CRAN Package Check Results for Package WGCNA

Last updated on 2015-07-29 23:47:33.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.47 11.38 146.99 158.38 NOTE
r-devel-linux-x86_64-debian-gcc 1.47 12.48 142.50 154.98 NOTE
r-devel-linux-x86_64-fedora-clang 1.47 301.32 NOTE
r-devel-linux-x86_64-fedora-gcc 1.47 287.92 NOTE
r-devel-osx-x86_64-clang 1.47 245.04 OK
r-devel-windows-ix86+x86_64 1.47 42.00 289.00 331.00 NOTE
r-patched-linux-x86_64 1.47 12.48 139.82 152.30 OK
r-patched-solaris-sparc 1.47 1743.00 OK
r-patched-solaris-x86 1.47 375.20 OK
r-release-linux-x86_64 1.47 13.76 139.78 153.54 OK
r-release-osx-x86_64-mavericks 1.47 NOTE
r-release-windows-ix86+x86_64 1.47 49.00 276.00 325.00 OK
r-oldrel-windows-ix86+x86_64 1.47 51.00 388.00 439.00 OK

Check Details

Version: 1.47
Check: R code for possible problems
Result: NOTE
    .ClusterCoef.fun: no visible global function definition for ‘as.dist’
    .NPC.direct: no visible global function definition for ‘as.dist’
    .alignedFirstPC: no visible global function definition for ‘cov’
    .clustOrder: no visible global function definition for ‘as.dist’
    .clusterCoeff: no visible global function definition for ‘as.dist’
    .colWeightedMeans.x: no visible global function definition for
     ‘weighted.mean’
    .consensusMEDissimilarity : <anonymous>: no visible global function
     definition for ‘as.dist’
    .consensusMEDissimilarity: no visible binding for global variable
     ‘quantile’
    .coreCalcForAdj: no visible global function definition for ‘as.dist’
    .coreCalcForExpr: no visible global function definition for ‘as.dist’
    .devianceResidual: no visible binding for global variable ‘na.exclude’
    .devianceResidual: no visible global function definition for ‘predict’
    .err.bp: no visible global function definition for ‘segments’
    .heatmap: no visible binding for global variable ‘dist’
    .heatmap : <anonymous>: no visible global function definition for
     ‘reorder’
    .heatmap: no visible global function definition for ‘as.dendrogram’
    .heatmap: no visible global function definition for ‘order.dendrogram’
    .heatmap: no visible binding for global variable ‘sd’
    .heatmap: no visible global function definition for ‘par’
    .heatmap: no visible global function definition for ‘layout’
    .heatmap: no visible global function definition for ‘image’
    .heatmap: no visible global function definition for ‘axis’
    .heatmap: no visible global function definition for ‘mtext’
    .heatmap: no visible global function definition for ‘plot’
    .heatmap: no visible global function definition for ‘frame’
    .heatmap: no visible global function definition for ‘title’
    .heatmapWithLegend: no visible global function definition for ‘barplot’
    .heatmapWithLegend: no visible global function definition for ‘par’
    .heatmapWithLegend: no visible global function definition for ‘rect’
    .heatmapWithLegend: no visible global function definition for ‘lines’
    .heatmapWithLegend: no visible global function definition for ‘text’
    .histogramsWithCommonBreaks: no visible binding for global variable
     ‘hist’
    .maxRowVariance : <anonymous>: no visible global function definition
     for ‘var’
    .pValueFromZ: no visible global function definition for ‘pnorm’
    .pValueFromZ: no visible binding for global variable ‘median’
    .panel.cor: no visible global function definition for ‘par’
    .panel.cor: no visible global function definition for ‘strwidth’
    .panel.cor: no visible global function definition for ‘text’
    .panel.hist: no visible global function definition for ‘par’
    .panel.hist: no visible global function definition for ‘hist’
    .panel.hist: no visible global function definition for ‘rect’
    .phyper2: no visible global function definition for ‘phyper’
    .qValueFromP: no visible binding for global variable ‘median’
    GOenrichmentAnalysis : ftp: no visible global function definition for
     ‘fisher.test’
    GTOMdist: no visible global function definition for ‘as.dist’
    TOMplot: no visible global function definition for ‘as.dendrogram’
    TOMplot: no visible global function definition for ‘terrain.colors’
    TrueTrait: no visible global function definition for ‘coef’
    TrueTrait: no visible global function definition for ‘lm’
    TrueTrait: no visible global function definition for ‘var’
    TrueTrait: no visible binding for global variable ‘na.exclude’
    TrueTrait: no visible global function definition for ‘predict’
    accuracyMeasures: no visible global function definition for ‘median’
    addErrorBars: no visible global function definition for ‘segments’
    addGrid: no visible global function definition for ‘par’
    addGrid: no visible global function definition for ‘lines’
    addGuideLines: no visible global function definition for ‘par’
    addGuideLines: no visible global function definition for ‘lines’
    adjacency.polyReg: no visible global function definition for ‘var’
    adjacency.polyReg: no visible global function definition for ‘glm’
    adjacency.polyReg: no visible global function definition for ‘predict’
    adjacency.splineReg: no visible global function definition for ‘var’
