CRAN Package Check Results for Package beadarrayMSV

Last updated on 2016-12-10 16:46:57.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.0 6.87 86.85 93.71 NOTE
r-devel-linux-x86_64-debian-gcc 1.1.0 6.99 87.39 94.38 NOTE
r-devel-linux-x86_64-fedora-clang 1.1.0 197.44 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.1.0 188.58 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.1.0 20.00 137.00 157.00 NOTE
r-patched-linux-x86_64 1.1.0 7.13 86.64 93.77 NOTE
r-release-linux-x86_64 1.1.0 7.17 85.97 93.14 NOTE
r-release-osx-x86_64-mavericks 1.1.0 ERROR
r-release-windows-ix86+x86_64 1.1.0 26.00 132.00 158.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1.0 26.00 138.00 164.00 NOTE

Check Details

Version: 1.1.0
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-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: 1.1.0
Check: R code for possible problems
Result: NOTE
    assignParalogues: no visible global function definition for ‘quantile’
    assignToAlleleSet: no visible global function definition for ‘as’
    assignToAlleleSet: no visible global function definition for ‘new’
    assignToAlleleSet: no visible global function definition for
     ‘validObject’
    callGenotypes: no visible global function definition for ‘median’
    callGenotypes: no visible global function definition for ‘quantile’
    callGenotypes: no visible binding for global variable ‘sd’
    callGenotypes: no visible binding for global variable ‘median’
    callGenotypes: no visible global function definition for ‘pf’
    callGenotypes: no visible global function definition for ‘plot.new’
    callGenotypes: no visible global function definition for ‘plot.window’
    callGenotypes: no visible global function definition for ‘axis’
    callGenotypes: no visible global function definition for ‘points’
    callGenotypes: no visible global function definition for ‘new’
    callGenotypes: no visible global function definition for ‘validObject’
    callGenotypes.interactive: no visible global function definition for
     ‘new’
    callGenotypes.interactive: no visible global function definition for
     ‘median’
    callGenotypes.interactive: no visible global function definition for
     ‘quantile’
    callGenotypes.interactive: no visible binding for global variable
     ‘median’
    callGenotypes.interactive: no visible binding for global variable ‘sd’
    callGenotypes.interactive: no visible global function definition for
     ‘pf’
    callGenotypes.interactive: no visible global function definition for
     ‘validObject’
    callGenotypes.verboseTest: no visible global function definition for
     ‘median’
    callGenotypes.verboseTest: no visible global function definition for
     ‘quantile’
    callGenotypes.verboseTest: no visible global function definition for
     ‘par’
    callGenotypes.verboseTest: no visible binding for global variable ‘sd’
    callGenotypes.verboseTest: no visible binding for global variable
     ‘median’
    callGenotypes.verboseTest: no visible global function definition for
     ‘pf’
    callGenotypes.verboseTest: no visible global function definition for
     ‘plot.new’
    callGenotypes.verboseTest: no visible global function definition for
     ‘plot.window’
    callGenotypes.verboseTest: no visible global function definition for
     ‘axis’
    callGenotypes.verboseTest: no visible global function definition for
     ‘title’
    callGenotypes.verboseTest: no visible global function definition for
     ‘points’
    countFailedSNP: no visible global function definition for ‘new’
    countFailedSNP: no visible global function definition for ‘validObject’
    createAlleleSet: no visible global function definition for ‘new’
    createAlleleSet: no visible global function definition for
     ‘validObject’
    createAlleleSetFromFiles: no visible global function definition for
     ‘read.table’
    createAlleleSetFromFiles: no visible global function definition for
     ‘new’
    createAlleleSetFromFiles: no visible global function definition for
     ‘validObject’
    createMultiSetFromFiles: no visible global function definition for
     ‘read.table’
    createMultiSetFromFiles: no visible global function definition for
     ‘new’
    createMultiSetFromFiles: no visible global function definition for
     ‘validObject’
    findClusters: no visible global function definition for ‘hist’
    findClusters: no visible global function definition for ‘embed’
    findPolyploidClusters: no visible global function definition for ‘hist’
    findPolyploidClusters: no visible global function definition for
     ‘median’
    findPolyploidClusters: no visible global function definition for
     ‘kmeans’
    findPolyploidClusters: no visible binding for global variable ‘median’
    findSeTheta: no visible global function definition for ‘integrate’
    getNoiseDistributions: no visible global function definition for ‘par’
    getNoiseDistributions: no visible binding for global variable ‘median’
    getNoiseDistributions: no visible binding for global variable ‘mad’
    getNoiseDistributions: no visible global function definition for ‘hist’
    getNoiseDistributions: no visible global function definition for
     ‘lines’
    getNoiseDistributions: no visible global function definition for
     ‘dnorm’
