BOTHlabels2: no visible global function definition for 'par'
BOTHlabels2: no visible global function definition for 'strwidth'
BOTHlabels2: no visible global function definition for 'strheight'
BOTHlabels2: no visible global function definition for 'xinch'
BOTHlabels2: no visible global function definition for 'yinch'
BOTHlabels2: no visible global function definition for 'rect'
BOTHlabels2: no visible global function definition for 'symbols'
BOTHlabels2: no visible global function definition for 'rainbow'
BOTHlabels2: no visible global function definition for 'segments'
BOTHlabels2: no visible global function definition for
  'floating.pie.asp'
BOTHlabels2: no visible global function definition for 'points'
FP.comp.subs: no visible global function definition for 'na.omit'
FP.comp.subs: no visible global function definition for 'quantile'
PosGroups: no visible global function definition for 'combinations'
Qcomp.subs: no visible global function definition for 'branching.times'
Qcomp.subs: no visible global function definition for 'na.omit'
Qcomp.subs: no visible global function definition for 'pchisq'
RemRedun: no visible global function definition for 'na.exclude'
birthdeath.tree.geiger1.3.1: no visible global function definition for
  'runif'
birthdeath.tree.geiger1.3.1: no visible global function definition for
  'rexp'
birthdeath.tree.geiger1.3.1: no visible global function definition for
  'old2new.phylo'
birthdeath.tree.geiger1.3.1: no visible global function definition for
  'read.tree'
birthdeath.tree.geiger1.3.1: no visible global function definition for
  'write.tree'
censor.lnorm.x: no visible global function definition for 'optim'
censor.vrat.x: no visible global function definition for 'optim'
censor.weib.x: no visible global function definition for 'optim'
color.tree.plot: no visible global function definition for 'rainbow'
color.tree.plot: no visible global function definition for 'p.adjust'
comBim: no visible global function definition for 'restrictedparts'
comp.subs: no visible global function definition for 'branching.times'
comp.subs: no visible global function definition for 'na.omit'
comp.subs: no visible global function definition for 'pchisq'
comp.subs.DF: no visible global function definition for
  'branching.times'
comp.subs.DF: no visible global function definition for 'na.omit'
comp.subs.DF: no visible global function definition for 'pchisq'
compareSubTrees: no visible global function definition for
  'branching.times'
drop.tip2.6: no visible global function definition for 'is.rooted'
drop.tip2.6: no visible global function definition for 'locator'
drop.tip2.6: no visible binding for global variable '.PlotPhyloEnv'
drop.tip2.6: no visible global function definition for 'root'
drop.tip2.6: no visible global function definition for 'reorder'
drop.tip2.6: no visible global function definition for
  'collapse.singles'
edgelabels2: no visible binding for global variable '.PlotPhyloEnv'
internds: no visible global function definition for 'branching.times'
min.lnorm: no visible global function definition for 'dlnorm'
min.lnorm: no visible global function definition for 'plnorm'
phylogram.plot2: no visible global function definition for 'segments'
plot.phylo2: no visible global function definition for 'par'
plot.phylo2: no visible global function definition for 'reorder'
plot.phylo2: no visible global function definition for 'unrooted.xy'
plot.phylo2: no visible global function definition for 'strwidth'
plot.phylo2: no visible global function definition for 'uniroot'
plot.phylo2: no visible global function definition for 'circular.plot'
plot.phylo2: no visible global function definition for 'cladogram.plot'
plot.phylo2: no visible global function definition for 'segments'
plot.phylo2: no visible global function definition for 'text'
plot.phylo2: no visible global function definition for 'strheight'
plot.phylo2: no visible binding for global variable '.PlotPhyloEnv'
subtrees2.6: no visible global function definition for 'Ntip'
subtrees2.6: no visible global function definition for 'Nnode'
subtrees2.6: no visible global function definition for 'drop.tip'
subtreez: no visible global function definition for 'Ntip'
subtreez: no visible global function definition for 'Nnode'
tree.rand.test: no visible global function definition for
  'branching.times'
treeSims: no visible global function definition for 'reorder'
trimTree: no visible global function definition for 'is.ultrametric'
trimTree: no visible global function definition for 'branching.times'
trimTree: no visible global function definition for 'multi2di'
trimTree: no visible global function definition for 'read.tree'
trimTree: no visible global function definition for 'write.tree'
trimTree: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  .PlotPhyloEnv Nnode Ntip branching.times circular.plot cladogram.plot
  collapse.singles combinations dlnorm drop.tip floating.pie.asp
  is.rooted is.ultrametric locator multi2di na.exclude na.omit
  old2new.phylo optim p.adjust par pchisq plnorm points quantile
  rainbow read.tree rect reorder restrictedparts rexp root runif
  segments strheight strwidth symbols text uniroot unrooted.xy
  write.tree xinch yinch
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "locator", "par", "points", "rect", "segments",
             "strheight", "strwidth", "symbols", "text", "xinch",
             "yinch")
  importFrom("stats", "dlnorm", "na.exclude", "na.omit", "optim",
             "p.adjust", "pchisq", "plnorm", "quantile", "reorder",
             "rexp", "runif", "uniroot")
to your NAMESPACE file.