Making Homebrew and R.app live together happily I just upgraded to Mavericks (10.9.2) and after years of using MacPorts I decided to use Homebrew.  I successfully installed Homebrew, but brew doctor shows:

brew doctor
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libtcl8.6.dylib
    /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .pc files:
    /usr/local/lib/pkgconfig/tcl.pc
    /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:
   /usr/local/lib/libtclstub8.6.a
   /usr/local/lib/libtkstub8.6.a


All this stuff comes from R.app, from the OSX specific website.  Now, I prefer to use the standard R.app rather than the Homebrew version (for a number of personal reasons).  Can I safely ignore these warnings or there will be a problem?
You can install R with hombrew so you avoid conflict.

brew tap homebrew/science
brew install gfortran r