    normalizeIllumina: no visible global function definition for ‘quantile’
    normalizeIllumina: no visible global function definition for ‘coef’
    normalizeIllumina: no visible global function definition for ‘lm’
    normalizeIllumina: no visible global function definition for ‘points’
    normalizeIllumina: no visible global function definition for ‘par’
    normalizeIllumina: no visible global function definition for ‘plot.new’
    normalizeIllumina: no visible global function definition for
     ‘plot.window’
    normalizeIllumina: no visible global function definition for ‘axis’
    normalizeIllumina: no visible global function definition for ‘lines’
    normalizeShearedChannels: no visible binding for global variable
     ‘median’
    normalizeShearedChannels: no visible binding for global variable
     ‘quantile’
    plotCountsChrom: no visible global function definition for ‘par’
    plotCountsChrom: no visible global function definition for ‘plot.new’
    plotCountsChrom: no visible global function definition for
     ‘plot.window’
    plotCountsChrom: no visible global function definition for ‘axis’
    plotCountsChrom: no visible global function definition for ‘lines’
    plotCountsChrom: no visible global function definition for ‘title’
    plotEstimatedNoise: no visible global function definition for ‘par’
    plotEstimatedNoise: no visible global function definition for ‘plot’
    plotEstimatedNoise: no visible global function definition for ‘lines’
    plotEstimatedNoise: no visible global function definition for ‘points’
    plotGenotypes: no visible global function definition for ‘par’
    plotGenotypes: no visible global function definition for ‘palette’
    plotGenotypes: no visible global function definition for ‘plot.new’
    plotGenotypes: no visible global function definition for ‘plot.window’
    plotGenotypes: no visible global function definition for ‘axis’
    plotGenotypes: no visible global function definition for ‘points’
    plotGenotypes: no visible global function definition for ‘title’
    plotGenotypes: no visible global function definition for ‘lines’
    plotPreprocessing: no visible global function definition for ‘par’
    preprocessBeadSet: no visible global function definition for ‘new’
    preprocessBeadSet: no visible global function definition for
     ‘validObject’
    readBeadSummaryOutput: no visible global function definition for ‘new’
    scatterArrays: no visible global function definition for ‘par’
    scatterArrays: no visible global function definition for
     ‘smoothScatter’
    scatterArrays: no visible global function definition for ‘plot’
    scatterArrays: no visible global function definition for ‘lines’
    shearRawSignal: no visible global function definition for ‘par’
    shearRawSignal: no visible global function definition for ‘validObject’
    testHardyWeinberg: no visible global function definition for ‘pchisq’
    translateThetaCombined: no visible global function definition for
     ‘validObject’
    translateThetaFromFiles: no visible global function definition for
     ‘read.table’
    translateThetaFromFiles: no visible global function definition for
     ‘new’
    translateThetaFromFiles: no visible global function definition for ‘as’
    translateThetaFromFiles: no visible global function definition for
     ‘write.table’
    validateCallsPedigree: no visible global function definition for ‘new’
    validateCallsPedigree: no visible global function definition for
     ‘validObject’
    writeAlleleSet: no visible global function definition for ‘write.table’
    initialize,AlleleSetIllumina: no visible global function definition for
     ‘new’
    initialize,AlleleSetIllumina: no visible global function definition for
     ‘callNextMethod’
    initialize,BeadSetIllumina: no visible global function definition for
     ‘new’
    initialize,BeadSetIllumina: no visible global function definition for
     ‘callNextMethod’
    Undefined global functions or variables:
     as axis callNextMethod coef dnorm embed hist integrate kmeans lines
     lm mad median new palette par pchisq pf plot plot.new plot.window
     points quantile read.table sd smoothScatter title validObject
     write.table
    Consider adding
     importFrom("grDevices", "palette")
     importFrom("graphics", "axis", "hist", "lines", "par", "plot",
     "plot.new", "plot.window", "points", "smoothScatter",
     "title")
     importFrom("methods", "as", "callNextMethod", "new", "validObject")
     importFrom("stats", "coef", "dnorm", "embed", "integrate", "kmeans",
     "lm", "mad", "median", "pchisq", "pf", "quantile", "sd")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.0
Flags: --no-stop-on-test-error
Check: installed package size
Result: NOTE
     installed size is 8.0Mb
     sub-directories of 1Mb or more:
     data 6.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1.0
Flags: --no-stop-on-test-error
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1.0
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    assignParalogues: no visible global function definition for ‘quantile’
    assignToAlleleSet: no visible global function definition for ‘as’
    assignToAlleleSet: no visible global function definition for ‘new’
    assignToAlleleSet: no visible global function definition for
