Repairing mysterious Python config scripts outside of the system

Question

I got this notice while doing a brew doctor today:

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:

/Library/Frameworks/Python.framework/Versions/3.3/bin/python3-config
/Library/Frameworks/Python.framework/Versions/3.3/bin/python3.3-config
/Library/Frameworks/Python.framework/Versions/3.3/bin/python3.3m-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2-config
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config

I'm on Mac OSX Mountain Lion, and have both Python & Python 3 installed via Homebrew. I think my broken setup has to do with this post, which I was following in an attempt to get my MacVim working properly.

Any ideas? I believe it could be a problem with symbolic links, and I'm pretty clueless on how to troubleshoot those.

Answer 1

Looks like you installed Python 2.7 and 3.3 via the python.org installer or something similar and set the path to include that listed directory. Try to clean your PATH variable from /Library/Frameworks/Python.framework/Versions/3.3/bin and /Library/Frameworks/Python.framework/Versions/2.7/bin (probably set in ~/.bash_profile.)

Answer 2

I had the same problem with both EPD and Anaconda Python. Since I find Homebrew Python unacceptable for numerical analysis I had to dump the Homebrew Package Manager because of little or no support. Please see the post that I made on Sep 25, 2013.

os x mountain lion with homebrew and EPD 7.3-2 (64-bit) not playing nice

Last login: Tue Sep 24 05:28:30 on ttys004 
~ ❯❯❯ echo $PATH 
/Users/mlb/.rbenv/shims:/usr/local/bin:/usr/local/sbin:
/Library/Frameworks/EPD64.framework/Versions/Current/bin:
/usr/bin:/bin:/usr/sbin:/sbin 

~ ❯❯❯ which python 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/python 

~ ❯❯❯ python --version 
Python 2.7.3 -- EPD 7.3-2 (64-bit) 

~ ❯❯❯ brew doctor 
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:

/Library/Frameworks/EPD64.framework/Versions/Current/bin/gdal-config 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/python-config 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/python2-config 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/python2.7-config 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/xml2-config 
/Library/Frameworks/EPD64.framework/Versions/Current/bin/xslt-config

Warning: Enthought Python was found in your PATH. 
This can cause build problems, as this software installs its own 
copies of iconv and libxml2 into directories that are picked up by 
other build systems.


.zprofile
---------
# Setting PATH for epd-7.3-2-macosx-x86_64
export EPDPATH="/Library/Frameworks/EPD64.framework/Versions/Current"
export PATH="$EPDPATH/bin:${PATH}"
export PYTHONPATH="$EPDPATH/lib/python2.7/site-packages"