BinBam: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
BinBam: no visible global function definition for 'seqlengths'
BinBam: no visible global function definition for 'assays'
BinBam: no visible global function definition for 'subsetByOverlaps'
ReadBed: no visible global function definition for 'read.table'
aggregateCounts: no visible global function definition for 'aggregate'
callUnknowns: no visible global function definition for 'dnorm'
callUnknowns: no visible global function definition for 'rnorm'
createReferenceSetFromCounts: no visible binding for global variable
  'sd'
createReferenceSetFromCounts: no visible global function definition for
  'cor'
createReferenceSetFromCounts: no visible global function definition for
  'write.csv'
createReferenceSetFromCounts: no visible global function definition for
  'write.table'
doPCA: no visible global function definition for 'prcomp'
find.excl.bins: no visible binding for global variable 'sd'
find.excl.bins: no visible global function definition for 'sd'
find.excl.bins: no visible global function definition for 'median'
findBaseline: no visible binding for global variable 'sd'
findBaseline: no visible global function definition for 'sd'
findBaseline: no visible global function definition for 'median'
findBaseline: no visible global function definition for 'mad'
gcCorrectOneSample: no visible global function definition for 'sd'
gcCorrectOneSample: no visible global function definition for 'pdf'
gcCorrectOneSample: no visible global function definition for 'boxplot'
gcCorrectOneSample: no visible global function definition for 'dev.off'
gcCorrectOneSample: no visible global function definition for
  'aggregate'
gcCorrectOneSampleLoess: no visible global function definition for
  'boxplot'
gcCorrectOneSampleLoess: no visible global function definition for
  'lowess'
makeBinnedCountsFile: no visible global function definition for
  'write.table'
makeGCContentData: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
makeGCContentData: no visible global function definition for
  'seqlengths'
makeGCContentPerPos: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
plotTestSample: no visible global function definition for 'par'
plotTestSample: no visible global function definition for 'plot'
plotTestSample: no visible global function definition for 'points'
plotTestSample: no visible global function definition for 'axis'
plotTestSample: no visible global function definition for 'title'
plotTestSample: no visible global function definition for 'abline'
testUnknowns: no visible global function definition for 'write.csv'
writeCleanedCountsFile: no visible global function definition for
  'write.table'
writeResultsToFile: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19 abline aggregate assays axis boxplot cor
  dev.off dnorm lowess mad median par pdf plot points prcomp read.table
  rnorm sd seqlengths subsetByOverlaps title write.csv write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "boxplot", "par", "plot",
             "points", "title")
  importFrom("stats", "aggregate", "cor", "dnorm", "lowess", "mad",
             "median", "prcomp", "rnorm", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.