    adjacency.splineReg: no visible global function definition for ‘glm’
    adjacency.splineReg: no visible global function definition for
     ‘predict’
    automaticNetworkScreening: no visible binding for global variable ‘var’
    automaticNetworkScreeningGS: no visible binding for global variable
     ‘var’
    bicorAndPvalue: no visible global function definition for ‘pt’
    bicovWeights: no visible global function definition for ‘qnorm’
    blockwiseConsensusModules: no visible global function definition for
     ‘plot’
    blockwiseConsensusModules: no visible binding for global variable
     ‘quantile’
    blockwiseConsensusModules: no visible global function definition for
     ‘pchisq’
    blockwiseIndividualTOMs: no visible global function definition for
     ‘as.dist’
    blockwiseModules: no visible global function definition for ‘as.dist’
    blueWhiteRed: no visible global function definition for ‘rgb’
    branchSplit: no visible global function definition for ‘predict’
    branchSplit: no visible global function definition for ‘lm’
    branchSplit.dissim: no visible binding for global variable ‘quantile’
    branchSplit.dissim : separation: no visible global function definition
     for ‘var’
    clusterCoef: no visible global function definition for ‘as.dist’
    coClustering.permutationTest: no visible binding for global variable
     ‘sd’
    consensusDissTOMandTree: no visible global function definition for
     ‘as.dist’
    consensusDissTOMandTree: no visible global function definition for
     ‘quantile’
    consensusKME: no visible binding for global variable ‘quantile’
    consensusKME: no visible binding for global variable ‘median’
    consensusKME: no visible global function definition for ‘pnorm’
    consensusTOM: no visible global function definition for ‘quantile’
    corAndPvalue: no visible global function definition for ‘pt’
    corPvalueFisher: no visible global function definition for ‘pnorm’
    corPvalueStudent: no visible global function definition for ‘pt’
    coxRegressionResiduals: no visible global function definition for
     ‘residuals’
    displayColors: no visible global function definition for ‘barplot’
    empiricalBayesLM: no visible global function definition for
     ‘model.matrix’
    empiricalBayesLM: no visible global function definition for ‘cov’
    empiricalBayesLM: no visible global function definition for ‘var’
    exportNetworkToCytoscape: no visible global function definition for
     ‘as.dist’
    exportNetworkToCytoscape: no visible global function definition for
     ‘write.table’
    exportNetworkToVisANT: no visible global function definition for
     ‘as.dist’
    exportNetworkToVisANT: no visible global function definition for
     ‘write.table’
    goodGenes: no visible binding for global variable ‘sd’
    goodGenesMS: no visible binding for global variable ‘sd’
    greenBlackRed: no visible global function definition for ‘rgb’
    greenWhiteRed: no visible global function definition for ‘rgb’
    kMEcomparisonScatterplot: no visible global function definition for
     ‘pdf’
    kMEcomparisonScatterplot: no visible global function definition for
     ‘dev.off’
    labelPoints: no visible global function definition for ‘par’
    labelPoints: no visible global function definition for ‘runif’
    labelPoints: no visible global function definition for ‘strwidth’
    labelPoints: no visible global function definition for ‘strheight’
    labelPoints: no visible global function definition for ‘text’
    labelPoints: no visible global function definition for ‘dist’
    labeledBarplot: no visible global function definition for ‘par’
    labeledBarplot: no visible global function definition for ‘barplot’
    labeledBarplot: no visible global function definition for ‘text’
    labeledBarplot: no visible global function definition for ‘rect’
    labeledBarplot: no visible global function definition for ‘axis’
    labeledHeatmap: no visible global function definition for ‘par’
    labeledHeatmap: no visible global function definition for ‘heat.colors’
    labeledHeatmap: no visible global function definition for ‘polygon’
    labeledHeatmap: no visible global function definition for ‘rect’
    labeledHeatmap: no visible global function definition for ‘text’
    labeledHeatmap: no visible global function definition for ‘lines’
    labeledHeatmap: no visible global function definition for ‘axis’
    mergeCloseModules: no visible global function definition for ‘as.dist’
    metaAnalysis: no visible global function definition for ‘qnorm’
    metaAnalysis: no visible global function definition for ‘pnorm’
    moduleEigengenes: no visible global function definition for ‘cov’
    moduleNumber: no visible global function definition for ‘cutree’
    modulePreservation: no visible global function definition for ‘pdf’
    modulePreservation: no visible binding for global variable ‘sd’
    modulePreservation: no visible global function definition for ‘lm’
    modulePreservation: no visible global function definition for ‘predict’
    modulePreservation: no visible global function definition for ‘par’
    modulePreservation: no visible global function definition for ‘lines’
