$ brew doctor

Error: "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:

    /usr/local/MacGPG2/bin/gpg-error-config
    /usr/local/MacGPG2/bin/ksba-config
    /usr/local/MacGPG2/bin/libassuan-config
    /usr/local/MacGPG2/bin/libgcrypt-config
    /usr/local/MacGPG2/bin/libusb-config
    /usr/local/MacGPG2/bin/pth-config
Error: You may have installed MacGPG2 via the package installer.
Several other checks in this script will turn up problems, such as stray
dylibs in /usr/local and permissions issues with share and man in /usr/local/.