error Ignoring "gem name" because its extensions are not built rails

Question

I install ruby 2.2.3 by rbenv and install rails 4.2.1

When i want see rails version in terminal by rails -v display this:

Ignoring json-1.8.2 because its extensions are not built.  Try: gem pristine json --version 1.8.2
Ignoring json-1.8.3 because its extensions are not built.  Try: gem pristine json --version 1.8.3
Ignoring nokogiri-1.6.6.2 because its extensions are not built.  Try: gem pristine nokogiri --version 1.6.6.2
Rails 4.2.1

or to craete new app by rails new app show me this:

Ignoring json-1.8.2 because its extensions are not built.  Try: gem pristine json --version 1.8.2
Ignoring json-1.8.3 because its extensions are not built.  Try: gem pristine json --version 1.8.3
Ignoring nokogiri-1.6.6.2 because its extensions are not built.  Try: gem pristine nokogiri --version 1.6.6.2
      create
      create  README.rdoc
      create  Rakefile
      create  config.ru
      create  .gitignore
      create  Gemfile
      create  app
      create  app/assets/javascripts/application.js
      create  app/assets/stylesheets/application.css
      create  app/controllers/application_controller.rb
      create  app/helpers/application_helper.rb
      create  app/views/layouts/application.html.erb
      create  app/assets/images/.keep
      create  app/mailers/.keep
      create  app/models/.keep
      create  app/controllers/concerns/.keep
      create  app/models/concerns/.keep
      create  bin
      create  bin/bundle
      create  bin/rails
      create  bin/rake
      create  bin/setup
      create  config
      create  config/routes.rb
      create  config/application.rb
      create  config/environment.rb
      create  config/secrets.yml
      create  config/environments
      create  config/environments/development.rb
      create  config/environments/production.rb
      create  config/environments/test.rb
      create  config/initializers
      create  config/initializers/assets.rb
      create  config/initializers/backtrace_silencers.rb
      create  config/initializers/cookies_serializer.rb
      create  config/initializers/filter_parameter_logging.rb
      create  config/initializers/inflections.rb
      create  config/initializers/mime_types.rb
      create  config/initializers/session_store.rb
      create  config/initializers/wrap_parameters.rb
      create  config/locales
      create  config/locales/en.yml
      create  config/boot.rb
      create  config/database.yml
      create  db
      create  db/seeds.rb
      create  lib
      create  lib/tasks
      create  lib/tasks/.keep
      create  lib/assets
      create  lib/assets/.keep
      create  log
      create  log/.keep
      create  public
      create  public/404.html
      create  public/422.html
      create  public/500.html
      create  public/favicon.ico
      create  public/robots.txt
      create  test/fixtures
      create  test/fixtures/.keep
      create  test/controllers
      create  test/controllers/.keep
      create  test/mailers
      create  test/mailers/.keep
      create  test/models
      create  test/models/.keep
      create  test/helpers
      create  test/helpers/.keep
      create  test/integration
      create  test/integration/.keep
      create  test/test_helper.rb
      create  tmp/cache
      create  tmp/cache/assets
      create  vendor/assets/javascripts
      create  vendor/assets/javascripts/.keep
      create  vendor/assets/stylesheets
      create  vendor/assets/stylesheets/.keep
         run  bundle install
Ignoring bcrypt-3.1.9 because its extensions are not built.  Try: gem pristine bcrypt --version 3.1.9
Ignoring binding_of_caller-0.7.2 because its extensions are not built.  Try: gem pristine binding_of_caller --version 0.7.2
Ignoring bcrypt-3.1.9 because its extensions are not built.  Try: gem pristine bcrypt --version 3.1.9
Ignoring binding_of_caller-0.7.2 because its extensions are not built.  Try: gem pristine binding_of_caller --version 0.7.2
Ignoring byebug-6.0.2 because its extensions are not built.  Try: gem pristine byebug --version 6.0.2
Ignoring byebug-5.0.0 because its extensions are not built.  Try: gem pristine byebug --version 5.0.0
Ignoring byebug-3.5.1 because its extensions are not built.  Try: gem pristine byebug --version 3.5.1
Ignoring debug_inspector-0.0.2 because its extensions are not built.  Try: gem pristine debug_inspector --version 0.0.2
Ignoring json-1.8.3 because its extensions are not built.  Try: gem pristine json --version 1.8.3
Ignoring json-1.8.2 because its extensions are not built.  Try: gem pristine json --version 1.8.2
Ignoring nokogiri-1.6.6.2 because its extensions are not built.  Try: gem pristine nokogiri --version 1.6.6.2
Ignoring sqlite3-1.3.10 because its extensions are not built.  Try: gem pristine sqlite3 --version 1.3.10


Your user account isn't allowed to install to the system Rubygems.
You can cancel this installation and run:

    bundle install --path vendor/bundle

to install the gems into ./vendor/bundle/, or you can enter your password
and install the bundled gems to Rubygems using sudo.

Password:
Fetching gem metadata from https://rubygems.org/............
Fetching version metadata from https://rubygems.org/...
Fetching dependency metadata from https://rubygems.org/..
Resolving dependencies....
Using rake 10.4.2
Using i18n 0.7.0
Using json 1.8.3
Using minitest 5.8.2
Using thread_safe 0.3.5
Using tzinfo 1.2.2
Using activesupport 4.2.1
Using builder 3.2.2
Using erubis 2.7.0
Using mini_portile 0.6.2
with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -r ./siteconf20151117-13935-1bujac5.rb extconf.rb
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
Ignoring bcrypt-3.1.9 because its extensions are not built.  Try: gem pristine bcrypt --version 3.1.9
Ignoring binding_of_caller-0.7.2 because its extensions are not built.  Try: gem pristine binding_of_caller --version 0.7.2
Ignoring byebug-6.0.2 because its extensions are not built.  Try: gem pristine byebug --version 6.0.2
Ignoring byebug-5.0.0 because its extensions are not built.  Try: gem pristine byebug --version 5.0.0
Ignoring byebug-3.5.1 because its extensions are not built.  Try: gem pristine byebug --version 3.5.1
Ignoring debug_inspector-0.0.2 because its extensions are not built.  Try: gem pristine debug_inspector --version 0.0.2
Ignoring json-1.8.3 because its extensions are not built.  Try: gem pristine json --version 1.8.3
Ignoring json-1.8.2 because its extensions are not built.  Try: gem pristine json --version 1.8.2
-----
The file "/usr/include/iconv.h" is missing in your build environment,
which means you haven't installed Xcode Command Line Tools properly.

To install Command Line Tools, try running `xcode-select --install` on
terminal and follow the instructions.  If it fails, open Xcode.app,
select from the menu "Xcode" - "Open Developer Tool" - "More Developer
Tools" to open the developer site, download the installer for your OS
version and run it.
-----
*** 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
    --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

extconf failed, exit code 1

Gem files will remain installed in /var/folders/89/03x00qyx4q9fps00mz9bns840000gn/T/bundler20151117-13935-p9edl4nokogiri-1.6.6.3/gems/nokogiri-1.6.6.3 for inspection.
Results logged to /var/folders/89/03x00qyx4q9fps00mz9bns840000gn/T/bundler20151117-13935-p9edl4nokogiri-1.6.6.3/extensions/universal-darwin-15/2.0.0/nokogiri-1.6.6.3/gem_make.out
An error occurred while installing nokogiri (1.6.6.3), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.6.3'` succeeds before bundling.
         run  bundle exec spring binstub --all
Ignoring bcrypt-3.1.9 because its extensions are not built.  Try: gem pristine bcrypt --version 3.1.9
Ignoring binding_of_caller-0.7.2 because its extensions are not built.  Try: gem pristine binding_of_caller --version 0.7.2
bundler: command not found: spring
Install missing gem executables with `bundle install`

And when i try to run for example gem pristine json --version 1.8.2 show me the error! how i can fix this issue?

Answer 1

I just had the same issue and I am a mac user. It is not clear if you are a mac user too but here I explain how I've got it fixed as I noticed a recent Command Line Tools for Xcode auto update.

Opening Xcode after a while, it prompted me with the screen below:

After clicking Install, it took a while installing components:

Then all I had to do was run the suggested gem pristine ... commands you mentioned above and all got back working fine.