I'm getting a little tired of this one popping up:

In x %in% other :
   Starting with BioC 2.12, the behavior of %in% on GenomicRanges objects
  has changed to use *equality* instead of *overlap* for comparing
  elements between GenomicRanges objects 'x' and 'table'. Now 'x[i]' and
  'table[j]' are considered to match when they are equal (i.e. 'x[i] ==
  table[j]'), instead of when they overlap. This new behavior is consistent
  with base::`%in%`(). If you need the old behavior, please use:

    query %over% subject

Now that even release is Bioc 2.13, can we remove it? And there might be
others.

Thanks,
Michael

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