CRAN Package Check Results for Package aroma.cn

Last updated on 2015-07-05 22:47:18.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.6.0 2.59 44.40 46.99 NOTE
r-devel-linux-x86_64-debian-gcc 1.6.0 2.57 40.54 43.11 NOTE
r-devel-linux-x86_64-fedora-clang 1.6.0 84.62 NOTE
r-devel-linux-x86_64-fedora-gcc 1.6.0 81.24 NOTE
r-devel-osx-x86_64-clang 1.6.0 77.67 NOTE
r-devel-windows-ix86+x86_64 1.6.0 18.00 61.00 79.00 NOTE
r-patched-linux-x86_64 1.6.0 2.71 40.88 43.59 OK
r-patched-solaris-sparc 1.6.0 521.00 OK
r-patched-solaris-x86 1.6.0 104.30 OK
r-release-linux-x86_64 1.6.0 2.93 41.38 44.31 OK
r-release-osx-x86_64-mavericks 1.6.0 NOTE
r-release-windows-ix86+x86_64 1.6.0 14.00 59.00 73.00 OK
r-oldrel-windows-ix86+x86_64 1.6.0 23.00 124.00 147.00 OK

Check Details

Version: 1.6.0
Check: R code for possible problems
Result: NOTE
    callAllelicBalanceByBAFs.PairedPSCBS: no visible global function
     definition for ‘density’
    callAllelicBalanceByBAFs.PairedPSCBS: no visible global function
     definition for ‘na.omit’
    doSegmentByPairedPSCBS.AromaUnitPscnBinarySet: no visible global
     function definition for ‘str’
    doSegmentByPairedPSCBS.AromaUnitPscnBinarySet : <anonymous>: no visible
     global function definition for ‘str’
    drawC1C2Density.PairedPSCBS: no visible global function definition for
     ‘density’
    drawC1C2Density.PairedPSCBS: no visible global function definition for
     ‘head’
    drawC1C2Density.PairedPSCBS: no visible global function definition for
     ‘abline’
    drawC1C2Density.PairedPSCBS: no visible global function definition for
     ‘box’
    findAtomicAberrations.CBS: no visible global function definition for
     ‘str’
    findAtomicAberrations.CopyNumberRegions : testEquality: no visible
     global function definition for ‘t.test’
    findAtomicAberrations.PairedPSCBS: no visible global function
     definition for ‘str’
    fit.PairedPscbsModel: no visible global function definition for ‘str’
    fitC1C2Densities.PairedPSCBS: no visible global function definition for
     ‘density’
    fitC1C2Peaks.PairedPSCBS: no visible global function definition for
     ‘lm’
    fitC1C2Peaks.PairedPSCBS: no visible global function definition for
     ‘coef’
    fitC1C2Peaks.PairedPSCBS: no visible global function definition for
     ‘str’
    fitLoessKD.matrix: no visible global function definition for ‘loess’
    fitLoessKD.matrix : predictY: no visible global function definition for
     ‘predict’
    fitOne.MultiSourceCopyNumberNormalization: no visible global function
     definition for ‘str’
    fitOne.MultiSourceCopyNumberNormalization: no visible global function
     definition for ‘cor’
    getOutputDataSet.AbstractCurveNormalization: no visible global function
     definition for ‘str’
    getOutputDataSet0.TotalCnSmoothing: no visible global function
     definition for ‘str’
    getOutputDataSets.MultiSourceCopyNumberNormalization: no visible global
     function definition for ‘str’
    getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization :
     smoother: no visible global function definition for ‘smooth.spline’
    getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization :
     smoother: no visible global function definition for ‘predict’
    getPrincipalCurveEstimator.MultiSourceCopyNumberNormalization :
     robustSmoother: no visible global function definition for ‘predict’
    getSubsetToFit.AbstractCurveNormalization: no visible global function
     definition for ‘str’
    getSubsetToFit.MultiSourceCopyNumberNormalization: no visible global
     function definition for ‘str’
    getTargetPositions.TotalCnSmoothing: no visible global function
     definition for ‘str’
    makeSmoothSplinePredict.numeric: no visible global function definition
     for ‘smooth.spline’
    makeSmoothSplinePredict.numeric : predFcn: no visible global function
     definition for ‘predict’
    normalizeMirroredBAFsByRegions.matrix: no visible global function
     definition for ‘str’
    normalizeMirroredBAFsByRegions.matrix: no visible global function
     definition for ‘plot’
    normalizeOne.MultiSourceCopyNumberNormalization: no visible global
     function definition for ‘str’
    normalizePrincipalCurve.matrix: no visible global function definition
     for ‘cor’
    normalizePrincipalCurve.matrix: no visible global function definition
     for ‘median’
    pairs2.principal.curve: no visible global function definition for
     ‘layout’
