title: R package with dependency on shiny gives RJSONIO warning
body: <p>My package CTDesignExplorer uses shiny (and shinyIncubator). When I include 
  <br>Depends: shiny<br>
  in the DESCRIPTION file, there are warnings upon loading the package in RStudio:
  <br></p>
  
  <blockquote>
    <p>Warning in .simpleDuplicateClass(def, prev) :
     the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from >package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class</p>
  </blockquote>
  
  <p>In command line R, loading shiny gets multiples warnings; in addition to "AsIs",  with "connect", "file", "pipe", and "textConnection".
  <br>
  At <a href="https://github.com/joey711/phyloseq/issues/128" rel="nofollow">https://github.com/joey711/phyloseq/issues/128</a>, the issue is supposedly solved 6 months ago, but here it is, even after update.packages("RJSONIO"). Version is 1.0-3, from 2013-03-27.<br>
  At <a href="https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004177.html" rel="nofollow">https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004177.html</a>, the suggestion was to remove RJSONIO from NAMESPACE. But it's not there (or in DESCRIPTION) in my package. In shiny, it's under Imports in DESCRIPTION.</p>
  
  <p>This probably has no impact on code execution, but it's hard to be sure. Anyway, sure is ugly for my users to see.  </p>