consensus.pyRAD: no visible global function definition for
  ‘write.table’
locus.dist: no visible global function definition for ‘as.dist’
match.lnL.to.trees: no visible global function definition for
  ‘read.delim’
plot.locus.dist: no visible global function definition for ‘layout’
plot.locus.dist: no visible global function definition for ‘plot’
plot.locus.dist: no visible global function definition for ‘points’
plot.locus.dist: no visible global function definition for ‘text’
plot.locus.dist: no visible global function definition for ‘segments’
plot.partitionedRAD: no visible global function definition for ‘pdf’
plot.partitionedRAD: no visible global function definition for ‘layout’
plot.partitionedRAD: no visible global function definition for ‘plot’
plot.partitionedRAD: no visible global function definition for ‘points’
plot.partitionedRAD: no visible global function definition for ‘lm’
plot.partitionedRAD: no visible global function definition for
  ‘predict’
plot.partitionedRAD: no visible global function definition for ‘lines’
plot.partitionedRAD: no visible global function definition for
  ‘matplot’
plot.partitionedRAD: no visible global function definition for
  ‘dev.off’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘pdf’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘layout’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘plot’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘points’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘lm’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘predict’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘lines’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘matplot’
plot.rankedPartitionedRAD: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  as.dist dev.off layout lines lm matplot pdf plot points predict
  read.delim segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "layout", "lines", "matplot", "plot", "points",
             "segments", "text")
  importFrom("stats", "as.dist", "lm", "predict")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file.