NB: .First.lib is obsolete and will not be used in R >= 3.0.0

BayesCptCI: no visible global function definition for ‘qbeta’
BayesCptCI: no visible global function definition for ‘quantile’
ScanCBSPlot: no visible global function definition for ‘lowess’
ScanCBSPlot: no visible global function definition for ‘pdf’
ScanCBSPlot: no visible global function definition for ‘par’
ScanCBSPlot: no visible global function definition for ‘plot’
ScanCBSPlot: no visible global function definition for ‘lines’
ScanCBSPlot: no visible global function definition for ‘abline’
ScanCBSPlot: no visible global function definition for ‘matplot’
ScanCBSPlot: no visible global function definition for ‘points’
ScanCBSPlot: no visible global function definition for ‘legend’
ScanCBSPlot: no visible global function definition for ‘dev.off’
ScanCBSPlot: no visible global function definition for ‘axis’
ScanCBSSimPlot: no visible global function definition for ‘lowess’
ScanCBSSimPlot: no visible global function definition for ‘pdf’
ScanCBSSimPlot: no visible global function definition for ‘par’
ScanCBSSimPlot: no visible global function definition for ‘plot’
ScanCBSSimPlot: no visible global function definition for ‘lines’
ScanCBSSimPlot: no visible global function definition for ‘abline’
ScanCBSSimPlot: no visible global function definition for ‘matplot’
ScanCBSSimPlot: no visible global function definition for ‘points’
ScanCBSSimPlot: no visible global function definition for ‘legend’
ScanCBSSimPlot: no visible global function definition for ‘dev.off’
ScanCBSSimPlot: no visible global function definition for ‘axis’
ScanIterateGrid: no visible binding for global variable ‘grid’
SegSeqResProcess: no visible global function definition for
  ‘read.delim’
getCountsInWindow: no visible global function definition for ‘tail’
getCountsInWindow: no visible global function definition for ‘hist’
hppSimulate: no visible global function definition for ‘rpois’
hppSimulate: no visible global function definition for ‘runif’
nhppRateEstimate: no visible global function definition for ‘lowess’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘read.delim’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘pdf’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘par’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘plot’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘matplot’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘legend’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘dev.off’
nhppSimConstWindowAnalysis: no visible global function definition for
  ‘abline’
nhppSimConstWindowGen: no visible global function definition for
  ‘write.table’
nhppSimulate: no visible global function definition for ‘runif’
nhppSpike: no visible global function definition for ‘rnbinom’
nhppSpike: no visible global function definition for ‘runif’
nhppSpikeConstWindow: no visible global function definition for ‘runif’
readListInputFile: no visible global function definition for
  ‘read.table’
readSeqChiang: no visible global function definition for ‘read.table’
readSeqELANDPaired: no visible global function definition for
  ‘read.table’
relCNComp: no visible global function definition for ‘binom.test’
Undefined global functions or variables:
  abline axis binom.test dev.off grid hist legend lines lowess matplot
  par pdf plot points qbeta quantile read.delim read.table rnbinom
  rpois runif tail write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "grid", "hist", "legend",
             "lines", "matplot", "par", "plot", "points")
  importFrom("stats", "binom.test", "lowess", "qbeta", "quantile",
             "rnbinom", "rpois", "runif")
  importFrom("utils", "read.delim", "read.table", "tail", "write.table")
to your NAMESPACE file.