rails : install nokogiri fails on Mac OSX Yosemite - ruby-on-rails

Question

I installed Rails 4.2.3 on Mac OS X Yosemite, but when I try to start the server, I get this error message
Companys-MacBook-Pro:App MyUser$ rails server
Could not find nokogiri-1.6.1 in any of the sources
Run `bundle install` to install missing gems.
Companys-MacBook-Pro:App MyUser$
so I tried this
sudo gem install nokogiri -v=1.6.1
then I got these errors
Companys-MacBook-Pro:~ MyUser$ sudo gem install nokogiri -v=1.6.1
Building native extensions. This could take a while...
ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby extconf.rb
Extracting libxml2-2.8.0.tar.gz into tmp/x86_64-apple-darwin14.4.0/ports/libxml2/2.8.0... OK
Running 'configure' for libxml2 2.8.0... OK
Running 'compile' for libxml2 2.8.0... OK
Running 'install' for libxml2 2.8.0... OK
Activating libxml2 2.8.0 (from /Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.1/ports/x86_64-apple-darwin14.4.0/libxml2/2.8.0)...
Extracting libxslt-1.1.26.tar.gz into tmp/x86_64-apple-darwin14.4.0/ports/libxslt/1.1.26... OK
Running 'configure' for libxslt 1.1.26... OK
Running 'compile' for libxslt 1.1.26... OK
Running 'install' for libxslt 1.1.26... OK
Activating libxslt 1.1.26 (from /Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.1/ports/x86_64-apple-darwin14.4.0/libxslt/1.1.26)...
checking for libxml/parser.h... yes
checking for libxslt/xslt.h... yes
checking for libexslt/exslt.h... yes
checking for iconv_open() in iconv.h... no
checking for iconv_open() in -liconv... yes
checking for xmlParseDoc() in -lxml2... no
-----
libxml2 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
--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=/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
--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-iconv-dir
--without-iconv-dir
--with-iconv-include
--without-iconv-include=${iconv-dir}/include
--with-iconv-lib
--without-iconv-lib=${iconv-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-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-pkg-config
--without-pkg-config
--with-libxml-2.0-config
--without-libxml-2.0-config
--with-pkg-config
--without-pkg-config
--with-libiconv-config
--without-libiconv-config
--with-pkg-config
--without-pkg-config
--with-iconvlib
--without-iconvlib
--with-xml2lib
--without-xml2lib
Gem files will remain installed in /Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.1 for inspection.
Results logged to /Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.1/ext/nokogiri/gem_make.out
Companys-MacBook-Pro:~ MyUser$
I then followed the instructions on nokogiri website to install libxslt, libxml2, and libiconv
Companys-MacBook-Pro:~ MyUser$ brew install libxml2
Warning: libxml2-2.9.2 already installed
Companys-MacBook-Pro:~ MyUser$ brew install libxslt
Warning: libxslt-1.1.28_1 already installed
Companys-MacBook-Pro:~ MyUser$ brew install libiconv
Error: No available formula for libiconv
==> Searching formulae...
==> Searching taps...
Companys-MacBook-Pro:~ MyUser$
and still no luck. I also tried
Companys-MacBook-Pro:~ MyUser$ sudo 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
unable to convert "\xCA" from ASCII-8BIT to UTF-8 for lib/nokogiri/nokogiri.bundle, skipping
1 gem installed
Companys-MacBook-Pro:~ MyUser$
but rails server still does not start because it requires nokogiri 1.6.1
Companys-MacBook-Pro:App MyUser$ rails server
Could not find nokogiri-1.6.1 in any of the sources
Run `bundle install` to install missing gems.
Companys-MacBook-Pro:App MyUser$
Anyone has an idea what's going on here?
EDIT 1
I did run bundle install and still the same issue ; this is the output
Companys-MacBook-Pro:App MyUser$ bundle install
Fetching gem metadata from http://rubygems.org/............
Fetching version metadata from http://rubygems.org/...
Fetching dependency metadata from http://rubygems.org/..
Resolving dependencies...
Using rake 0.9.2.2
Using multi_json 1.0.3
Using activesupport 3.1.0
Using bcrypt-ruby 3.0.0
Using builder 3.0.0
Using i18n 0.6.0
Using activemodel 3.1.0
Using erubis 2.7.0
Using rack 1.3.2
Using rack-cache 1.0.3
Using rack-mount 0.8.3
Using rack-test 0.6.1
Using hike 1.2.1
Using tilt 1.3.3
