CRAN Package Check Results for Package rnaseqWrapper

Last updated on 2019-05-24 15:48:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-1 4.46 55.55 60.01 NOTE
r-devel-linux-x86_64-debian-gcc 1.0-1 3.22 41.99 45.21 NOTE
r-devel-linux-x86_64-fedora-clang 1.0-1 73.67 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0-1 67.72 NOTE
r-devel-windows-ix86+x86_64 1.0-1 7.00 124.00 131.00 NOTE
r-patched-linux-x86_64 1.0-1 3.56 54.53 58.09 NOTE
r-patched-solaris-x86 1.0-1 107.50 NOTE
r-release-linux-x86_64 1.0-1 4.56 55.53 60.09 NOTE
r-release-windows-ix86+x86_64 1.0-1 8.00 88.00 96.00 NOTE
r-release-osx-x86_64 1.0-1 NOTE
r-oldrel-windows-ix86+x86_64 1.0-1 7.00 68.00 75.00 NOTE
r-oldrel-osx-x86_64 1.0-1 NOTE

Check Details

Version: 1.0-1
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0-1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     'DESeq' 'seqinr' 'topGO'
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
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, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0-1
Check: R code for possible problems
Result: NOTE
    DESeqWrapper: no visible global function definition for
     'newCountDataSet'
    DESeqWrapper: no visible global function definition for
     'estimateSizeFactors'
    DESeqWrapper: no visible global function definition for 'counts'
    DESeqWrapper: no visible global function definition for 'write.table'
    DESeqWrapper: no visible global function definition for
     'estimateDispersions'
    DESeqWrapper: no visible global function definition for 'nbinomTest'
    DESeqWrapper: no visible global function definition for 'pdf'
    DESeqWrapper: no visible global function definition for 'hist'
    DESeqWrapper: no visible global function definition for
     'getVarianceStabilizedData'
    DESeqWrapper: no visible global function definition for
     'colorRampPalette'
    DESeqWrapper: no visible global function definition for 'legend'
    DESeqWrapper: no visible global function definition for 'dist'
    DESeqWrapper: no visible global function definition for 'heatmap'
    DESeqWrapper: no visible global function definition for 'pData'
    DESeqWrapper: no visible global function definition for 'dev.off'
    heatmap.mark: no visible binding for global variable 'dist'
    heatmap.mark: no visible binding for global variable 'hclust'
    heatmap.mark: no visible global function definition for 'par'
    heatmap.mark: no visible global function definition for 'median'
    heatmap.mark: no visible global function definition for
     'colorRampPalette'
    heatmap.mark: no visible global function definition for
     'order.dendrogram'
    heatmap.mark: no visible global function definition for 'as.dendrogram'
    heatmap.mark: no visible global function definition for 'reorder'
    heatmap.mark: no visible binding for global variable 'sd'
    heatmap.mark: no visible global function definition for 'layout'
    heatmap.mark: no visible global function definition for 'image'
    heatmap.mark: no visible global function definition for 'axis'
    heatmap.mark: no visible global function definition for 'text'
    heatmap.mark: no visible global function definition for 'strheight'
    heatmap.mark: no visible global function definition for 'strwidth'
    heatmap.mark: no visible global function definition for 'mtext'
    heatmap.mark: no visible global function definition for 'rect'
    heatmap.mark: no visible global function definition for 'abline'
    heatmap.mark: no visible global function definition for 'lines'
    heatmap.mark: no visible global function definition for 'plot'
    heatmap.mark: no visible global function definition for 'plot.new'
    heatmap.mark: no visible global function definition for 'title'
    heatmap.mark: no visible global function definition for 'density'
    heatmap.mark: no visible global function definition for 'hist'
    kaksFromVariants : <anonymous>: no visible global function definition
     for 'as.alignment'
    kaksFromVariants : <anonymous>: no visible global function definition
     for 'kaks'
    mergeCountFiles: no visible global function definition for 'read.table'
    nSynNonSites : <anonymous>: no visible global function definition for
     'as.alignment'
    nSynNonSites : <anonymous>: no visible global function definition for
     'kaks'
    parseVarScan: no visible global function definition for 'read.table'
    plotDE: no visible global function definition for 'plot'
    plotDispEsts: no visible global function definition for 'plot'
    plotDispEsts: no visible global function definition for 'counts'
    plotDispEsts: no visible global function definition for 'fitInfo'
    plotDispEsts: no visible global function definition for 'lines'
    readVariantFiles: no visible global function definition for
     'read.table'
    runGOAnalysis: no visible global function definition for 'new'
    runGOAnalysis: no visible binding for global variable 'annFUN.gene2GO'
    runGOAnalysis: no visible global function definition for 'runTest'
    runGOAnalysis: no visible global function definition for 'score'
    runGOAnalysis: no visible global function definition for 'termStat'
    runGOAnalysis: no visible global function definition for 'Term'
    runGOAnalysis: no visible binding for global variable 'GOTERM'
    runGOAnalysis: no visible global function definition for
     'showSigOfNodes'
    Undefined global functions or variables:
     GOTERM Term abline annFUN.gene2GO as.alignment as.dendrogram axis
     colorRampPalette counts density dev.off dist estimateDispersions
     estimateSizeFactors fitInfo getVarianceStabilizedData hclust heatmap
     hist image kaks layout legend lines median mtext nbinomTest new
     newCountDataSet order.dendrogram pData par pdf plot plot.new
     read.table rect reorder runTest score sd showSigOfNodes strheight
     strwidth termStat text title write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
     importFrom("graphics", "abline", "axis", "hist", "image", "layout",
     "legend", "lines", "mtext", "par", "plot", "plot.new",
     "rect", "strheight", "strwidth", "text", "title")
     importFrom("methods", "new")
     importFrom("stats", "as.dendrogram", "density", "dist", "hclust",
     "heatmap", "median", "order.dendrogram", "reorder", "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-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0-1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'topGO', 'DESeq'
Flavor: r-release-osx-x86_64

Version: 1.0-1
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
Flavor: r-release-osx-x86_64