If this post saves one person the headache of several hours of trying to build Nokogiri via Bundler on a Mac, maybe my time wasn't wasted, but it was painful.
Trying to install Nokogiri 1.6.1 as a dependency for other gems via Capistrano's bundle:install task, I continually ran into "Failed to build gem native extension" error. Scrolling through the errors, the one item that stuck out was "You have to install development tools first."
Although 100% certain my server had Xcode Command Line tools installed (it was recently updated at noted in the App Store), I reinstalled manually and tried to deploy again. Same error.
I then proceeded down the path of using Homebrew to install the various Nokogiri dependencies (e.g. libxml2, libxslt). Deploy...build...fail.
I ran "gem install nokogiri" locally on the server. Build...success. Tried to deploy again...build...fail.
Finally, I dug up the make log for Nokogiri (path below for reference) where I noted a message indicating that "gcc-4.2" was not installed. gcc is installed, but the build script seems specific. Not finding a switch to change the name of gcc, I went brute force:
sudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2
Deploy...build...success! Annoying problem, solved.
Better suggestions welcome.
Make log: /shared/bundle/ruby/2.0.0/gems/nokogiri-1.6.1/ports/x86_64-apple-darwin13.1.0/ext/nokogiri/mkmf.log
After all that, I noticed a warning: "Nokogiri was built against LibXML version 2.8.0, but has dynamically loaded 2.9.1". After trying a few paths, I was able to rectify the warning via the steps in the comments of this :
The commenter notes that Nokogiri 1.6+ now bundle the necessary libraries so there is no need to use the Homebrew versions.