title: Gem File won't update or install with bundler
body: <p>I'm working on Michael Hartl's RoR tutorials. I'm on chapter 3. Unfortunately, copy and pasting the gem files won't work for me, but I figured out which gem is the problem. It's the capybara gem. I've commented it out and continued the tutorial, but I'm at the point where I need to use the gem.</p>
  
  <p>Here is an example $bundle update giving me an error:</p>
  
  <pre><code>$ bundle update
  Fetching gem metadata from https://rubygems.org/.........
  
  (Removed a bunch of text)
  
  Building nokogiri using system libraries.
  
  Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native extension.
  
      /Users/dbz/.rvm/rubies/ruby-2.0.0-p481/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.
  
  (Removed a bunch of text)
  
  
  Gem files will remain installed in /Users/dbz/.rvm/gems/ruby-2.0.0-p481/gems/nokogiri-1.6.3.1 for inspection.
  Results logged to /Users/dbz/.rvm/gems/ruby-2.0.0-p481/gems/nokogiri-1.6.3.1/ext/nokogiri/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.
  </code></pre>
  
  <p>I tried going to the nokogiri website and fixing the problem, but when I try to update the missing libraries (an earlier part of the error), my machine says I already have them. </p>
  
  <p>Here is my Gemfile:</p>
  
  <pre><code>source 'https://rubygems.org'
  ruby '2.0.0'
  #ruby-gemset=railstutorial_rails_4_0
  
  gem 'rails', '4.0.8'
  
  group :development, :test do
    gem 'sqlite3', '1.3.8'
    gem 'rspec-rails', '2.13.1'
  end
  
  group :test do
    gem 'selenium-webdriver', '2.35.1'
    #gem 'capybara', '2.1.0'   # This line breaks everything
  end
  
  gem 'sass-rails', '4.0.1'
  gem 'uglifier', '2.1.1'
  gem 'coffee-rails', '4.0.1'
  gem 'jquery-rails', '3.0.4'
  gem 'turbolinks', '1.1.1'
  gem 'jbuilder', '1.0.2'
  
  group :doc do
    gem 'sdoc', '0.3.20', require: false
  end
  
  group :production do
    gem 'pg', '0.15.1'
    gem 'rails_12factor', '0.0.2'
  end
  </code></pre>
  
  <p>EDIT: From the <a href="http://nokogiri.org/tutorials/installing_nokogiri.html" rel="nofollow">http://nokogiri.org/tutorials/installing_nokogiri.html</a> install page</p>
  
  <p>I followed all of the steps and at the final step where I need to run the command</p>
  
  <pre><code>gem install nokogiri -- --with-xml2-include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2 
                      --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib 
                      --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26 
                      --with-iconv-include=/usr/local/Cellar/libiconv/1.13.1/include 
                      --with-iconv-lib=/usr/local/Cellar/libiconv/1.13.1/lib
  </code></pre>
  
  <p>The output from my console is:</p>
  
  <pre><code>Daniels-MacBook-Air:libiconv-1.13.1 dbz$ pwd
  /Users/dbz/libiconv-1.13.1
  Daniels-MacBook-Air:libiconv-1.13.1 dbz$ gem install nokogiri -- --with-xml2-    include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2 
                      --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib 
                      --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26 
                      --with-iconv-include=/usr/local/Cellar/libiconv/1.13.1/include 
                      --with-iconv-lib=/usr/local/Cellar/libiconv/1.13.1/lib
  Building native extensions with: '--with-xml2-    include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2'
  This could take a while...
  Building nokogiri using packaged libraries.
  ERROR:  Error installing nokogiri:
      ERROR: Failed to build gem native extension.
  
      /Users/dbz/.rvm/rubies/ruby-2.0.0-p481/bin/ruby extconf.rb --with-xml2-    include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2
  Building nokogiri using packaged libraries.
  -----
  libiconv is missing.  please visit     http://nokogiri.org/tutorials/installing_nokogiri.html for help with installing dependencies.
  -----
  *** 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
      --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/dbz/.rvm/rubies/ruby-2.0.0-p481/bin/ruby
      --help
      --clean
      --use-system-libraries
      --enable-static
      --disable-static
      --with-zlib-dir
      --without-zlib-dir
      --with-zlib-include
      --without-zlib-include=${zlib-dir}/include
      --with-zlib-lib
      --without-zlib-lib=${zlib-dir}/lib
      --enable-cross-build
      --disable-cross-build
  
  
  Gem files will remain installed in /Users/dbz/.rvm/gems/ruby-2.0.0-p481@railstutorial_rails_4_0/gems/nokogiri-1.6.3.1 for inspection.
  Results logged to /Users/dbz/.rvm/gems/ruby-2.0.0-p481@railstutorial_rails_4_0/gems/nokogiri-1.6.3.1/ext/nokogiri/gem_make.out
  Daniels-MacBook-Air:libiconv-1.13.1 dbz$                         --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib 
  -bash: --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib: No such file or directory
  Daniels-MacBook-Air:libiconv-1.13.1 dbz$                         --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26 
  -bash: --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26: No such file or directory
  Daniels-MacBook-Air:libiconv-1.13.1 dbz$                         --with-iconv-include=/usr/local/Cellar/libiconv/1.13.1/include 
  -bash: --with-iconv-include=/usr/local/Cellar/libiconv/1.13.1/include: No such file or directory
  Daniels-MacBook-Air:libiconv-1.13.1 dbz$                         --with-iconv-lib=/usr/local/Cellar/libiconv/1.13.1/lib
  -bash: --with-iconv-lib=/usr/local/Cellar/libiconv/1.13.1/lib: No such file or directory
  </code></pre>