cgraph: no visible global function definition for ‘combn’
cgraph: no visible global function definition for ‘segments’
dataStat: no visible global function definition for ‘median’
haploAccum: no visible global function definition for ‘as.roman’
haploAccum: no visible binding for global variable ‘sd’
heatmapSpp: no visible global function definition for ‘image’
heatmapSpp: no visible global function definition for ‘axis’
localMinima: no visible global function definition for ‘density’
monophyly: no visible global function definition for ‘prop.part’
monophylyBoot: no visible global function definition for ‘nj’
monophylyBoot: no visible global function definition for ‘boot.phylo’
monophylyBoot : <anonymous>: no visible global function definition for
  ‘root’
monophylyBoot : <anonymous>: no visible global function definition for
  ‘nj’
monophylyBoot: no visible global function definition for ‘prop.part’
ordinDNA: no visible global function definition for ‘cmdscale’
plot.haploAccum: no visible global function definition for ‘par’
plot.haploAccum: no visible global function definition for ‘segments’
plot.haploAccum: no visible global function definition for ‘matlines’
plot.haploAccum: no visible global function definition for ‘polygon’
plot.haploAccum: no visible global function definition for ‘lines’
plot.ordinDNA: no visible global function definition for ‘aggregate’
plot.ordinDNA : maxDist: no visible global function definition for
  ‘dist’
plot.ordinDNA: no visible global function definition for ‘symbols’
plot.ordinDNA: no visible global function definition for ‘points’
plot.ordinDNA: no visible global function definition for ‘text’
plot.slidWin : distM: no visible global function definition for
  ‘abline’
plot.slidWin: no visible global function definition for ‘layout’
plot.slidWin: no visible global function definition for ‘axis’
plot.slidWin: no visible global function definition for ‘bxp’
plot.slidWin: no visible global function definition for ‘median’
polyBalance: no visible global function definition for ‘node.depth’
rankSlidWin: no visible global function definition for ‘head’
read.BOLD: no visible global function definition for ‘as.DNAbin’
read.GB: no visible global function definition for ‘as.DNAbin’
seeBarcode: no visible global function definition for ‘abline’
seqStat: no visible global function definition for ‘median’
slideAnalyses: no visible global function definition for ‘nj’
slideAnalyses: no visible global function definition for ‘node.depth’
slideAnalyses: no visible global function definition for ‘median’
slideAnalyses: no visible binding for global variable ‘nj’
slideBoxplots : <anonymous>: no visible global function definition for
  ‘boxplot’
tree.comp: no visible global function definition for ‘unroot’
tree.comp: no visible global function definition for ‘prop.part’
tree.comp: no visible global function definition for ‘node.depth’
tree.comp: no visible global function definition for ‘median’
Undefined global functions or variables:
  abline aggregate as.DNAbin as.roman axis boot.phylo boxplot bxp
  cmdscale combn density dist head image layout lines matlines median
  nj node.depth par points polygon prop.part root sd segments symbols
  text unroot
Consider adding
  importFrom("graphics", "abline", "axis", "boxplot", "bxp", "image",
             "layout", "lines", "matlines", "par", "points", "polygon",
             "segments", "symbols", "text")
  importFrom("stats", "aggregate", "cmdscale", "density", "dist",
             "median", "sd")
  importFrom("utils", "as.roman", "combn", "head")
to your NAMESPACE file.