adjust.linearmodel: no visible global function definition for 'lm'
adjust.linearmodel: no visible global function definition for 'rlm'
combat : aprior: no visible global function definition for 'var'
combat : bprior: no visible global function definition for 'var'
combat : L: no visible global function definition for 'dnorm'
combat: no visible binding for global variable 'var'
combat: no visible global function definition for 'par'
combat: no visible global function definition for 'density'
combat: no visible global function definition for 'plot'
combat: no visible global function definition for 'lines'
combat: no visible global function definition for 'dnorm'
combat: no visible global function definition for 'qqnorm'
combat: no visible global function definition for 'qqline'
combat: no visible global function definition for 'rgamma'
combat: no visible global function definition for 'qqplot'
combat: no visible global function definition for 'title'
confounding: no visible global function definition for 'heat.colors'
confounding: no visible global function definition for 'fisher.test'
confounding: no visible global function definition for 'chisq.test'
confounding: no visible global function definition for 'lm'
confounding: no visible global function definition for 'pf'
confounding: no visible global function definition for 'heatmap.2'
corrected.p: no visible global function definition for 'p.adjust'
dense.plot: no visible global function definition for 'density'
dense.plot: no visible global function definition for 'plot'
dense.plot: no visible global function definition for 'lines'
feature.assoc: no visible binding for global variable 'cor'
feature.assoc : <anonymous>: no visible global function definition for
  'cor.test'
feature.assoc: no visible global function definition for 't.test'
feature.assoc: no visible global function definition for 'wilcox.test'
feature.assoc: no visible global function definition for 'na.omit'
feature.assoc: no visible global function definition for 'lm'
feature.assoc: no visible global function definition for 'pf'
hca.plot: no visible global function definition for 'palette'
hca.plot: no visible global function definition for 'colorpanel'
hca.plot: no visible global function definition for 'hcluster'
hca.plot: no visible global function definition for 'as.dendrogram'
hca.plot: no visible global function definition for 'par'
hca.plot: no visible global function definition for 'layout'
hca.plot: no visible global function definition for 'plot'
hca.plot: no visible global function definition for 'rect'
hca.plot: no visible global function definition for 'axis'
hca.test: no visible global function definition for 'hcluster'
hca.test: no visible global function definition for 'cutree'
hca.test: no visible global function definition for 'fisher.test'
hca.test: no visible global function definition for 'chisq.test'
hca.test: no visible global function definition for 'lm'
hca.test: no visible global function definition for 'pf'
kill.pc: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'prcomp'
prince: no visible global function definition for 'lm'
prince: no visible global function definition for 'pf'
prince.plot: no visible global function definition for 'heat.colors'
prince.plot: no visible global function definition for 'heatmap.2'
prince.var.plot: no visible global function definition for 'impute.knn'
prince.var.plot: no visible global function definition for 'prcomp'
prince.var.plot: no visible binding for global variable 'median'
prince.var.plot: no visible global function definition for 'plot'
prince.var.plot: no visible global function definition for 'points'
prince.var.plot: no visible global function definition for 'legend'
quickadjust.ref: no visible binding for global variable 'median'
quickadjust.ref: no visible global function definition for 'median'
quickadjust.zero: no visible binding for global variable 'median'
Undefined global functions or variables:
  as.dendrogram axis chisq.test colorpanel cor cor.test cutree density
  dnorm fisher.test hcluster heat.colors heatmap.2 impute.knn layout
  legend lines lm median na.omit p.adjust palette par pf plot points
  prcomp qqline qqnorm qqplot rect rgamma rlm t.test title var
  wilcox.test
Consider adding
  importFrom("grDevices", "heat.colors", "palette")
  importFrom("graphics", "axis", "layout", "legend", "lines", "par",
             "plot", "points", "rect", "title")
  importFrom("stats", "as.dendrogram", "chisq.test", "cor", "cor.test",
             "cutree", "density", "dnorm", "fisher.test", "lm", "median",
             "na.omit", "p.adjust", "pf", "prcomp", "qqline", "qqnorm",
             "qqplot", "rgamma", "t.test", "var", "wilcox.test")
to your NAMESPACE file.