Download: no visible global function definition for 'download.file'
GMT2List: no visible global function definition for '%dopar%'
GMT2List: no visible global function definition for 'foreach'
GMT2List: no visible global function definition for 'iter'
GMT2List: no visible binding for global variable 'x'
GetEWPval: no visible global function definition for 'pchisq'
GetPVal : t.test2: no visible global function definition for 'pt'
GetPVal : <anonymous>: no visible global function definition for
  't.test'
GetPVal : <anonymous>: no visible global function definition for 'lm'
GetPVal : <anonymous>: no visible global function definition for
  'coxph'
MetaQC: no visible global function definition for 'proto'
MetaQC: no visible global function definition for 'registerDoMC'
MetaQC: no visible global function definition for 'registerDoSNOW'
MetaQC: no visible global function definition for 'makeCluster'
MetaQC : .Initialize: no visible global function definition for '%do%'
MetaQC : .Initialize: no visible global function definition for
  'foreach'
MetaQC : .Initialize: no visible global function definition for 'iter'
MetaQC : .FilterGenes: no visible global function definition for
  '%dopar%'
MetaQC : .FilterGenes: no visible global function definition for
  'foreach'
MetaQC : .FilterGenes: no visible global function definition for 'iter'
MetaQC : .FilterGenes: no visible binding for global variable 'd'
MetaQC : .ConvertToGeneSetIdx: no visible global function definition
  for '%dopar%'
MetaQC : .ConvertToGeneSetIdx: no visible global function definition
  for 'foreach'
MetaQC : .ConvertToGeneSetIdx: no visible global function definition
  for 'iter'
MetaQC : .ConvertToGeneSetIdx: no visible global function definition
  for '%do%'
MetaQC : .ConvertToGeneSetIdx: no visible global function definition
  for 'na.omit'
MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
  'g'
MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
  'd'
MetaQC : .CalcPval: no visible global function definition for '%do%'
MetaQC : .CalcPval: no visible global function definition for 'foreach'
MetaQC : .CalcPval: no visible binding for global variable 'i'
MetaQC : .CalcPval: no visible global function definition for '%dopar%'
MetaQC : .CalcPval: no visible binding for global variable 'w'
MetaQC : .CalcPval: no visible global function definition for 'as.dist'
MetaQC : .CalcPval: no visible global function definition for 'cor'
MetaQC : .CalcPval: no visible global function definition for 'iter'
MetaQC : .CalcPval: no visible binding for global variable 'j'
MetaQC : .CalcPval : <anonymous>: no visible global function definition
  for 'as.dist'
MetaQC : .CalcPval : <anonymous>: no visible global function definition
  for 'cor'
MetaQC : .CalcPval: no visible binding for global variable 'b'
MetaQC : EQC: no visible global function definition for '%do%'
MetaQC : EQC: no visible global function definition for 'foreach'
MetaQC : EQC: no visible global function definition for '%dopar%'
MetaQC : EQC: no visible global function definition for 'iter'
MetaQC : EQC: no visible global function definition for 'as.dist'
MetaQC : EQC: no visible global function definition for 'cor'
MetaQC : EQC: no visible binding for global variable 'g'
MetaQC : EQC: no visible global function definition for 'na.omit'
MetaQC : EQC: no visible binding for global variable 'w'
MetaQC : AQCg: no visible global function definition for '%dopar%'
MetaQC : AQCg: no visible global function definition for 'foreach'
MetaQC : AQCg: no visible binding for global variable 'i'
MetaQC : AQCg: no visible global function definition for 'p.adjust'
MetaQC : AQCg: no visible global function definition for 'fisher.test'
MetaQC : AQCp: no visible global function definition for '%dopar%'
MetaQC : AQCp: no visible global function definition for 'foreach'
MetaQC : AQCp: no visible binding for global variable 'i'
MetaQC : AQCp: no visible global function definition for 'p.adjust'
MetaQC : AQCp: no visible global function definition for 'fisher.test'
MetaQC : CQCg: no visible global function definition for '%dopar%'
MetaQC : CQCg: no visible global function definition for 'foreach'
