After installing Anaconda, I get constant “KeyError: 'PYTHONPATH'” messages

Question

After installing Anaconda for Python 3.4 on my Mac I get constant messages saying:

Error in sitecustomize; set PYTHONVERBOSE for traceback: 
KeyError: \'PYTHONP         


        

Answer 1

Going to necro-answer here with more detail for folks that might hit this page after searching for the error shown…

If your Mac has messages referencing /usr/local/, I'm going to go ahead and assume you've used homebrew to install something. In this case, Python.

When Anaconda's Python distribution is installed, one of the things it'll check is if there are any site customizations applied to your existing Python installation. If you installed any version of Python using Homebrew, you likely have such a site customization.

1. Running conda info -a | grep dirs will get your Anaconda install info and look for a line with dirs included. Only one should match, if it exists:

   user site dirs: ~/.local/lib/python3.5

2. If it does exist, cd to that directory (whatever it is), and get a directory listing (ls). You'll then (likely) find a file called homebrew.pth.

3. Remove that file, and the error goes away.

Reason: Anaconda is referencing that homebrew.pth file, which then goes on to include the sitecustomize.py from your earlier homebrew-installed version of Python.

Answer 2

If your PYTHONPATH environment variable is set, unset it. You can check with echo $PYTHONPATH. If it is set it is probably coming from something in ~/.profile or ~/.bash_profile.

The issue is the file /usr/local/lib/python2.7/site-packages/sitecustomize.py. You may want to check what that file is and where it comes from, but removing it should fix the problem.