brew doctor

brew_doctor.txt

Warning: You have leftover files from an older version of Xcode.
You should delete them using:
  /Developer/Library/uninstall-developer-folder

Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:

    autoconf

Warning: /usr/bin occurs before /usr/local/bin
This means that system-provided programs will be used instead of those
provided by Homebrew. The following tools exist at both paths:

    2to3
    git
    git-cvsserver
    git-receive-pack
    git-shell
    git-upload-archive
    git-upload-pack
    idle
    pydoc
    python
    python-config
    python2.7
    python2.7-config
    pythonw
    pythonw2.7
    smtpd.py
    sqlite3

Consider setting your PATH so that /usr/local/bin
occurs before /usr/bin. Here is a one-liner:
    echo export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

Warning: Some keg-only formula are linked into the Cellar.
Linking a keg-only formula, such as gettext, into the cellar with
`brew link <formula>` will cause other formulae to detect them during
the `./configure` step. This may cause problems when compiling those
other formulae.

Binaries provided by keg-only formulae may override system binaries
with other strange results.

You may wish to `brew unlink` these brews:

    readline

https://gist.github.com/katorie/8316677 のメッセージにも出ているリンク先の、

https://github.com/Homebrew/homebrew/wiki/troubleshooting にある
"1) Check for Common Issues"も確認してみてください。

お手元のMacの環境によるものなのか、そうでないのかを切り分けるエスパー力は低いので、
これぐらいの通りいっぺんのことしか書けませんが…。