Using sprockets 2.0.0
Using actionpack 3.1.0
Using mime-types 1.16
Using polyglot 0.3.2
Using treetop 1.4.10
Using mail 2.3.0
Using actionmailer 3.1.0
Using arel 2.2.1
Using tzinfo 0.3.29
Using activerecord 3.1.0
Using activeresource 3.1.0
Using addressable 2.3.6
Using bundler 1.10.6
Using coderay 1.0.8
Using coffee-script-source 1.1.2
Using execjs 1.2.4
Using coffee-script 2.2.0
Using rack-ssl 1.3.2
Using rdoc 3.9.4
Using thor 0.14.6
Using railties 3.1.0
Using coffee-rails 3.1.0
Using crack 0.3.1
Using diff-lcs 1.1.3
Using multipart-post 1.2.0
Using faraday 0.7.6
Using git 1.2.6
Using hashie 1.2.0
Using oauth2 0.5.2
Using github_api 0.4.10
Using highline 1.6.21
Using mini_portile 0.5.3
Installing nokogiri 1.6.1 with native extensions
Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby extconf.rb --with-xml2-dir=/usr --with-xslt-dir=/opt/local --with-iconv-dir=/opt/local
Extracting libxml2-2.8.0.tar.gz into tmp/x86_64-apple-darwin14.4.0/ports/libxml2/2.8.0... OK
Running 'configure' for libxml2 2.8.0... OK
Running 'compile' for libxml2 2.8.0... OK
Running 'install' for libxml2 2.8.0... OK
Activating libxml2 2.8.0 (from /private/var/folders/x4/01wntm8j66lf6mwbtmg8t3lm0000gn/T/bundler20150801-30338-1m943xrnokogiri-1.6.1/gems/nokogiri-1.6.1/ports/x86_64-apple-darwin14.4.0/libxml2/2.8.0)...
Extracting libxslt-1.1.26.tar.gz into tmp/x86_64-apple-darwin14.4.0/ports/libxslt/1.1.26... OK
Running 'configure' for libxslt 1.1.26... OK
Running 'compile' for libxslt 1.1.26... OK
Running 'install' for libxslt 1.1.26... OK
Activating libxslt 1.1.26 (from /private/var/folders/x4/01wntm8j66lf6mwbtmg8t3lm0000gn/T/bundler20150801-30338-1m943xrnokogiri-1.6.1/gems/nokogiri-1.6.1/ports/x86_64-apple-darwin14.4.0/libxslt/1.1.26)...
checking for libxml/parser.h... no
-----
libxml2 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
--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=/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
--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-iconv-dir
--with-iconv-include
--without-iconv-include=${iconv-dir}/include
--with-iconv-lib
--without-iconv-lib=${iconv-dir}/lib
--with-xml2-dir
--with-xml2-include
--without-xml2-include=${xml2-dir}/include
--with-xml2-lib
--without-xml2-lib=${xml2-dir}/lib
--with-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-pkg-config
--without-pkg-config
--with-libxml-2.0-config
--without-libxml-2.0-config
--with-pkg-config
--without-pkg-config
--with-libiconv-config
--without-libiconv-config
--with-pkg-config
--without-pkg-config
Gem files will remain installed in /var/folders/x4/01wntm8j66lf6mwbtmg8t3lm0000gn/T/bundler20150801-30338-1m943xrnokogiri-1.6.1/gems/nokogiri-1.6.1 for inspection.
Results logged to /var/folders/x4/01wntm8j66lf6mwbtmg8t3lm0000gn/T/bundler20150801-30338-1m943xrnokogiri-1.6.1/gems/nokogiri-1.6.1/ext/nokogiri/gem_make.out
An error occurred while installing nokogiri (1.6.1), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.1'` succeeds before bundling.
Companys-MacBook-Pro:App MyUser$

Answer 1

One of issues was that you were manually installing Nokogiri 1.6.6.2, but not including the nokogiri gem entry in your Gemfile. Bundler will specifically only show your app the gems that are listed in the file.
It wasn't clear to me if you were tied to nokogiri 1.6.1 because it was a dependency of another gem. If there was another gem calling for 1.6.1 then you would investigate a newer version of that gem, which hopefully depended on the newer Nokogiri. bundle update <othergem> would attempt to do so.
Just wanted to be clear that I wasn't suggesting modifying another gem's dependencies in your lock file as they were set for a reason by that gem's author.
Since you initially specified gem 'nokogiri', '~> 1.6.1' in your Gemfile you were locked to that after the first bundle install. bundle update nokogiri would try to update you to the latest. Or manually changing the Gemfile to 1.6.6.2 or more loosely ~> 1.6 or 1.6.6.
Also, as #the Tin Man mentioned using sudo install to put gems into the Apple system ruby isn't the best way to go. I definitely recommend using one of the Ruby version managers like RVM or rbenv as he linked in his comment.