est.s0: no visible global function definition for ‘quantile’
est.s0: no visible global function definition for ‘mad’
est.s0: no visible global function definition for ‘var’
foldchange.seq.twoclass.paired: no visible global function definition
  for ‘rowMedians’
foldchange.seq.twoclass.unpaired: no visible global function definition
  for ‘rowMedians’
localfdr: no visible global function definition for ‘median’
localfdr: no visible global function definition for ‘smooth.spline’
paired.ttest.func: no visible global function definition for ‘var’
patterndiscovery.func: no visible global function definition for
  ‘quantile’
patterndiscovery.func: no visible global function definition for
  ‘median’
permute.rows: no visible global function definition for ‘runif’
predictlocalfdr: no visible global function definition for ‘predict’
resample: no visible global function definition for ‘rpois’
resample: no visible global function definition for ‘runif’
samr: no visible global function definition for ‘impute.knn’
samr: no visible binding for global variable ‘median’
samr: no visible global function definition for ‘quantile’
samr.assess.samplesize: no visible global function definition for
  ‘quantile’
samr.assess.samplesize: no visible global function definition for
  ‘median’
samr.assess.samplesize.plot: no visible global function definition for
  ‘par’
samr.assess.samplesize.plot: no visible global function definition for
  ‘plot’
samr.assess.samplesize.plot: no visible global function definition for
  ‘lines’
samr.assess.samplesize.plot: no visible global function definition for
  ‘mtext’
samr.assess.samplesize.plot: no visible global function definition for
  ‘abline’
samr.assess.samplesize.plot: no visible global function definition for
  ‘title’
samr.assess.samplesize.plot: no visible global function definition for
  ‘dev.off’
samr.compute.delta.table.array: no visible binding for global variable
  ‘var’
samr.compute.delta.table.array: no visible binding for global variable
  ‘median’
samr.compute.delta.table.array: no visible binding for global variable
  ‘quantile’
samr.compute.delta.table.seq: no visible binding for global variable
  ‘median’
samr.compute.delta.table.seq: no visible binding for global variable
  ‘quantile’
samr.estimate.depth: no visible global function definition for
  ‘quantile’
samr.missrate: no visible global function definition for ‘quantile’
samr.plot: no visible global function definition for ‘plot’
samr.plot: no visible global function definition for ‘points’
samr.plot: no visible global function definition for ‘abline’
samr.tail.strength: no visible global function definition for ‘var’
samr.xl.compute.plot.xy: no visible global function definition for
  ‘points’
samr.xl.compute.plot.xy: no visible global function definition for
  ‘abline’
samr.xl.impute.data: no visible global function definition for
  ‘impute.knn’
samr.xl.impute.data: no visible binding for global variable
  ‘samr.xl.var.knn.neighbors’
Undefined global functions or variables:
  abline dev.off impute.knn lines mad median mtext par plot points
  predict quantile rowMedians rpois runif samr.xl.var.knn.neighbors
  smooth.spline title var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "lines", "mtext", "par", "plot",
             "points", "title")
  importFrom("stats", "mad", "median", "predict", "quantile", "rpois",
             "runif", "smooth.spline", "var")
to your NAMESPACE file.