BOTHlabels2: no visible global function definition for
  'floating.pie.asp'
PosGroups: no visible global function definition for 'combinations'
Qcomp.subs: no visible global function definition for 'branching.times'
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'
comBim: no visible global function definition for 'restrictedparts'
comp.subs: no visible global function definition for 'branching.times'
comp.subs.DF: no visible global function definition for
  'branching.times'
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 binding for global variable '.PlotPhyloEnv'
drop.tip2.6: no visible global function definition for 'root'
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'
plot.phylo2: no visible global function definition for 'unrooted.xy'
plot.phylo2: no visible global function definition for 'circular.plot'
plot.phylo2: no visible global function definition for 'cladogram.plot'
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'
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'