I'm currently using pyenv and pyenv-virtualenv, which i've installed via Homebrew. I've added if which pyenv > /dev/null; then eval "$(pyenv init -)"; fi to enable shims and autocompletion and if which pyenv-virtualenv-init > /dev/null; then eval "$(pyenv virtualenv- init -)"; fi in order to enable auto-activation to my .bash_profile.

Suddendly, running brew doctor, the following message shows up:

"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:


What should i do to fix the problem?

  • report as a bug to Homebrew :) The pyenv port should have dealt with putting the files in the correct place and telling the rest of the ports about them as in effect they are Homebre supplied scripts. I suspect they will cause no issue as I would count anything else except peen looks in pyenv/shims
    – mmmmmm
    May 13, 2016 at 17:40
  • What's the peen port?
    – g_rmz
    May 13, 2016 at 17:41
  • So, what should i do? Upgrade pyenv via brew upgrade pyenv?
    – g_rmz
    May 13, 2016 at 17:44
  • I left as a comment as I don;t use Homebrew and so can't check the details but just working on running a port should not break the port system
    – mmmmmm
    May 13, 2016 at 17:45


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