An error occurred while installing nokogiri (1.6.3.1), and Bundler cannot continue.

bundle install

してたら下記のエラーが起きた場合の対処。

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    /Users/me/.rbenv/versions/2.1.6/bin/ruby extconf.rb --use-system-libraries
Building nokogiri using system libraries.
libxml2 version 2.6.21 or later is required!
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
    --with-opt-dir
    --without-opt-dir
    --with-opt-include
    --without-opt-include=${opt-dir}/include
    --with-opt-lib
    --without-opt-lib=${opt-dir}/lib
    --with-make-prog
    --without-make-prog
    --srcdir=.
    --curdir
    --ruby=/Users/me/.rbenv/versions/2.1.6/bin/ruby
    --help
    --clean
    --use-system-libraries=true
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --with-xml2-dir
    --without-xml2-dir
    --with-xml2-include
    --without-xml2-include=${xml2-dir}/include
    --with-xml2-lib
    --without-xml2-lib=${xml2-dir}/lib
    --with-libxml-2.0-config
    --without-libxml-2.0-config
    --with-pkg-config
    --without-pkg-config
    --with-xslt-dir
    --without-xslt-dir
    --with-xslt-include
    --without-xslt-include=${xslt-dir}/include
    --with-xslt-lib
    --without-xslt-lib=${xslt-dir}/lib
    --with-libxslt-config
    --without-libxslt-config
    --with-exslt-dir
    --without-exslt-dir
    --with-exslt-include
    --without-exslt-include=${exslt-dir}/include
    --with-exslt-lib
    --without-exslt-lib=${exslt-dir}/lib
    --with-libexslt-config
    --without-libexslt-config

extconf failed, exit code 1

Gem files will remain installed in /Users/me/dev/work/zzz/xxx/vendor/bundle/ruby/2.1.0/gems/nokogiri-1.6.3.1 for inspection.
Results logged to /Users/me/dev/work/zzz/xxx/vendor/bundle/ruby/2.1.0/extensions/x86_64-darwin-14/2.1.0-static/nokogiri-1.6.3.1/gem_make.out
An error occurred while installing nokogiri (1.6.3.1), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.3.1'` succeeds before bundling.

下記によると、

> brew update
> brew install libxml2 libxslt libiconv

> brew --prefix libxml2
/usr/local/opt/libxml2

> brew --prefix libxslt
/usr/local/opt/libxslt

> brew --prefix libiconv
/usr/local/opt/libiconv

> gem uninstall nokogiri

> gem install nokogiri -v 1.6.3.1 -- --with-xslt-dir=/usr/local/opt/libxslt --with-iconv-dir=/usr/local/opt/libiconv --with-xml2-config=/usr/local/opt/libxml2/bin/xml2-config --with-xslt-config=/usr/local/opt/libxslt/bin/xslt-config

で、上記は本家サイトの下記にも書かれていたことだったので従っておくべきなのでしょう。

私の手元ではこれで問題なくいけた様子です。一旦gemを綺麗にした方が良いかもしれません。