assignParalogues: no visible global function definition for 'quantile'
assignToAlleleSet: no visible global function definition for 'as'
assignToAlleleSet: no visible global function definition for 'new'
assignToAlleleSet: no visible global function definition for
  'validObject'
callGenotypes: no visible global function definition for 'median'
callGenotypes: no visible global function definition for 'quantile'
callGenotypes: no visible binding for global variable 'sd'
callGenotypes: no visible binding for global variable 'median'
callGenotypes: no visible global function definition for 'pf'
callGenotypes: no visible global function definition for 'plot.new'
callGenotypes: no visible global function definition for 'plot.window'
callGenotypes: no visible global function definition for 'axis'
callGenotypes: no visible global function definition for 'points'
callGenotypes: no visible global function definition for 'new'
callGenotypes: no visible global function definition for 'validObject'
callGenotypes.interactive: no visible global function definition for
  'new'
callGenotypes.interactive: no visible global function definition for
  'median'
callGenotypes.interactive: no visible global function definition for
  'quantile'
callGenotypes.interactive: no visible binding for global variable
  'median'
callGenotypes.interactive: no visible binding for global variable 'sd'
callGenotypes.interactive: no visible global function definition for
  'pf'
callGenotypes.interactive: no visible global function definition for
  'validObject'
callGenotypes.verboseTest: no visible global function definition for
  'median'
callGenotypes.verboseTest: no visible global function definition for
  'quantile'
callGenotypes.verboseTest: no visible global function definition for
  'par'
callGenotypes.verboseTest: no visible binding for global variable 'sd'
callGenotypes.verboseTest: no visible binding for global variable
  'median'
callGenotypes.verboseTest: no visible global function definition for
  'pf'
callGenotypes.verboseTest: no visible global function definition for
  'plot.new'
callGenotypes.verboseTest: no visible global function definition for
  'plot.window'
callGenotypes.verboseTest: no visible global function definition for
  'axis'
callGenotypes.verboseTest: no visible global function definition for
  'title'
callGenotypes.verboseTest: no visible global function definition for
  'points'
countFailedSNP: no visible global function definition for 'new'
countFailedSNP: no visible global function definition for 'validObject'
createAlleleSet: no visible global function definition for 'new'
createAlleleSet: no visible global function definition for
  'validObject'
createAlleleSetFromFiles: no visible global function definition for
  'read.table'
createAlleleSetFromFiles: no visible global function definition for
  'new'
createAlleleSetFromFiles: no visible global function definition for
  'validObject'
createMultiSetFromFiles: no visible global function definition for
  'read.table'
createMultiSetFromFiles: no visible global function definition for
  'new'
createMultiSetFromFiles: no visible global function definition for
  'validObject'
findClusters: no visible global function definition for 'hist'
findClusters: no visible global function definition for 'embed'
findPolyploidClusters: no visible global function definition for 'hist'
findPolyploidClusters: no visible global function definition for
  'median'
findPolyploidClusters: no visible global function definition for
  'kmeans'
findPolyploidClusters: no visible binding for global variable 'median'
findSeTheta: no visible global function definition for 'integrate'
getNoiseDistributions: no visible global function definition for 'par'
getNoiseDistributions: no visible binding for global variable 'median'
getNoiseDistributions: no visible binding for global variable 'mad'
getNoiseDistributions: no visible global function definition for 'hist'
getNoiseDistributions: no visible global function definition for
  'lines'
getNoiseDistributions: no visible global function definition for
  'dnorm'
normalizeIllumina: no visible global function definition for 'quantile'
normalizeIllumina: no visible global function definition for 'coef'
normalizeIllumina: no visible global function definition for 'lm'
normalizeIllumina: no visible global function definition for 'points'
normalizeIllumina: no visible global function definition for 'par'
normalizeIllumina: no visible global function definition for 'plot.new'
normalizeIllumina: no visible global function definition for
  'plot.window'
normalizeIllumina: no visible global function definition for 'axis'
normalizeIllumina: no visible global function definition for 'lines'
normalizeShearedChannels: no visible binding for global variable
  'median'
normalizeShearedChannels: no visible binding for global variable
  'quantile'
plotCountsChrom: no visible global function definition for 'par'
plotCountsChrom: no visible global function definition for 'plot.new'
plotCountsChrom: no visible global function definition for
  'plot.window'
plotCountsChrom: no visible global function definition for 'axis'
plotCountsChrom: no visible global function definition for 'lines'
plotCountsChrom: no visible global function definition for 'title'
plotEstimatedNoise: no visible global function definition for 'par'
plotEstimatedNoise: no visible global function definition for 'lines'
plotEstimatedNoise: no visible global function definition for 'points'
plotGenotypes: no visible global function definition for 'par'
plotGenotypes: no visible global function definition for 'palette'
plotGenotypes: no visible global function definition for 'plot.new'
plotGenotypes: no visible global function definition for 'plot.window'
plotGenotypes: no visible global function definition for 'axis'
plotGenotypes: no visible global function definition for 'points'
plotGenotypes: no visible global function definition for 'title'
plotGenotypes: no visible global function definition for 'lines'
plotPreprocessing: no visible global function definition for 'par'
preprocessBeadSet: no visible global function definition for 'new'
preprocessBeadSet: no visible global function definition for
  'validObject'
readBeadSummaryOutput: no visible global function definition for 'new'
scatterArrays: no visible global function definition for 'par'
scatterArrays: no visible global function definition for
  'smoothScatter'
scatterArrays: no visible global function definition for 'lines'
shearRawSignal: no visible global function definition for 'par'
shearRawSignal: no visible global function definition for 'validObject'
testHardyWeinberg: no visible global function definition for 'pchisq'
translateThetaCombined: no visible global function definition for
  'validObject'
translateThetaFromFiles: no visible global function definition for
  'read.table'
translateThetaFromFiles: no visible global function definition for
  'new'
translateThetaFromFiles: no visible global function definition for 'as'
translateThetaFromFiles: no visible global function definition for
  'write.table'
validateCallsPedigree: no visible global function definition for 'new'
validateCallsPedigree: no visible global function definition for
  'validObject'
writeAlleleSet: no visible global function definition for 'write.table'
initialize,AlleleSetIllumina: no visible global function definition for
  'new'
initialize,AlleleSetIllumina: no visible global function definition for
  'callNextMethod'
initialize,BeadSetIllumina: no visible global function definition for
  'new'
initialize,BeadSetIllumina: no visible global function definition for
  'callNextMethod'
Undefined global functions or variables:
  as axis callNextMethod coef dnorm embed hist integrate kmeans lines
  lm mad median new palette par pchisq pf plot.new plot.window points
  quantile read.table sd smoothScatter title validObject write.table
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot.new",
             "plot.window", "points", "smoothScatter", "title")
  importFrom("methods", "as", "callNextMethod", "new", "validObject")
  importFrom("stats", "coef", "dnorm", "embed", "integrate", "kmeans",
             "lm", "mad", "median", "pchisq", "pf", "quantile", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').