title: Error installing Nokogiri on bundle install but already installed
body: <p>I'm having issues with bundling my Gemfile. I have Nokogiri installed already yet when I run <code>bundle install</code> it fails to load Nokogiri.  </p>
  
  <p>Installing Nokogiri:</p>
  
  <pre><code>gem install nokogiri
  Building native extensions.  This could take a while...
  Successfully installed nokogiri-1.6.6.2
  Parsing documentation for nokogiri-1.6.6.2
  Done installing documentation for nokogiri after 2 seconds
  1 gem installed
  </code></pre>
  
  <p>Bundle install:</p>
  
  <pre><code>bundle install   sic@ANTHONYs-iMac
  Fetching gem metadata from https://rubygems.org/.........
  Fetching version metadata from https://rubygems.org/...
  Fetching dependency metadata from https://rubygems.org/..
  Resolving dependencies...
  Using rake 10.4.2
  Using i18n 0.7.0
  Using json 1.8.2
  Using minitest 5.5.1
  Using thread_safe 0.3.4
  Using tzinfo 1.2.2
  Using activesupport 4.2.0
  Using builder 3.2.2
  Using erubis 2.7.0
  Using mini_portile 0.6.2
  
  Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
  
      /Users/sic/.rvm/rubies/ruby-2.2.0/bin/ruby -r ./siteconf20150312-7195-1d8tq46.rb extconf.rb 
  checking if the C compiler accepts ... yes
  checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
  Building nokogiri using packaged libraries.
  checking for gzdopen() in -lz... yes
  checking for iconv using --with-opt-* flags... yes
  ************************************************************************
  IMPORTANT NOTICE:
  
  Building Nokogiri with a packaged version of libxml2-2.9.2
  with the following patches applied:
    - 0001-Revert-Missing-initialization-for-the-catalog-module.patch
    - 0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch
  
  Team Nokogiri will keep on doing their best to provide security
  updates in a timely manner, but if this is a concern for you and want
  to use the system library instead; abort this installation process and
  reinstall nokogiri as follows:
  
      gem install nokogiri -- --use-system-libraries
          [--with-xml2-config=/path/to/xml2-config]
          [--with-xslt-config=/path/to/xslt-config]
  
  If you are using Bundler, tell it to use the option:
  
      bundle config build.nokogiri --use-system-libraries
      bundle install
  
  Note, however, that nokogiri is not fully compatible with arbitrary
  versions of libxml2 provided by OS/package vendors.
  ************************************************************************
  Extracting libxml2-2.9.2.tar.gz into tmp/x86_64-apple-darwin14.1.0/ports/libxml2/2.9.2... OK
  Running patch with /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxml2/0001-Revert-Missing-initialization-for-the-catalog-module.patch...
  Running 'patch' for libxml2 2.9.2... ERROR, review '/Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/nokogiri-1.6.6.2/ext/nokogiri/tmp/x86_64-apple-darwin14.1.0/ports/libxml2/2.9.2/patch.log' to see what happened.
  *** 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/sic/.rvm/rubies/ruby-2.2.0/bin/$(RUBY_BASE_NAME)
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --enable-cross-build
    --disable-cross-build
  /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:279:in `block in execute': Failed to complete patch task (RuntimeError)
    from /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `chdir'
    from /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `execute'
    from extconf.rb:311:in `block in patch'
    from extconf.rb:308:in `each'
    from extconf.rb:308:in `patch'
    from /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:108:in `cook'
    from extconf.rb:278:in `block in process_recipe'
    from extconf.rb:177:in `tap'
    from extconf.rb:177:in `process_recipe'
    from extconf.rb:475:in `&lt;main&gt;'
  
  extconf failed, exit code 1
  
  Gem files will remain installed in /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/gems/nokogiri-1.6.6.2 for inspection.
  Results logged to /Users/sic/home/ruby/rails/Vl2/vendor/bundle /ruby/2.2.0/extensions/x86_64-darwin-14/2.2.0/nokogiri-1.6.6.2/gem_make.out
  An error occurred while installing nokogiri (1.6.6.2), and Bundler cannot
  continue.
  Make sure that `gem install nokogiri -v '1.6.6.2'` succeeds before
  bundling.`
  </code></pre>
  
  <p>My Gemfile contents:</p>
  
  <pre><code>source 'https://rubygems.org'
  
  # Standard Rails gems
  gem 'rails', '4.2.0'
  gem 'sass-rails', '5.0.1'
  gem 'uglifier', '2.7.1'
  gem 'coffee-rails', '4.1.0'
  gem 'jquery-rails', '4.0.3'
  gem 'turbolinks', '2.5.3'
  gem 'jbuilder', '2.2.11'
  gem 'bcrypt', '3.1.10'
  
  
  gem 'pg'
  gem 'devise', '3.4.1'
  gem 'redcarpet', '3.2.2'
  gem 'kaminari', '0.16.3'
  gem 'friendly_id', '5.1.0'
  gem 'font-awesome-sass', '4.3.1'
  gem 'bootstrap-sass', '3.3.3'
  
  
  # OmniAuth
  gem 'omniauth'
  gem 'omniauth-facebook'
  gem 'omniauth-twitter'
  gem 'omniauth-linkedin'
  
  group :development, :test do
    gem 'better_errors'
    gem 'binding_of_caller'
    gem 'meta_request'
    gem 'byebug'
    gem 'web-console', '~&gt; 2.0'
    gem 'figaro', '1.1.0'
    gem 'spring', '1.3.3'
  end
  
  
  
  # Necessary for Windows OS (won't install on *nix systems)
  gem 'tzinfo-data', platforms: [:mingw, :mswin]
  </code></pre>