    pairs2.principal.curve: no visible global function definition for ‘par’
    pairs2.principal.curve: no visible global function definition for
     ‘plot.new’
    pairs2.principal.curve: no visible global function definition for
     ‘plot’
    pairs2.principal.curve: no visible global function definition for
     ‘abline’
    pairs2.principal.curve: no visible global function definition for
     ‘points’
    pairs2.principal.curve: no visible global function definition for
     ‘lines’
    plot.C1C2: no visible global function definition for ‘plot’
    plot.C1C2: no visible global function definition for ‘abline’
    plot.C1C2: no visible global function definition for ‘grid’
    plot.C1C2: no visible global function definition for ‘points’
    plot.CartesianSnpData: no visible binding for global variable ‘data’
    plot.CopyNumberRegions: no visible global function definition for
     ‘plot’
    plot.CopyNumberRegions: no visible global function definition for
     ‘lines’
    plotBacktransforms.PrincipalCurve: no visible global function
     definition for ‘plot’
    plotBacktransforms.PrincipalCurve: no visible global function
     definition for ‘abline’
    plotBacktransforms.PrincipalCurve: no visible global function
     definition for ‘lines’
    plotC1C2Grid.PairedPSCBS: no visible global function definition for
     ‘title’
    plotSmoothedPairsOne.MultiSourceCopyNumberNormalization : panel: no
     visible global function definition for ‘abline’
    plotSmoothedPairsOne.MultiSourceCopyNumberNormalization : panel: no
     visible global function definition for ‘points’
    plotSmoothedPairsOne.MultiSourceCopyNumberNormalization: no visible
     global function definition for ‘str’
    plotSmoothedPairsOne.MultiSourceCopyNumberNormalization: no visible
     global function definition for ‘pairs’
    plotTracks.PruneCNA: no visible global function definition for ‘par’
    plotTracks.PruneCNA: no visible global function definition for ‘abline’
    plotTracks.PruneCNA: no visible global function definition for ‘lines’
    process.AbstractCurveNormalization: no visible global function
     definition for ‘str’
    process.MultiSourceCopyNumberNormalization: no visible global function
     definition for ‘str’
    process.PairedPscbsCaller: no visible global function definition for
     ‘str’
    process.TotalCnSmoothing: no visible global function definition for
     ‘str’
    process.TumorBoostNormalization: no visible global function definition
     for ‘str’
    process.TumorBoostNormalization: no visible global function definition
     for ‘median’
    pruneCNA.AbstractCBS: no visible global function definition for ‘str’
    resampleA.PairedPSCBS: no visible global function definition for ‘str’
    segmentByPruneCBS.RawGenomicSignals: no visible global function
     definition for ‘plot’
    segmentByPruneCBS.RawGenomicSignals: no visible global function
     definition for ‘axis’
    segmentByPruneCBSv1.RawGenomicSignals: no visible global function
     definition for ‘plot’
    segmentByPruneCBSv1.RawGenomicSignals: no visible global function
     definition for ‘axis’
    smoothRawCopyNumbers.TotalCnBinnedSmoothing: no visible global function
     definition for ‘str’
    smoothRawCopyNumbers.TotalCnKernelSmoothing: no visible global function
     definition for ‘str’
    testAllelicBalanceByBAFs.default: no visible global function definition
     for ‘str’
    testAllelicBalanceByBAFs.default: no visible global function definition
     for ‘var.test’
    testAllelicBalanceByBAFs.default: no visible global function definition
     for ‘sd’
    testAllelicBalanceByBAFs.default: no visible global function definition
     for ‘pnorm’
    testEqualityC1C2ByChiSq : <anonymous>: no visible global function
     definition for ‘t.test’
    testEqualityC1C2ByChiSq: no visible global function definition for
     ‘qnorm’
    testEqualityC1C2ByChiSq: no visible global function definition for
     ‘pchisq’
    testEqualityC1orC2ByT : <anonymous>: no visible global function
     definition for ‘t.test’
    testEqualityTcnByT: no visible global function definition for ‘t.test’
    Undefined global functions or variables:
     abline axis box coef cor data density grid head layout lines lm loess
     median na.omit pairs par pchisq plot plot.new pnorm points predict
     qnorm sd smooth.spline str t.test title var.test
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: 1.6.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks