merge collab branch

* collab:
  update vignettes/Makefile
  update .gitignore
  update table in CopyNumberViewiew
  bump dependency on oligoClasses version
  Update alias for "[" method for PredictionRegion objects
  Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch.  The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358
@<- has been moved from methods to base, so it no longer needs to
be imported in package NAMESPACEs.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72298 bc3139a8-67e5-0310-9ffc-ced21a209358
run texi2dvi with R CMD to avoid windows build error

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72377 bc3139a8-67e5-0310-9ffc-ced21a209358
merge local changes with dan's changes on bioc

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72708 bc3139a8-67e5-0310-9ffc-ced21a209358