Homebrew doctor warnings requesting library deletions
I got the same warnings, and worked it around with the following:

So first back up these files:


mv /usr/local/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib.bak
...


Then install tcl/tk with Homebrew:


brew tap homebrew/dupes
brew install tcl-tk --with-tk


Then link the files, so that R can find the tcl/tk installed by Homebrew:


ln -s /usr/local/Cellar/tcl-tk/8.6.1/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib
ln -s /usr/local/Cellar/tcl-tk/8.6.1/lib/libtk8.6.dylib /usr/local/lib/libtk8.6.dylib


Please double check that the linked location is where tcl-tk is installed.

Now both Homebrew and R are happy.

More details can be found on my blog. Hope this helps.