MetaQC : CQCg: no visible global function definition for 'iter'
MetaQC : CQCg: no visible binding for global variable 'dat'
MetaQC : CQCg: no visible binding for global variable 'pv'
MetaQC : CQCg: no visible binding for global variable 'i'
MetaQC : CQCg: no visible global function definition for 'cor.test'
MetaQC : CQCp: no visible global function definition for '%dopar%'
MetaQC : CQCp: no visible global function definition for 'foreach'
MetaQC : CQCp: no visible global function definition for 'iter'
MetaQC : CQCp: no visible binding for global variable 'dat'
MetaQC : CQCp: no visible binding for global variable 'pv'
MetaQC : CQCp: no visible global function definition for '%do%'
MetaQC : CQCp: no visible binding for global variable 'ii'
MetaQC : CQCp: no visible binding for global variable 'jj'
MetaQC : CQCp: no visible global function definition for 'na.omit'
MetaQC : CQCp: no visible global function definition for 'ks.test'
MetaQC : CQCp: no visible binding for global variable 'i'
MetaQC : CQCp: no visible global function definition for 'cor.test'
MetaQC : IQC: no visible global function definition for '%dopar%'
MetaQC : IQC: no visible global function definition for 'foreach'
MetaQC : IQC: no visible binding for global variable 'i'
MetaQC : IQC: no visible global function definition for 'wilcox.test'
MetaQC : IQC: no visible global function definition for 'pnorm'
MetaQC : IQC: no visible global function definition for 'qnorm'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  '%dopar%'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'foreach'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'iter'
MetaQC : .CalcDistOfStudies: no visible binding for global variable
  'ii'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  '%do%'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'as.dist'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'cor'
MetaQC : .CalcDistOfStudies: no visible binding for global variable
  'jj'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'na.omit'
MetaQC : .CalcDistOfStudies: no visible global function definition for
  'median'
MetaQC : .CalcScores: no visible global function definition for '%do%'
MetaQC : .CalcScores: no visible global function definition for
  'foreach'
MetaQC : .CalcScores: no visible global function definition for 'iter'
MetaQC : .CalcScores: no visible binding for global variable 'd'
MetaQC : Plot : <anonymous>: no visible global function definition for
  'sd'
MetaQC : Plot: no visible global function definition for 'prcomp'
MetaQC : Plot: no visible global function definition for 'plot'
MetaQC : Plot: no visible global function definition for 'axis'
MetaQC : Plot: no visible global function definition for 'box'
MetaQC : Plot: no visible global function definition for 'abline'
MetaQC : Plot: no visible global function definition for 'arrows'
MetaQC : Plot: no visible global function definition for 'gray'
MetaQC : Plot: no visible global function definition for 'text'
MetaQC : Plot: no visible global function definition for 'points'
MetaQC : GetDistOfStudies: no visible global function definition for
  'as.dist'
requireAll: no visible global function definition for
  'installed.packages'
requireAll: no visible binding for global variable 'biocLite'
requireAll: no visible global function definition for 'biocLite'
Undefined global functions or variables:
  %do% %dopar% abline arrows as.dist axis b biocLite box cor cor.test
  coxph d dat download.file fisher.test foreach g gray i ii
  installed.packages iter j jj ks.test lm makeCluster median na.omit
  p.adjust pchisq plot pnorm points prcomp proto pt pv qnorm
  registerDoMC registerDoSNOW sd t.test text w wilcox.test x
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "arrows", "axis", "box", "plot",
             "points", "text")
  importFrom("stats", "as.dist", "cor", "cor.test", "fisher.test",
             "ks.test", "lm", "median", "na.omit", "p.adjust", "pchisq",
             "pnorm", "prcomp", "pt", "qnorm", "sd", "t.test",
             "wilcox.test")
  importFrom("utils", "download.file", "installed.packages")
to your NAMESPACE file.