    modulePreservation: no visible global function definition for ‘abline’
    modulePreservation: no visible global function definition for ‘dev.off’
    modulePreservation: no visible binding for global variable ‘median’
    mtd.branchEigengeneDissim: no visible global function definition for
     ‘quantile’
    nearestCentroidPredictor: no visible binding for global variable ‘sd’
    networkScreening: no visible global function definition for ‘pt’
    networkScreeningGS: no visible binding for global variable ‘var’
    overlapTable: no visible global function definition for ‘fisher.test’
    pickHardThreshold: no visible global function definition for ‘pt’
    pickHardThreshold: no visible global function definition for ‘median’
    pickSoftThreshold: no visible global function definition for ‘median’
    plotClusterTreeSamples: no visible global function definition for
     ‘dist’
    plotClusterTreeSamples: no visible global function definition for ‘par’
    plotClusterTreeSamples: no visible global function definition for
     ‘plot’
    plotClusterTreeSamples: no visible global function definition for
     ‘median’
    plotCor: no visible global function definition for ‘image’
    plotCor: no visible global function definition for ‘axis’
    plotCor: no visible global function definition for ‘mtext’
    plotCor: no visible global function definition for ‘box’
    plotDendroAndColors: no visible global function definition for ‘par’
    plotDendroAndColors: no visible global function definition for ‘layout’
    plotDendroAndColors: no visible global function definition for ‘plot’
    plotDendroAndColors: no visible global function definition for ‘abline’
    plotEigengeneNetworks: no visible global function definition for
     ‘heat.colors’
    plotEigengeneNetworks: no visible global function definition for ‘par’
    plotEigengeneNetworks: no visible global function definition for
     ‘as.dist’
    plotEigengeneNetworks: no visible global function definition for ‘plot’
    plotMEpairs: no visible global function definition for ‘hist’
    plotMEpairs: no visible global function definition for ‘as.dist’
    plotMEpairs: no visible global function definition for ‘pairs’
    plotMEpairs: no visible binding for global variable ‘panel.smooth’
    plotMat: no visible global function definition for ‘image’
    plotMat: no visible global function definition for ‘axis’
    plotMat: no visible global function definition for ‘mtext’
    plotMat: no visible global function definition for ‘box’
    plotModuleSignificance: no visible global function definition for
     ‘kruskal.test’
    plotModuleSignificance: no visible global function definition for
     ‘barplot’
    plotNetworkHeatmap: no visible global function definition for ‘plot’
    plotNetworkHeatmap: no visible global function definition for ‘as.dist’
    plotNetworkHeatmap: no visible global function definition for ‘heatmap’
    plotNetworkHeatmap: no visible global function definition for
     ‘as.dendrogram’
    plotOrderedColors: no visible global function definition for ‘barplot’
    plotOrderedColors: no visible global function definition for ‘strwidth’
    plotOrderedColors: no visible global function definition for
     ‘strheight’
    plotOrderedColors: no visible global function definition for ‘par’
    plotOrderedColors: no visible global function definition for ‘rect’
    plotOrderedColors: no visible global function definition for ‘text’
    plotOrderedColors: no visible global function definition for ‘lines’
    populationMeansInAdmixture: no visible global function definition for
     ‘lm’
    pquantile: no visible binding for global variable ‘quantile’
    proportionsInAdmixture: no visible global function definition for ‘lm’
    qvalue: no visible global function definition for ‘smooth.spline’
    qvalue: no visible global function definition for ‘predict’
    rankPvalue: no visible global function definition for ‘pnorm’
    recutConsensusTrees: no visible binding for global variable ‘quantile’
    recutConsensusTrees: no visible global function definition for ‘pchisq’
    redWhiteGreen: no visible global function definition for ‘rgb’
    relativeCorPredictionSuccess: no visible global function definition for
     ‘kruskal.test’
    removePrincipalComponents: no visible global function definition for
     ‘lm’
    removePrincipalComponents: no visible global function definition for
     ‘residuals’
    returnGeneSetsAsList: no visible global function definition for
     ‘read.csv’
    returnGeneSetsAsList: no visible global function definition for ‘data’
    rgcolors.func: no visible global function definition for ‘rgb’
    scaleFreeFitIndex: no visible global function definition for ‘hist’
    scaleFreeFitIndex: no visible global function definition for ‘lm’
    scaleFreePlot: no visible global function definition for ‘hist’
    scaleFreePlot: no visible global function definition for ‘lm’
    scaleFreePlot: no visible global function definition for ‘plot’
    scaleFreePlot: no visible global function definition for ‘lines’
    scaleFreePlot: no visible global function definition for ‘predict’
    signedKME: no visible binding for global variable ‘var’
    simulateDatExpr: no visible global function definition for ‘rnorm’
    simulateDatExpr5Modules: no visible global function definition for
     ‘rnorm’
    simulateEigengeneNetwork: no visible global function definition for
     ‘rnorm’
    simulateModule: no visible global function definition for ‘rnorm’
    simulateModule: no visible global function definition for ‘var’
    simulateSmallLayer: no visible global function definition for ‘rexp’
    simulateSmallLayer: no visible global function definition for ‘rnorm’
    sizeGrWindow: no visible global function definition for ‘par’
    sizeGrWindow: no visible global function definition for ‘dev.off’
    standardScreeningBinaryTrait: no visible global function definition for
     ‘t.test’
    standardScreeningBinaryTrait: no visible global function definition for
     ‘kruskal.test’
    standardScreeningBinaryTrait: no visible global function definition for
     ‘qnorm’
    standardScreeningBinaryTrait : stderr1: no visible global function
     definition for ‘var’
    standardScreeningCensoredTime: no visible binding for global variable
     ‘na.exclude’
    standardScreeningCensoredTime: no visible global function definition
     for ‘predict’
    standardScreeningCensoredTime: no visible global function definition
     for ‘var’
    standardScreeningCensoredTime: no visible global function definition
     for ‘quantile’
    standardScreeningNumericTrait: no visible global function definition
     for ‘pt’
    stdErr: no visible global function definition for ‘var’
    stratifiedBarplot : <anonymous>: no visible global function definition
     for ‘sd’
    stratifiedBarplot: no visible global function definition for
     ‘kruskal.test’
    stratifiedBarplot: no visible global function definition for ‘sd’
    stratifiedBarplot: no visible global function definition for ‘barplot’
    updateProgInd: no visible global function definition for
     ‘flush.console’
    userListEnrichment: no visible global function definition for
     ‘read.csv’
    userListEnrichment: no visible global function definition for ‘data’
    userListEnrichment: no visible global function definition for
     ‘fisher.test’
    userListEnrichment: no visible global function definition for
     ‘write.csv’
    verboseBarplot : stderr1: no visible global function definition for
     ‘var’
    verboseBarplot : err.bp: no visible global function definition for
     ‘segments’
    verboseBarplot: no visible global function definition for
     ‘kruskal.test’
    verboseBarplot: no visible global function definition for ‘anova’
    verboseBarplot: no visible global function definition for ‘lm’
    verboseBarplot: no visible global function definition for ‘fisher.test’
    verboseBarplot: no visible global function definition for ‘barplot’
    verboseBarplot: no visible global function definition for ‘mtext’
    verboseBarplot: no visible global function definition for ‘abline’
    verboseBoxplot: no visible global function definition for
     ‘kruskal.test’
    verboseBoxplot: no visible global function definition for ‘boxplot’
    verboseIplot: no visible global function definition for ‘lm’
    verboseIplot : whiteBlueGreenRedBlack: no visible global function
     definition for ‘rgb’
    verboseIplot: no visible global function definition for ‘image’
    verboseScatterplot: no visible binding for global variable ‘lm’
    verboseScatterplot: no visible global function definition for ‘plot’
    votingLinearPredictor: no visible binding for global variable ‘sd’
    Undefined global functions or variables:
     abline anova as.dendrogram as.dist axis barplot box boxplot coef cov
     cutree data dev.off dist fisher.test flush.console frame glm
     heat.colors heatmap hist image kruskal.test layout lines lm median
     model.matrix mtext na.exclude order.dendrogram pairs panel.smooth par
     pchisq pdf phyper plot pnorm polygon predict pt qnorm quantile
     read.csv rect reorder residuals rexp rgb rnorm runif sd segments
     smooth.spline strheight strwidth t.test terrain.colors text title var
     weighted.mean write.csv write.table
    Consider adding
     importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
     "terrain.colors")
     importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
     "frame", "hist", "image", "layout", "lines", "mtext",
     "pairs", "panel.smooth", "par", "plot", "polygon", "rect",
     "segments", "strheight", "strwidth", "text", "title")
     importFrom("stats", "anova", "as.dendrogram", "as.dist", "coef", "cov",
     "cutree", "dist", "fisher.test", "glm", "heatmap",
     "kruskal.test", "lm", "median", "model.matrix",
     "na.exclude", "order.dendrogram", "pchisq", "phyper",
     "pnorm", "predict", "pt", "qnorm", "quantile", "reorder",
     "residuals", "rexp", "rnorm", "runif", "sd",
     "smooth.spline", "t.test", "var", "weighted.mean")
     importFrom("utils", "data", "flush.console", "read.csv", "write.csv",
     "write.table")
    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: 1.47
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘minet’
Flavor: r-release-osx-x86_64-mavericks