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').