     ‘validObject’
    callGenotypes: no visible global function definition for ‘median’
    callGenotypes: no visible global function definition for ‘quantile’
    callGenotypes: no visible binding for global variable ‘sd’
    callGenotypes: no visible binding for global variable ‘median’
    callGenotypes: no visible global function definition for ‘pf’
    callGenotypes: no visible global function definition for ‘plot.new’
    callGenotypes: no visible global function definition for ‘plot.window’
    callGenotypes: no visible global function definition for ‘axis’
    callGenotypes: no visible global function definition for ‘points’
    callGenotypes: no visible global function definition for ‘new’
    callGenotypes: no visible global function definition for ‘validObject’
    callGenotypes.interactive: no visible global function definition for
     ‘new’
    callGenotypes.interactive: no visible global function definition for
     ‘median’
    callGenotypes.interactive: no visible global function definition for
     ‘quantile’
    callGenotypes.interactive: no visible binding for global variable
     ‘median’
    callGenotypes.interactive: no visible binding for global variable ‘sd’
    callGenotypes.interactive: no visible global function definition for
     ‘pf’
    callGenotypes.interactive: no visible global function definition for
     ‘validObject’
    callGenotypes.verboseTest: no visible global function definition for
     ‘median’
    callGenotypes.verboseTest: no visible global function definition for
     ‘quantile’
    callGenotypes.verboseTest: no visible global function definition for
     ‘par’
    callGenotypes.verboseTest: no visible binding for global variable ‘sd’
    callGenotypes.verboseTest: no visible binding for global variable
     ‘median’
    callGenotypes.verboseTest: no visible global function definition for
     ‘pf’
    callGenotypes.verboseTest: no visible global function definition for
     ‘plot.new’
    callGenotypes.verboseTest: no visible global function definition for
     ‘plot.window’
    callGenotypes.verboseTest: no visible global function definition for
     ‘axis’
    callGenotypes.verboseTest: no visible global function definition for
     ‘title’
    callGenotypes.verboseTest: no visible global function definition for
     ‘points’
    countFailedSNP: no visible global function definition for ‘new’
    countFailedSNP: no visible global function definition for ‘validObject’
    createAlleleSet: no visible global function definition for ‘new’
    createAlleleSet: no visible global function definition for
     ‘validObject’
    createAlleleSetFromFiles: no visible global function definition for
     ‘read.table’
    createAlleleSetFromFiles: no visible global function definition for
     ‘new’
    createAlleleSetFromFiles: no visible global function definition for
     ‘validObject’
    createMultiSetFromFiles: no visible global function definition for
     ‘read.table’
    createMultiSetFromFiles: no visible global function definition for
     ‘new’
    createMultiSetFromFiles: no visible global function definition for
     ‘validObject’
    findClusters: no visible global function definition for ‘hist’
    findClusters: no visible global function definition for ‘embed’
    findPolyploidClusters: no visible global function definition for ‘hist’
    findPolyploidClusters: no visible global function definition for
     ‘median’
    findPolyploidClusters: no visible global function definition for
     ‘kmeans’
    findPolyploidClusters: no visible binding for global variable ‘median’
    findSeTheta: no visible global function definition for ‘integrate’
    getNoiseDistributions: no visible global function definition for ‘par’
    getNoiseDistributions: no visible binding for global variable ‘median’
    getNoiseDistributions: no visible binding for global variable ‘mad’
    getNoiseDistributions: no visible global function definition for ‘hist’
    getNoiseDistributions: no visible global function definition for
     ‘lines’
    getNoiseDistributions: no visible global function definition for
     ‘dnorm’
    normalizeIllumina: no visible global function definition for ‘quantile’
    normalizeIllumina: no visible global function definition for ‘coef’
    normalizeIllumina: no visible global function definition for ‘lm’
    normalizeIllumina: no visible global function definition for ‘points’
    normalizeIllumina: no visible global function definition for ‘par’
    normalizeIllumina: no visible global function definition for ‘plot.new’
    normalizeIllumina: no visible global function definition for
     ‘plot.window’
    normalizeIllumina: no visible global function definition for ‘axis’
    normalizeIllumina: no visible global function definition for ‘lines’
    normalizeShearedChannels: no visible binding for global variable
     ‘median’
    normalizeShearedChannels: no visible binding for global variable
     ‘quantile’
    plotCountsChrom: no visible global function definition for ‘par’
    plotCountsChrom: no visible global function definition for ‘plot.new’
    plotCountsChrom: no visible global function definition for
     ‘plot.window’
    plotCountsChrom: no visible global function definition for ‘axis’
    plotCountsChrom: no visible global function definition for ‘lines’
    plotCountsChrom: no visible global function definition for ‘title’
    plotEstimatedNoise: no visible global function definition for ‘par’
    plotEstimatedNoise: no visible global function definition for ‘plot’
    plotEstimatedNoise: no visible global function definition for ‘lines’
    plotEstimatedNoise: no visible global function definition for ‘points’
    plotGenotypes: no visible global function definition for ‘par’
    plotGenotypes: no visible global function definition for ‘palette’
    plotGenotypes: no visible global function definition for ‘plot.new’
    plotGenotypes: no visible global function definition for ‘plot.window’
    plotGenotypes: no visible global function definition for ‘axis’
    plotGenotypes: no visible global function definition for ‘points’
    plotGenotypes: no visible global function definition for ‘title’
    plotGenotypes: no visible global function definition for ‘lines’
    plotPreprocessing: no visible global function definition for ‘par’
    preprocessBeadSet: no visible global function definition for ‘new’
    preprocessBeadSet: no visible global function definition for
     ‘validObject’
    readBeadSummaryOutput: no visible global function definition for ‘new’
    scatterArrays: no visible global function definition for ‘par’
    scatterArrays: no visible global function definition for
     ‘smoothScatter’
    scatterArrays: no visible global function definition for ‘plot’
    scatterArrays: no visible global function definition for ‘lines’
    shearRawSignal: no visible global function definition for ‘par’
    shearRawSignal: no visible global function definition for ‘validObject’
    testHardyWeinberg: no visible global function definition for ‘pchisq’
    translateThetaCombined: no visible global function definition for
     ‘validObject’
    translateThetaFromFiles: no visible global function definition for
     ‘read.table’
    translateThetaFromFiles: no visible global function definition for
     ‘new’
    translateThetaFromFiles: no visible global function definition for ‘as’
    translateThetaFromFiles: no visible global function definition for
     ‘write.table’
    validateCallsPedigree: no visible global function definition for ‘new’
    validateCallsPedigree: no visible global function definition for
     ‘validObject’
    writeAlleleSet: no visible global function definition for ‘write.table’
    initialize,AlleleSetIllumina: no visible global function definition for
     ‘new’
    initialize,AlleleSetIllumina: no visible global function definition for
     ‘callNextMethod’
    initialize,BeadSetIllumina: no visible global function definition for
     ‘new’
    initialize,BeadSetIllumina: no visible global function definition for
     ‘callNextMethod’
    Undefined global functions or variables:
     as axis callNextMethod coef dnorm embed hist integrate kmeans lines
     lm mad median new palette par pchisq pf plot plot.new plot.window
     points quantile read.table sd smoothScatter title validObject
     write.table
    Consider adding
     importFrom("grDevices", "palette")
     importFrom("graphics", "axis", "hist", "lines", "par", "plot",
     "plot.new", "plot.window", "points", "smoothScatter",
     "title")
     importFrom("methods", "as", "callNextMethod", "new", "validObject")
     importFrom("stats", "coef", "dnorm", "embed", "integrate", "kmeans",
     "lm", "mad", "median", "pchisq", "pf", "quantile", "sd")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1.0
Check: installed package size
Result: NOTE
     installed size is 7.9Mb
     sub-directories of 1Mb or more:
     data 6.6Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘rggobi’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1.0
Check: R code for possible problems
Result: NOTE
    assignParalogues: no visible global function definition for 'quantile'
    callGenotypes: no visible global function definition for 'median'
    callGenotypes: no visible global function definition for 'quantile'
    callGenotypes: no visible binding for global variable 'sd'
    callGenotypes: no visible binding for global variable 'median'
    callGenotypes: no visible global function definition for 'pf'
    callGenotypes: no visible global function definition for 'plot.new'
    callGenotypes: no visible global function definition for 'plot.window'
    callGenotypes: no visible global function definition for 'axis'
    callGenotypes: no visible global function definition for 'points'
    callGenotypes.interactive: no visible global function definition for
     'median'
    callGenotypes.interactive: no visible global function definition for
     'quantile'
    callGenotypes.interactive: no visible binding for global variable
     'median'
    callGenotypes.interactive: no visible binding for global variable 'sd'
    callGenotypes.interactive: no visible global function definition for
     'pf'
    callGenotypes.verboseTest: no visible global function definition for
     'median'
    callGenotypes.verboseTest: no visible global function definition for
     'quantile'
    callGenotypes.verboseTest: no visible global function definition for
     'par'
    callGenotypes.verboseTest: no visible binding for global variable 'sd'
