DDL: no visible global function definition for 'nlm'
DDX: no visible global function definition for 'nlm'
bd: no visible global function definition for 'optim'
birthdeathSim: no visible global function definition for 'sim.bdtree'
birthdeathSim: no visible binding for global variable 'drop.tip'
birthdeathSim : fx: no visible global function definition for
  'branching.times'
fitBOTHVAR: no visible global function definition for 'optim'
fitEXVAR: no visible global function definition for 'optim'
fitSPVAR: no visible global function definition for 'optim'
gamStat: no visible global function definition for 'pnorm'
getBtimes: no visible global function definition for 'read.tree'
getBtimes: no visible global function definition for 'is.ultrametric'
getBtimes: no visible global function definition for 'branching.times'
getBtimes.batch : btfx: no visible global function definition for
  'branching.times'
getBtimes.batch: no visible global function definition for 'read.tree'
getBtimes.batch: no visible binding for global variable
  'branching.times'
lambda.stem.ml: no visible global function definition for 'nlm'
mccrTest: no visible global function definition for 'sim.bdtree'
mccrTest: no visible global function definition for 'drop.tip'
mccrTest: no visible global function definition for 'read.tree'
mccrTest: no visible binding for global variable 'gammaStat'
mccrTest: no visible global function definition for 'quantile'
pTt.BOTHVAR: no visible global function definition for 'integrate'
pTt.EXVAR: no visible global function definition for 'integrate'
pTt.SPVAR: no visible global function definition for 'integrate'
plotLtt: no visible global function definition for 'plot'
plotNodeNumbers.phylo: no visible global function definition for
  'plot.phylo'
plotRate: no visible global function definition for 'plot.new'
plotRate: no visible global function definition for 'plot.window'
plotRate: no visible global function definition for 'lines'
plotRate: no visible global function definition for 'axis'
yuleSim: no visible global function definition for 'rexp'
Undefined global functions or variables:
  axis branching.times drop.tip gammaStat integrate is.ultrametric
  lines nlm optim plot plot.new plot.phylo plot.window pnorm quantile
  read.tree rexp sim.bdtree
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "integrate", "nlm", "optim", "pnorm", "quantile",
             "rexp")
to your NAMESPACE file.