rails server bin/rails:6: warning: already initial

I'm using Ubuntu 14.04 and I'm a beginner using Ruby on Rails

I recently installed rbenv, ruby 2.3.0 and rails 4.2.4 following the tutorial: https://gorails.com/setup/ubuntu/14.04

After installation, I ran ruby -v and rails -v and got the expected versions. So far so good. Then I ran rails s and I got:

rails server bin/rails:6: warning: already initialized constant APP_PATH error

To fix it I ran: rake rails:update:bin following this StackOverflow question: rails server bin/rails:6: warning: already initialized constant APP_PATH error which resulted to a new error (I also removed Spring gem):

Gem::LoadError: You have already activated rake 10.4.2, but your Gemfile requires rake 10.5.0. Prepending `bundle exec` to your command may solve this.
/my-home-directory/my-ruby-on-rails-project/config/boot.rb:3:in `<top (required)>'
/my-home-directory/my-ruby-on-rails-project/config/application.rb:1:in `<top (required)>'
/my-home-directory/my-ruby-on-rails-project/Rakefile:4:in `<top (required)>'
LoadError: cannot load such file -- bundler/setup
/my-home-directory/my-ruby-on-rails-project/config/boot.rb:3:in `<top (required)>'
/my-home-directory/my-ruby-on-rails-project/config/application.rb:1:in `<top (required)>'
/my-home-directory/my-ruby-on-rails-project/Rakefile:4:in `<top (required)>'
(See full trace by running task with --trace)

I prepend 'bundle exec' and got the following error:

/my-home-directory/my-ruby-on-rails-project/.bundle/gems/nokogiri-1.6.7.2/lib/nokogiri.rb:29:in `require': libruby.so.2.2: cannot open shared object file: No such file or directory - /my-home-directory/my-ruby-on-rails-project/.bundle/gems/nokogiri-1.6.7.2/lib/nokogiri/nokogiri.so (LoadError)
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/nokogiri-1.6.7.2/lib/nokogiri.rb:29:in `rescue in <top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/nokogiri-1.6.7.2/lib/nokogiri.rb:25:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/fog-1.23.0/lib/fog/xml.rb:1:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/fog-1.23.0/lib/fog/xml.rb:1:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/fog-1.23.0/lib/fog.rb:11:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/fog-1.23.0/lib/fog.rb:11:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave/storage/fog.rb:3:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave/storage/fog.rb:3:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave/storage.rb:9:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave/storage.rb:9:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave.rb:78:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/carrierwave-0.10.0/lib/carrierwave.rb:78:in `<top (required)>'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:77:in `require'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:77:in `block (2 levels) in require'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:72:in `each'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:72:in `block in require'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:61:in `each'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:61:in `require'
from /my-home-directory/.rbenv/versions/2.3.0/lib/ruby/gems/2.3.0/gems/bundler-1.11.2/lib/bundler.rb:99:in `require'
from /my-home-directory/my-ruby-on-rails-project/config/application.rb:7:in `<top (required)>'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands/commands_tasks.rb:78:in `require'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands/commands_tasks.rb:78:in `block in server'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands/commands_tasks.rb:75:in `tap'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands/commands_tasks.rb:75:in `server'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands/commands_tasks.rb:39:in `run_command!'
from /my-home-directory/my-ruby-on-rails-project/.bundle/gems/railties-4.2.4/lib/rails/commands.rb:17:in `<top (required)>'
from bin/rails:8:in `require'
from bin/rails:8:in `<main>'

Before installing rbenv, I was using RVM and I had the same errors popping around. I can't figure out what changes I've done when I started having these issues.

For the sake of my sanity, any help is very appreciated!

Thank you all!

A friend of mine just helped me and fixed this. What he suggested:

Create a file .ruby-version in my project directory with one line: ruby-2.3.0 - This will make sure that we're not loading another nokogiri version
Remove the bundler by running: rm -rfv .bundle
Then run: bundle
Run: bundle exec rails s

Works like a charm. I asked him why he thinks I had these issues and said: Hard to say, a messed up .bundle directory can do a lot of funky stuff.