MotifModel.plotFits: no visible global function definition for
  ‘colorRampPalette’
MotifModel.plotFits: no visible global function definition for
  ‘barplot’
MotifModel.plotPositions: no visible global function definition for
  ‘par’
MotifModel.plotPositions: no visible global function definition for
  ‘barplot’
MotifModel.plotPositions: no visible global function definition for
  ‘hcl’
MotifModel.plotPositions: no visible global function definition for
  ‘text’
MotifModel.plotStartingPosition: no visible global function definition
  for ‘par’
MotifModel.plotStartingPosition: no visible global function definition
  for ‘barplot’
MotifModel.plotStartingPosition: no visible global function definition
  for ‘hcl’
ROC: no visible global function definition for ‘lines’
autocorrelation: no visible global function definition for ‘var’
descriptors: no visible global function definition for ‘var’
descriptors: no visible binding for global variable ‘var’
descriptors: no visible global function definition for ‘wilcox.test’
modelStep: no visible global function definition for ‘cor’
motifModelSet: no visible global function definition for ‘lines’
plot.Descriptors: no visible global function definition for ‘cor’
plot.Descriptors: no visible global function definition for ‘hist’
plot.Descriptors: no visible global function definition for ‘par’
plot.Descriptors: no visible global function definition for ‘barplot’
plot.Descriptors: no visible global function definition for ‘prcomp’
plot.Descriptors: no visible global function definition for ‘biplot’
plot.MotifModel: no visible global function definition for ‘barplot’
plot.MotifModel: no visible global function definition for ‘par’
plot.MotifModel: no visible global function definition for
  ‘colorRampPalette’
plot.MotifModelSet: no visible global function definition for ‘hcl’
plot.MotifModelSet: no visible global function definition for ‘prcomp’
plot.MotifModelSet: no visible global function definition for ‘par’
plot.MotifModelSet: no visible global function definition for ‘legend’
plot.Sequences: no visible global function definition for ‘hcl’
plot.Sequences: no visible global function definition for ‘prcomp’
plot.Sequences: no visible global function definition for ‘legend’
read.sequences: no visible global function definition for ‘read.table’
write.sequences: no visible global function definition for
  ‘write.table’
plotFits,MotifModel: no visible global function definition for
  ‘colorRampPalette’
plotFits,MotifModel: no visible global function definition for
  ‘barplot’
plotPositions,MotifModel: no visible global function definition for
  ‘par’
plotPositions,MotifModel: no visible global function definition for
  ‘barplot’
plotPositions,MotifModel: no visible global function definition for
  ‘hcl’
plotPositions,MotifModel: no visible global function definition for
  ‘text’
plotStartingPosition,MotifModel: no visible global function definition
  for ‘par’
plotStartingPosition,MotifModel: no visible global function definition
  for ‘barplot’
plotStartingPosition,MotifModel: no visible global function definition
  for ‘hcl’
Undefined global functions or variables:
  barplot biplot colorRampPalette cor hcl hist legend lines par prcomp
  read.table text var wilcox.test write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "hcl")
  importFrom("graphics", "barplot", "hist", "legend", "lines", "par",
             "text")
  importFrom("stats", "biplot", "cor", "prcomp", "var", "wilcox.test")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.