no visible global function
     definition for ‘col2rgb’
    drawCytoband2.default : seqPalette: no visible global function
     definition for ‘rgb’
    drawCytoband2.default: no visible global function definition for ‘par’
    drawCytoband2.default: no visible global function definition for
     ‘symbols’
    drawCytoband2.default: no visible global function definition for
     ‘arrows’
    drawCytoband2.default: no visible global function definition for ‘text’
    drawDensity.RawGenomicSignals: no visible global function definition
     for ‘density’
    drawLevels.CopyNumberOutliers : <anonymous>: no visible global function
     definition for ‘lines’
    drawLevels.CopyNumberRegions : <anonymous>: no visible global function
     definition for ‘lines’
    extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList :
     <anonymous>: no visible global function definition for ‘median’
    extractNonPairedPSCNData.PairedPSCNData: no visible global function
     definition for ‘na.omit’
    findPngDevice.default: no visible binding for global variable ‘png’
    findPngDevice.default : png2trans: no visible global function
     definition for ‘par’
    findPngDevice.default : pngtrans: no visible global function definition
     for ‘png’
    fit2d.matrix: no visible global function definition for ‘predict’
    fitGenotypeConeByExpectile.matrix: no visible global function
     definition for ‘median’
    fitProbePositionEffects.numeric: no visible global function definition
     for ‘lm.fit’
    fitProbePositionEffects.numeric: no visible global function definition
     for ‘coefficients’
    fitSplineBlockPolish.matrix : effectFcn: no visible global function
     definition for ‘smooth.spline’
    fitSplineBlockPolish.matrix : effectFcn: no visible global function
     definition for ‘predict’
    gaussKernel: no visible global function definition for ‘dnorm’
    getDensity.CopyNumberRegions: no visible global function definition for
     ‘density’
    getDeviceResolution.default: no visible global function definition for
     ‘par’
    getFullNames.AromaMicroarrayDataSetTuple : getFullNameOfList :
     <anonymous>: no visible global function definition for ‘na.omit’
    getStateColors.SegmentedGenomicSignalsInterface: no visible global
     function definition for ‘na.omit’
    lines.CopyNumberOutliers: no visible global function definition for
     ‘lines’
    lines.CopyNumberRegions: no visible global function definition for
     ‘lines’
    lines.RawGenomicSignals: no visible global function definition for
     ‘lines’
    log2center: no visible global function definition for ‘median’
    newPlot.CopyNumberChromosomalModel: no visible global function
     definition for ‘par’
    newPlot.CopyNumberChromosomalModel: no visible global function
     definition for ‘plot’
    normalizeGenotypeCone.matrix: no visible binding for global variable
     ‘median’
    onFitAddGenotypeCalls.GladModel: no visible global function definition
     for ‘par’
    onFitAddGenotypeCalls.GladModel: no visible global function definition
     for ‘points’
    plot.BinnedScatter: no visible global function definition for ‘plot’
    plot.CopyNumberSegmentationModel : drawXAxisRuler: no visible global
     function definition for ‘par’
    plot.CopyNumberSegmentationModel : drawXAxisRuler: no visible global
     function definition for ‘axis’
    plot.CopyNumberSegmentationModel : drawXAxisRuler: no visible global
     function definition for ‘text’
    plot.CopyNumberSegmentationModel : screenDev: no visible global
     function definition for ‘dev.new’
    plot.CopyNumberSegmentationModel : <anonymous>: no visible global
     function definition for ‘par’
    plot.CopyNumberSegmentationModel : <anonymous>: no visible global
     function definition for ‘abline’
    plot.CopyNumberSegmentationModel : <anonymous>: no visible global
     function definition for ‘dev.off’
    plot.ProbePositionEffects: no visible global function definition for
     ‘matplot’
    plot.ProbePositionEffects: no visible global function definition for
     ‘abline’
    plot.RawGenomicSignals: no visible global function definition for
     ‘plot’
    plotAxesLayers.CopyNumberChromosomalModel : drawXAxisRuler: no visible
     global function definition for ‘par’
    plotAxesLayers.CopyNumberChromosomalModel : drawXAxisRuler: no visible
     global function definition for ‘axis’
    plotAxesLayers.CopyNumberChromosomalModel : drawXAxisRuler: no visible
     global function definition for ‘text’
    plotChromosomesLayers.CopyNumberChromosomalModel : screenDev: no
     visible global function definition for ‘dev.new’
    plotChromosomesLayers.CopyNumberChromosomalModel: no visible global
     function definition for ‘par’
    plotChromosomesLayers.CopyNumberChromosomalModel: no visible global
     function definition for ‘dev.off’
    plotCoverageMap.AromaUgpFile: no visible global function definition for
     ‘plot’
    plotCoverageMap.AromaUgpFile: no visible global function definition for
     ‘axis’
    plotCoverageMap.AromaUgpFile: no visible global function definition for
     ‘par’
    plotCoverageMap.AromaUgpFile: no visible global function definition for
     ‘text’
    plotCoverageMap.AromaUgpFile: no visible global function definition for
     ‘points’
    plotFitLayers.CopyNumberChromosomalModel : screenDev: no visible global
     function definition for ‘dev.new’
    plotFitLayers.CopyNumberChromosomalModel : <anonymous>: no visible
     global function definition for ‘par’
    plotFitLayers.CopyNumberChromosomalModel : <anonymous>: no visible
     global function definition for ‘dev.off’
    plotGridHorizontalLayers.CopyNumberChromosomalModel : <anonymous>: no
     visible global function definition for ‘abline’
    plotProfile2.profileCGH: no visible global function definition for
     ‘aggregate’
    plotProfile2.profileCGH: no visible global function definition for
     ‘par’
    plotProfile2.profileCGH: no visible global function definition for
     ‘abline’
    plotRawCNs.profileCGH: no visible global function definition for
     ‘aggregate’
    plotRawCNs.profileCGH: no visible global function definition for ‘par’
    plotRawCNs.profileCGH: no visible global function definition for ‘plot’
    plotRawCopyNumbers.CopyNumberChromosomalModel : <anonymous>: no visible
     global function definition for ‘points’
    plotSampleLayers.CopyNumberChromosomalModel : screenDev: no visible
     global function definition for ‘dev.new’
    plotSampleLayers.CopyNumberChromosomalModel: no visible global function
     definition for ‘par’
    plotSampleLayers.CopyNumberChromosomalModel: no visible global function
     definition for ‘dev.off’
    plotTracks.PairedPSCNData: no visible global function definition for
     ‘par’
    plotTracks.PairedPSCNData: no visible global function definition for
     ‘points’
    plotTracks.PairedPSCNData: no visible global function definition for
     ‘plot’
    plotTracks.PairedPSCNData: no visible global function definition for
     ‘abline’
    points.BinnedScatter: no visible global function definition for
     ‘points’
    points.RawGenomicSignals: no visible global function definition for
     ‘points’
    pointsRawCNs.default: no visible global function definition for
     ‘points’
    pointsRawCNs.profileCGH: no visible global function definition for
     ‘par’
    pointsRawCNs.profileCGH: no visible global function definition for
     ‘points’
    pointsSequence.ProbePositionEffects: no visible global function
     definition for ‘points’
    segmentByCBS.RawGenomicSignals: no visible global function definition
     for ‘median’
    segmentByGLAD.RawGenomicSignals: no visible global function definition
     for ‘median’
    segmentByHaarSeg.RawGenomicSignals: no visible global function
     definition for ‘median’
    shakyText.default: no visible global function definition for ‘text’
    simulateRawCopyNumbers.CopyNumberRegions : <anonymous>: no visible
     global function definition for ‘rnorm’
    sqrtcenter: no visible global function definition for ‘median’
    text.ProbePositionEffects: no visible global function definition for
     ‘text’
    textSequence.ProbePositionEffects: no visible global function
     definition for ‘text’
    writeGraphs.ChromosomeExplorer: no visible global function definition
     for ‘plot’
    yellow.colors: no visible global function definition for ‘hsv’
    Undefined global functions or variables:
     abline aggregate arrows as.raster axis coefficients col2rgb density
     dev.new dev.off dnorm gray.colors hsv lines lm.fit mad matplot median
     na.omit par plot png points predict quantile rasterImage rgb rnorm sd
     smooth.spline symbols text
    Consider adding
     importFrom("grDevices", "as.raster", "col2rgb", "dev.new", "dev.off",
     "gray.colors", "hsv", "png", "rgb")
     importFrom("graphics", "abline", "arrows", "axis", "lines", "matplot",
     "par", "plot", "points", "rasterImage", "symbols", "text")
     importFrom("stats", "aggregate", "coefficients", "density", "dnorm",
     "lm.fit", "mad", "median", "na.omit", "predict", "quantile",
     "rnorm", "sd", "smooth.spline")
    to your NAMESPACE.
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-windows-ix86+x86_64

Version: 2.13.1
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-mavericks

Version: 2.13.1
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-release-osx-x86_64-mavericks

Version: 2.13.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86