XHMM_plots: no visible global function definition for 'pdf'
XHMM_plots: no visible global function definition for 'hist'
XHMM_plots: no visible global function definition for 'dev.off'
XHMM_plots: no visible global function definition for 'cor'
XHMM_plots: no visible global function definition for 'rainbow'
XHMM_plots: no visible global function definition for 'matplot'
XHMM_plots: no visible global function definition for 'points'
XHMM_plots: no visible global function definition for 'legend'
XHMM_plots: no visible global function definition for 'par'
XHMM_plots: no visible binding for global variable 'sd'
col2rgbString: no visible global function definition for 'col2rgb'
col2rgbString : <anonymous>: no visible global function definition for
  'rgb'
loadTargetsToGenes: no visible global function definition for
  'read.table'
loadXCNVcalls: no visible global function definition for 'read.table'
plotAllChromosomeValues: no visible global function definition for
  'png'
plotAllChromosomeValues: no visible global function definition for
  'axis'
plotAllChromosomeValues: no visible global function definition for
  'dev.off'
plot_XHMM_targets_helper: no visible global function definition for
  'graphics.off'
plot_XHMM_targets_helper: no visible global function definition for
  'heat.colors'
plot_XHMM_targets_helper: no visible global function definition for
  'pdf'
plot_XHMM_targets_helper: no visible global function definition for
  'png'
plot_XHMM_targets_helper: no visible global function definition for
  'par'
plot_XHMM_targets_helper: no visible global function definition for
  't.test'
plot_XHMM_targets_helper: no visible global function definition for
  'points'
plot_XHMM_targets_helper: no visible global function definition for
  'grconvertY'
plot_XHMM_targets_helper: no visible global function definition for
  'segments'
plot_XHMM_targets_helper: no visible global function definition for
  'text'
plot_XHMM_targets_helper: no visible global function definition for
  'legend'
plot_XHMM_targets_helper: no visible global function definition for
  'dev.off'
plot_XHMM_targets_helper: no visible global function definition for
  'layout'
plot_XHMM_targets_helper: no visible global function definition for
  'layout.show'
plot_XHMM_targets_helper: no visible global function definition for
  'plot.new'
readPedigreeFile: no visible global function definition for
  'read.table'
readPhenotypesFile: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  axis col2rgb cor dev.off graphics.off grconvertY heat.colors hist
  layout layout.show legend matplot par pdf plot.new png points rainbow
  read.table rgb sd segments t.test text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "graphics.off",
             "heat.colors", "pdf", "png", "rainbow", "rgb")
  importFrom("graphics", "axis", "grconvertY", "hist", "layout",
             "layout.show", "legend", "matplot", "par", "plot.new",
             "points", "segments", "text")
  importFrom("stats", "cor", "sd", "t.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.