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/b…

Accepted Answer

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:

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

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.

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.

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`)

Existing config scripts when brew doctor is prompted

Solution

Problem