DiffAnalysis: no visible global function definition for 'read.table'
DiffAnalysis: no visible global function definition for 'write.table'
DiffAnalysis: no visible global function definition for 'pt'
DiffAnalysis : <anonymous>: no visible global function definition for
  'p.adjust'
DiffAnalysis: no visible global function definition for 'qchisq'
DiffAnalysis: no visible global function definition for 'pnorm'
DiffAnalysis: no visible global function definition for 'var'
DiffAnalysis : <anonymous>: no visible global function definition for
  'pnorm'
DiffAnalysis.unpaired: no visible global function definition for
  'read.table'
DiffAnalysis.unpaired: no visible global function definition for
  'write.table'
DiffAnalysis.unpaired : <anonymous>: no visible global function
  definition for 'bartlett.test'
DiffAnalysis.unpaired: no visible global function definition for 'pt'
DiffAnalysis.unpaired : <anonymous>: no visible global function
  definition for 'p.adjust'
DiffAnalysis.unpaired: no visible global function definition for
  'qchisq'
DiffAnalysis.unpaired: no visible global function definition for
  'pnorm'
DiffAnalysis.unpaired: no visible global function definition for 'var'
DiffAnalysis.unpaired : <anonymous>: no visible global function
  definition for 'pnorm'
Intensity.Norm: no visible global function definition for 'read.table'
LBI: no visible global function definition for 'png'
LBI: no visible global function definition for 'plot'
LBI: no visible global function definition for 'dev.off'
LocalFDR: no visible global function definition for 'loess'
LocalFDR: no visible global function definition for 'pdf'
LocalFDR: no visible global function definition for 'plot'
LocalFDR: no visible global function definition for 'lines'
LocalFDR: no visible global function definition for 'dev.off'
LocalFDR: no visible global function definition for 'isoreg'
LocalFDR: no visible global function definition for 'write.table'
MeanBySpot: no visible global function definition for 'aggregate'
fdr.estimate.eta0: no visible global function definition for
  'smooth.spline'
fdr.estimate.eta0: no visible global function definition for 'predict'
filterByDefault: no visible global function definition for 'read.table'
filterByDefault: no visible global function definition for
  'write.table'
mixgamma: no visible global function definition for 'dgamma'
mixgamma : <anonymous>: no visible global function definition for
  'dgamma'
normalisation: no visible global function definition for 'write.table'
normalisation: no visible global function definition for 'pdf'
normalisation: no visible global function definition for 'read.table'
normalisation: no visible global function definition for 'lowess'
normalisation: no visible global function definition for 'plot'
normalisation: no visible global function definition for 'lines'
normalisation: no visible global function definition for 'boxplot'
normalisation: no visible global function definition for 'median'
normalisation: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  aggregate bartlett.test boxplot dev.off dgamma isoreg lines loess
  lowess median p.adjust pdf plot png pnorm predict pt qchisq
  read.table smooth.spline var write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "png")
  importFrom("graphics", "boxplot", "lines", "plot")
  importFrom("stats", "aggregate", "bartlett.test", "dgamma", "isoreg",
             "loess", "lowess", "median", "p.adjust", "pnorm", "predict",
             "pt", "qchisq", "smooth.spline", "var")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.