* using log directory 'd:/Rcompile/CRANpkg/local/3.3/rnaseqWrapper.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'rnaseqWrapper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaseqWrapper' version '1.0-1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rnaseqWrapper' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [26s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs