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 ‘plot’
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 ‘plot’
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 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",
             "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').