Gem File won't update or install with bundler

Question

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.

Here is an example $bundle update giving me an error:

$ 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.

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.

Here is my Gemfile:

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

EDIT: From the http://nokogiri.org/tutorials/installing_nokogiri.html install page

I followed all of the steps and at the final step where I need to run the command

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

The output from my console is:

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

Answer 1

You might be missing some packages. Try installing them manually

For Mac OSX:

$ sudo port install libxml2 libxslt

With homebrew

$ brew install libxml2

Checkout this LINK here for more information. Goodluck!

Answer 2

I found a solution that worked:

gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2

From: Nokogiri 'Failed to build gem native extension' when I run bundle install

Source's source: https://github.com/sparklemotion/nokogiri/issues/1099#issuecomment-43023208

Answer 3

Just type this in console: gem install nokogiri -v '1.6.3.1' then hit enter... After that finishes... run bundle

If you're using homebrew.. type: brew update then type brew doctor

Answer 4

Just resolved the same issue after I saw your post. It's a problem with Homebrew not including libicov with versions 9.0 and up. You'll need to manually install the library then install with the lib paths defined. See http://nokogiri.org/tutorials/installing_nokogiri.html