correct.taxanames: no visible global function definition for ‘fix’
correct.taxanames: no visible global function definition for
  ‘flush.console’
flist.data: no visible global function definition for ‘data’
formtomat: no visible global function definition for ‘D’
get.dupe.sel: no visible global function definition for ‘select.list’
get.dupe.sel: no visible global function definition for ‘flush.console’
get.otu: no visible global function definition for ‘select.list’
get.otu: no visible global function definition for ‘write.table’
infergui : getfile: no visible global function definition for
  ‘read.delim’
infergui : select.te: no visible global function definition for ‘data’
infergui : compute.inf: no visible global function definition for
  ‘flush.console’
infergui : export.res: no visible global function definition for
  ‘write.table’
load.itis: no visible global function definition for ‘data’
load.itis: no visible binding for global variable ‘itis.ttable’
load.revised.otu: no visible global function definition for
  ‘read.delim’
load.revised.species: no visible global function definition for
  ‘read.delim’
makess: no visible global function definition for ‘flush.console’
makess: no visible global function definition for ‘dev.new’
makess: no visible global function definition for ‘hist’
mlsolve: no visible global function definition for ‘par’
mlsolve: no visible global function definition for ‘contour’
mlsolve: no visible global function definition for ‘box’
mlsolve: no visible global function definition for ‘axis’
mlsolve: no visible global function definition for ‘mtext’
mlsolve: no visible global function definition for ‘optim’
mlsolve: no visible global function definition for ‘points’
output.tax.table: no visible global function definition for
  ‘write.table’
sel.coeffile: no visible global function definition for ‘data’
taxon.env: no visible global function definition for ‘na.omit’
taxon.env: no visible global function definition for ‘glm’
taxon.env: no visible global function definition for ‘as.formula’
taxon.env: no visible global function definition for ‘predict’
taxon.env: no visible global function definition for ‘coef’
view.te: no visible global function definition for ‘pdf’
view.te: no visible global function definition for ‘par’
view.te: no visible global function definition for ‘dev.new’
view.te: no visible global function definition for ‘contour’
view.te: no visible global function definition for ‘box’
view.te: no visible global function definition for ‘axis’
view.te: no visible global function definition for ‘mtext’
view.te: no visible global function definition for ‘quantile’
view.te: no visible global function definition for ‘points’
view.te: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  D as.formula axis box coef contour data dev.new dev.off fix
  flush.console glm hist itis.ttable mtext na.omit optim par pdf points
  predict quantile read.delim select.list write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "axis", "box", "contour", "hist", "mtext",
             "par", "points")
  importFrom("stats", "D", "as.formula", "coef", "glm", "na.omit",
             "optim", "predict", "quantile")
  importFrom("utils", "data", "fix", "flush.console", "read.delim",
             "select.list", "write.table")
to your NAMESPACE file.