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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?

  • Yes Homebrew might use R's libraries rather then the ones brew knows work this might be OK but Homebrew does not know - This use od /usr/local is one reason I use macports rather than Homebrew – user151019 Feb 27 '14 at 21:42
  • In general, having a warning like that is because mixing libraries can cause really hard to debug problems when linking programs. What is your definition of safe? Do you rely on either R or other homebrew tools to work or are they something you care to tend to and don't mind tracking down why odd things happen or unexcited compile errors crop up? – bmike Feb 27 '14 at 22:59
  • @bmike for me safe means 'no random stuff happening'. I plan to use Homebrew to get stuff like gcc, gsl python 3 and ffmpeg. Aside from python 3 I doubt any other program I might install through Homebrew will use TCL or TK libraries (and python 3 might also not care). – user1256923 Feb 28 '14 at 10:42
  • Roll the dice, take your chances. With tk and tcl, you have very common libraries that likely will be used at one point by another package you choose to install. Ignoring the warning means he tool may not catch a collision in versioning for you. – bmike Feb 28 '14 at 12:02
  • This use of/usr/local is why macports and fink use another directory - from experience using /usr/local might work then on the odd occasion it will fail and is difficult to debug but it will fail – user151019 Apr 9 '14 at 12:38
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You can install R with hombrew so you avoid conflict.

brew tap homebrew/science
brew install gfortran r
  • Many colleagues do that but I am old and set in my old ways... – user1256923 Oct 21 '14 at 13:47

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