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

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.

Update:

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.

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