Existing config scripts when brew doctor is prompted

Question

I'm completely new to Homebrew and Anaconda installation and I hope someone could help me out with the warning after executing brew doctor. I'm running on Snow Leopard 10.6.8. The warning is as follows:

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

    /Users/user.name/anaconda/bin/freetype-config
    /Users/user.name/anaconda/bin/libpng-config
    /Users/user.name/anaconda/bin/libpng15-config
    /Users/user.name/anaconda/bin/llvm-config
    /Users/user.name/anaconda/bin/python-config
    /Users/user.name/anaconda/bin/python2-config
    /Users/user.name/anaconda/bin/python2.7-config
    /Users/user.name/anaconda/bin/xml2-config
    /Users/user.name/anaconda/bin/xslt-config

I executed brew --config and the following shows the configuration (hope it helps w/ the issue):

HOMEBREW_VERSION: 0.9.4
ORIGIN: (none)
HEAD: (none)
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: dual-core 64-bit penryn
OS X: 10.6.8-i386
Xcode: 3.2.6
GCC-4.0: build 5494
GCC-4.2: build 5666
LLVM-GCC: build 2335
Clang: 1.7 build 77
X11: 2.7.4 => /opt/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /Users/user.name/anaconda/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby

Really appreciate your help. Thank you.

Answer 1

tl;dr: you can't really fix this but you can probably ignore it

Those scripts ending in -config provide information for other packages that want to link to them during installation. Let's take libpng for example. If brew (or anything really) compiles a package that depends on libpng it might execute libpng-config to find out some details about the library.

The problem is that brew brings its own version of libpng so if both are installed brew might pick up the wrong libpng-config when installing additional software.

You can do one of four things now:

1. Ignore the warning if you're confident that the stuff you install with homebrew will not conflict with the stuff that comes with anaconda.

2. Edit your ~/.bash_profile and remove anaconda from the PATH. If you do this you will have to specify the full path every time you want to run anaconda python.

3. Move those anaconda config files aside (out of your PATH, e.g. into a config subdirectory). This will likely prevent additional software from linking to anaconda components but should be ok if you intend to keep anaconda isolated.

4. Remove anaconda completely (just delete the folder) and install brew's version of python. This will also give you pip which should make it easy to reinstall most of the other packages that come with anaconda.

   i.e.

   brew install python
   

   Then to install e.g. numpy, simply:

   pip install numpy
   

   (To make brew's python your default add export PATH="/usr/local/bin:$PATH" to your ~/.bash_profile)