Homebrew brew doctor warning about /Library/Frameworks/Python.framework, even with brew's Python installed

When I ran Homebrew's brew doctor (Mac OS X 10.9.2), I get the following warning message:

Warning: Python is installed at /Library/Frameworks/Python.framework

Homebrew only supports building against the System-provided Python or a brewed Python. In particular, Pythons installed to /Library can interfere with other software installs.

Therefore, I ran brew install and followed the steps provided in the installation's caveats output to install Homebrew's version of Python. Running which python confirms that Homebrew's version of it is indeed at the top of my PATH. Output is /usr/local/bin/python.

Despite all this, when I rerun brew doctor, I am still getting the same warning message. How do I suppress this warning? Do I need to delete the /Library/Frameworks/Python.framework directory from my computer? Am I just supposed to ignore it? Is there a different application on my computer that may be causing this warning to emit?

Note that I don't have any applications in particular that are running into errors due to this warning from brew doctor. Also note that this warning message didn't always print out when I ran brew doctor, it was something that started to appear recently. Also, I am using Python 2.7 on my computer, trying to stay away from Python 3.

I had the same problem. When I upgraded python3 through Homebrew, I started getting this:

    -bash: python3: command not found

I had the same conflict with Python somehow being installed in /Library/Framework/Python.framework. I just did a brew link overwrite and everything is working fine now. There is some info about what to do with the Python version in the /Library/Framework/Python.framework here.

I guess you could try deleting that version as the link suggests, just make sure that version isn't being used. When I got into the Python.framework directory I was seeing some EPD version of Python, which I think is Enthought. You could delete it, but I if it isn't causing you any problems besides the unsightly Homebrew warning message, then I think you should just ignore it for now.


I did delete the Python.framework directory which, through some poking around inside that directory, I started seeing a few old versions of Python that I didn't install with Homebrew. One was from Enthought, and another was a distribution of Python3.3. I think some of these installs in the Framework directory are user installs. I installed R on my system, and there is also an R.framework directory, so I think most of these are user installs. After I deleted the directory, I just had to call brew prune to remove the old symlinks. I checked both brew versions of python 2.7.6 and 3.3.4, and they seem to be in good working order with all of my installed packages. I guess I leave the decision to remove that directory, or python version, to your discretion.

From: stackoverflow.com/q/22255579