Found the following significant warnings:

  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotWGassociation 8.770  1.633   7.857
interactionPval   6.718  0.104   7.501
permTest          5.412  0.876   6.266
Examples with CPU time > 2.5 times elapsed time
             user system elapsed  ratio
plotMissing 3.641  0.873   0.375 12.037
resHapMap   0.950  0.279   0.298  4.124