Please at first remove Gemfile.lock file to make sure that bundle rebuild all dependencies, and install all gem as for a first time, and recreate the file, then:
$ bundle install
Please verify, that the nokogiri gem has presented in the Gemfile.lock. Then to make sure that the nokogiri gem is properly installed type:
$ bundle show nokogiri
/path/to/nokogiri/gem
I above command shows an error others to Could not find gem 'nokogiri' that means that the setup of your systems is incorrect. So please don't use root account, and use simple user as holder of the project. And to separate project gem versions from each other use rvm
to install gems into its gemsets as it has been written here.