    callGenotypes.verboseTest: no visible binding for global variable
     'median'
    callGenotypes.verboseTest: no visible global function definition for
     'pf'
    callGenotypes.verboseTest: no visible global function definition for
     'plot.new'
    callGenotypes.verboseTest: no visible global function definition for
     'plot.window'
    callGenotypes.verboseTest: no visible global function definition for
     'axis'
    callGenotypes.verboseTest: no visible global function definition for
     'title'
    callGenotypes.verboseTest: no visible global function definition for
     'points'
    createAlleleSetFromFiles: no visible global function definition for
     'read.table'
    createMultiSetFromFiles: no visible global function definition for
     'read.table'
    findClusters: no visible global function definition for 'hist'
    findClusters: no visible global function definition for 'embed'
    findPolyploidClusters: no visible global function definition for 'hist'
    findPolyploidClusters: no visible global function definition for
     'median'
    findPolyploidClusters: no visible global function definition for
     'kmeans'
    findPolyploidClusters: no visible binding for global variable 'median'
    findSeTheta: no visible global function definition for 'integrate'
    getNoiseDistributions: no visible global function definition for 'par'
    getNoiseDistributions: no visible binding for global variable 'median'
    getNoiseDistributions: no visible binding for global variable 'mad'
    getNoiseDistributions: no visible global function definition for 'hist'
    getNoiseDistributions: no visible global function definition for
     'lines'
    getNoiseDistributions: no visible global function definition for
     'dnorm'
    normalizeIllumina: no visible global function definition for 'quantile'
    normalizeIllumina: no visible global function definition for 'coef'
    normalizeIllumina: no visible global function definition for 'lm'
    normalizeIllumina: no visible global function definition for 'points'
    normalizeIllumina: no visible global function definition for 'par'
    normalizeIllumina: no visible global function definition for 'plot.new'
    normalizeIllumina: no visible global function definition for
     'plot.window'
    normalizeIllumina: no visible global function definition for 'axis'
    normalizeIllumina: no visible global function definition for 'lines'
    normalizeShearedChannels: no visible binding for global variable
     'median'
    normalizeShearedChannels: no visible binding for global variable
     'quantile'
    plotCountsChrom: no visible global function definition for 'par'
    plotCountsChrom: no visible global function definition for 'plot.new'
    plotCountsChrom: no visible global function definition for
     'plot.window'
    plotCountsChrom: no visible global function definition for 'axis'
    plotCountsChrom: no visible global function definition for 'lines'
    plotCountsChrom: no visible global function definition for 'title'
    plotEstimatedNoise: no visible global function definition for 'par'
    plotEstimatedNoise: no visible global function definition for 'plot'
    plotEstimatedNoise: no visible global function definition for 'lines'
    plotEstimatedNoise: no visible global function definition for 'points'
    plotGenotypes: no visible global function definition for 'par'
    plotGenotypes: no visible global function definition for 'palette'
    plotGenotypes: no visible global function definition for 'plot.new'
    plotGenotypes: no visible global function definition for 'plot.window'
    plotGenotypes: no visible global function definition for 'axis'
    plotGenotypes: no visible global function definition for 'points'
    plotGenotypes: no visible global function definition for 'title'
    plotGenotypes: no visible global function definition for 'lines'
    plotPreprocessing: no visible global function definition for 'par'
    scatterArrays: no visible global function definition for 'par'
    scatterArrays: no visible global function definition for
     'smoothScatter'
    scatterArrays: no visible global function definition for 'plot'
    scatterArrays: no visible global function definition for 'lines'
    shearRawSignal: no visible global function definition for 'par'
    testHardyWeinberg: no visible global function definition for 'pchisq'
    translateThetaFromFiles: no visible global function definition for
     'read.table'
    translateThetaFromFiles: no visible global function definition for
     'write.table'
    writeAlleleSet: no visible global function definition for 'write.table'
    Undefined global functions or variables:
     axis coef dnorm embed hist integrate kmeans lines lm mad median
     palette par pchisq pf plot plot.new plot.window points quantile
     read.table sd smoothScatter title write.table
    Consider adding
     importFrom("grDevices", "palette")
     importFrom("graphics", "axis", "hist", "lines", "par", "plot",
     "plot.new", "plot.window", "points", "smoothScatter",
     "title")
     importFrom("stats", "coef", "dnorm", "embed", "integrate", "kmeans",
     "lm", "mad", "median", "pchisq", "pf", "quantile", "sd")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file.
Flavor: r-release-windows-ix86+x86_64