RFLPdist: no visible binding for global variable 'dist'
RFLPdist2: no visible binding for global variable 'dist'
RFLPdist2 : dfun1: no visible global function definition for 'combn'
RFLPdist2 : dfun2: no visible global function definition for 'combn'
RFLPdist2ref: no visible binding for global variable 'dist'
RFLPplot: no visible binding for global variable 'dist'
RFLPplot: no visible global function definition for 'order.dendrogram'
RFLPplot: no visible global function definition for 'as.dendrogram'
RFLPplot: no visible global function definition for 'hclust'
RFLPplot: no visible global function definition for 'par'
RFLPplot: no visible global function definition for 'axis'
RFLPplot: no visible global function definition for 'abline'
RFLPplot: no visible global function definition for 'box'
RFLPplot: no visible global function definition for 'title'
RFLPplot: no visible global function definition for 'colorRampPalette'
RFLPplot: no visible global function definition for 'matlines'
RFLPrefplot: no visible binding for global variable 'dist'
RFLPrefplot: no visible global function definition for 'par'
RFLPrefplot: no visible global function definition for 'dev.new'
RFLPrefplot: no visible global function definition for 'axis'
RFLPrefplot: no visible global function definition for 'abline'
RFLPrefplot: no visible global function definition for 'box'
RFLPrefplot: no visible global function definition for 'title'
RFLPrefplot: no visible global function definition for
  'colorRampPalette'
RFLPrefplot: no visible global function definition for 'matlines'
diffDist: no visible global function definition for 'dist'
read.blast: no visible global function definition for 'read.table'
read.rflp: no visible global function definition for 'read.delim'
read.rflp : <anonymous>: no visible global function definition for
  'tail'
sim2dist: no visible global function definition for 'as.dist'
simulateRFLPdata: no visible global function definition for 'runif'
write.hclust: no visible global function definition for 'cutree'
write.hclust: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline as.dendrogram as.dist axis box colorRampPalette combn cutree
  dev.new dist hclust matlines order.dendrogram par read.delim
  read.table runif tail title write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "matlines", "par",
             "title")
  importFrom("stats", "as.dendrogram", "as.dist", "cutree", "dist",
             "hclust", "order.dendrogram", "runif")
  importFrom("utils", "combn", "read.delim", "read.table", "tail",
             "write.table")
to your NAMESPACE file.