コマンドラインでbrew doctorすると警告だらけになっちゃった助けて

なんかbrew doctorしたら警告だらけになったので１つずつ解決していきます

$ brew doctor
    Warning: Broken symlinks were found. Remove them with `brew prune`:
        /usr/local/bin/c++-4.9
        /usr/local/bin/cpp-4.9
        /usr/local/bin/g++-4.9
        /usr/local/bin/gcc-4.9
        /usr/local/bin/gcc-ar-4.9
        /usr/local/bin/gcc-nm-4.9
        /usr/local/bin/gcc-ranlib-4.9
        /usr/local/bin/gcov-4.9
        /usr/local/bin/gfortran
        /usr/local/bin/gfortran-4.9
        /usr/local/bin/github
        /usr/local/bin/x86_64-apple-darwin13.2.0-c++-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-g++-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-gcc-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-gcc-4.9.1
        /usr/local/bin/x86_64-apple-darwin13.2.0-gcc-ar-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-gcc-nm-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-gcc-ranlib-4.9
        /usr/local/bin/x86_64-apple-darwin13.2.0-gfortran-4.9
        /usr/local/lib/gcc/x86_64-apple-darwin13.2.0
        /usr/local/lib/libmpfr.4.dylib
        /usr/local/lib/libmpfr.a
        /usr/local/lib/libmpfr.dylib
        /usr/local/lib/python2.7/site-packages/site-packages
        /usr/local/lib/python3.4/site-packages/site-packages
        /usr/local/share/doc/mpfr
        /usr/local/share/gcc-4.9.1
        /usr/local/share/info/mpfr.info
        /usr/local/share/man/man1/cpp-4.9.1
        /usr/local/share/man/man1/g++-4.9.1
        /usr/local/share/man/man1/gcc-4.9.1
        /usr/local/share/man/man1/gcov-4.9.1
        /usr/local/share/man/man1/gfortran-4.9.1
        /usr/local/share/man/man1/git-lost-found.1
        /usr/local/share/man/man1/git-peek-remote.1
        /usr/local/share/man/man1/git-repo-config.1
        /usr/local/share/man/man1/git-tar-tree.1
        /usr/local/share/man/man7/fsf-funding-4.9.7
        /usr/local/share/man/man7/gfdl-4.9.7
        /usr/local/share/man/man7/gpl-4.9.7
        /usr/local/share/python
        /usr/local/Frameworks/Python.framework/Headers
        /usr/local/Frameworks/Python.framework/Python
        /usr/local/Frameworks/Python.framework/Resources
        /usr/local/Frameworks/Python.framework/Versions/2.7
        /usr/local/Frameworks/Python.framework/Versions/3.4
        /usr/local/Frameworks/Python.framework/Versions/Current

    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:
        mpfr
        node_modules
        python
        python3

    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:

        emacs
        emacsclient
        erb
        etags
        gem
        git
        git-cvsserver
        git-receive-pack
        git-shell
        git-upload-archive
        git-upload-pack
        irb
        rake
        rdoc
        ri
        ruby
        testrb

    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

問題1: Warning: Broken symlinks were found. Remove them with brew prune:

解決法 #1
このコマンドを打つだけ

$ brew prune 
Pruned 47 symbolic links and 19 directories from /usr/local

問題2: You have unlinked kegs in your Cellar

解決法 #2
何か一部のツールが unlink になっているらしいので、brew link コマンドを使用する。

$ brew link mpfr
Linking /usr/local/Cellar/mpfr/3.1.2-p8... 0 symlinks created

$ brew link node_modules
Error: Multiple kegs installed to /usr/local/Cellar/node_modules
However we don't know which one you refer to.
Please delete (with rm -rf!) all but one and then try again.

$ brew link python
Linking /usr/local/Cellar/python/2.7.8... 0 symlinks created

$ brew link python3
Linking /usr/local/Cellar/python/2.7.8... 0 symlinks created

$ brew link python3
Linking /usr/local/Cellar/python3/3.4.1... 0 symlinks created

node_modulesだけ何かおかしい...
エラー内容を読むとnpmでインストールされているパッケージのどれを参照しているのか分からないらしい。

$ ls /usr/local/Cellar/node_modules
http     mtwitter ntwitter oauth    twitter

とりあえず応急処置的にtwitterだけ残して残りは全部アンインストールしてみる。

$ npm uninstall mtwitter
unbuild mtwitter@1.6.4
$ npm uninstall ntwitter
unbuild ntwitter@0.5.0
$ npm uninstall http
unbuild http@0.0.0
$ npm uninstall oauth
unbuild oauth@0.9.12

ここでbrew linkを使う

$ brew link node_modules
Linking /usr/local/Cellar/node_modules/twitter... 3 symlinks created

問題3: Warning: /usr/bin occurs before /usr/local/bin

解決法 #3
Consider amending 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

このメッセージの通り、".bash_profile"のPATHを設定する。

コマンドラインにてvimで.bash_profileを開く。

$ vim ~/.bash_profile
export PATH=/usr/local/bin:$PATH  # 1行目に追加。

最後にbrew doctorを叩く

$ brew doctor
Your system is ready to brew.

全て正常に戻りました！٩('ω' )و
結構時間かかりました。。。

参考にしたサイトとか

Homebrewのエラーを治す
http://qiita.com/cubdesign/items/176e655a14d47b374a75

homebrew brew doctorトラブルシューティング
http://bismar.hatenablog.com/entry/2012/12/06/022457

brew doctorのwarningを解決する
http://mrk1869.com/blog/brew_doctor/

Mountain Lion環境へのHomebrew & gitインストール手順
http://blog.pinkpinkpink.net/2012/07/homebrew.html

ヾ(oﾟωﾟo)ﾉﾞbrew updateでエラーでたった[Homebrew]
http://qiita.com/harapeko_wktk/items/f4f44ddb5d3912e15ea2