Homebrew warnings about unbrewed dylibs installed by R
Aug 25, 2014If you install R on Mac OS X from the official binaries, it will install tcl/tk to /usr/local/lib. The problem is, if you use homebrew to manage other packages, when running brew doctor, it complains:
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
Although it does not break anything for now, it may if other homebrew packages depend on tcl/tk.
Simply deleting these files will cause R to complain:
> library("Rcmdr")
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
...
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.
Further note:
The above solution does not completely remove the tcl/tk installed by R, so it may cause complications (please let me know if this is indeed the case).
R installed through the official binaries can be removed as is instructed here. However, the tcl/tk files are not removed.
Running pkgutil --files org.r-project.x86_64.tcltk.x11 will list all files installed by the specified package. Run man pkgutil for details.
These files can be manually removed, but it is advised against doing so.
Lesson learned:
Do not install things from .pkg files if possible. Use homebrew.
To install R with Homebrew:
brew tap homebrew/science
brew install r