Rails5へアップグレード後にUserControllerを作りたい。

【環境】
cloud9
rails5.0.0
ruby2.3.1

【やりたいこと】
rails5.0.0のファイルでコントローラーを作りたい。

【現状】

こんにちは。
表題の件です。

cloud9でrails5にアップグレードした後に

rails g controller Users new

を実行するとエラーがでます....

【エラー内容】

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-9.0.5 because its extensions are not built.  Try: gem pristine byebug --version 9.0.5
Ignoring debug_inspector-0.0.2 because its extensions are not built.  Try: gem pristine debug_inspector --version 0.0.2
Ignoring executable-hooks-1.3.2 because its extensions are not built.  Try: gem pristine executable-hooks --version 1.3.2
Ignoring ffi-1.9.14 because its extensions are not built.  Try: gem pristine ffi --version 1.9.14
Ignoring gem-wrappers-1.2.7 because its extensions are not built.  Try: gem pristine gem-wrappers --version 1.2.7
Ignoring nio4r-1.2.1 because its extensions are not built.  Try: gem pristine nio4r --version 1.2.1
Ignoring nokogiri-1.6.8 because its extensions are not built.  Try: gem pristine nokogiri --version 1.6.8
Ignoring sqlite3-1.3.11 because its extensions are not built.  Try: gem pristine sqlite3 --version 1.3.11
Ignoring sqlite3-1.3.9 because its extensions are not built.  Try: gem pristine sqlite3 --version 1.3.9
Ignoring websocket-driver-0.6.4 because its extensions are not built.  Try: gem pristine websocket-driver --version 0.6.4
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-9.0.5 because its extensions are not built.  Try: gem pristine byebug --version 9.0.5
Ignoring debug_inspector-0.0.2 because its extensions are not built.  Try: gem pristine debug_inspector --version 0.0.2
/usr/local/rvm/gems/ruby-2.3.0/gems/sqlite3-1.3.9/lib/sqlite3.rb:6:in `require': incompatible library version - /usr/local/rvm/gems/ruby-2.3.0/gems/sqlite3-1.3.9/lib/sqlite3/sqlite3_native.so (LoadError)
        from /usr/local/rvm/gems/ruby-2.3.0/gems/sqlite3-1.3.9/lib/sqlite3.rb:6:in `rescue in <top (required)>'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/sqlite3-1.3.9/lib/sqlite3.rb:2:in `<top (required)>'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:86:in `require'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:86:in `block (2 levels) in require'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:81:in `each'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:81:in `block in require'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:70:in `each'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler/runtime.rb:70:in `require'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/bundler-1.12.5/lib/bundler.rb:102:in `require'
        from /home/ubuntu/workspace/config/application.rb:7:in `<top (required)>'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands/commands_tasks.rb:156:in `require'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands/commands_tasks.rb:156:in `require_application_and_environment!'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands/commands_tasks.rb:143:in `generate_or_destroy'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands/commands_tasks.rb:60:in `generate'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands/commands_tasks.rb:49:in `run_command!'
        from /usr/local/rvm/gems/ruby-2.3.0/gems/railties-5.0.0/lib/rails/commands.rb:18:in `<top (required)>'
        from bin/rails:4:in `require'
        from bin/rails:4:in `<main>'

おそらく環境構築が上手くいっていないんだと思いますが原因がわかりません。。。
何が原因なのでしょう？？

gem listも載せておきます。

【gemlist】

actioncable (5.0.0)
actionmailer (5.0.0, 4.2.5)
actionpack (5.0.0, 4.2.5)
actionview (5.0.0, 4.2.5)
activejob (5.0.0, 4.2.5)
activemodel (5.0.0, 4.2.5)
activerecord (5.0.0, 4.2.5)
activesupport (5.0.0, 4.2.5)
ansi (1.5.0)
arel (7.1.2, 6.0.3)
bigdecimal (1.2.8)
binding_of_caller (0.7.2)
bootstrap-sass (3.2.0.0)
builder (3.2.2)
bundler (1.12.5)
bundler-unload (1.0.2)
byebug (9.0.5, 3.4.0)
coderay (1.1.1)
coffee-rails (4.1.1)
coffee-script (2.4.1)
coffee-script-source (1.10.0)
columnize (0.9.0)
concurrent-ruby (1.0.2)
debug_inspector (0.0.2)
debugger-linecache (1.2.0)
did_you_mean (1.0.0)
erubis (2.7.0)
execjs (2.7.0)
executable-hooks (1.3.2)
ffi (1.9.14)
formatador (0.2.5)
gem-wrappers (1.2.7)
globalid (0.3.7)
guard (2.14.0)
guard-minitest (2.3.1)
i18n (0.7.0)
io-console (0.4.5)
jbuilder (2.6.0)
jquery-rails (4.2.1)
json (1.8.3)
listen (3.1.5)
loofah (2.0.3)
lumberjack (1.0.10)
mail (2.6.4)
method_source (0.8.2)
mime-types (3.1)
mime-types-data (3.2016.0521)
mini_backtrace (0.1.3)
mini_portile2 (2.1.0)
minitest (5.9.0, 5.8.3)
minitest-reporters (1.0.5)
multi_json (1.12.1)
nenv (0.3.0)
net-telnet (0.1.1)
nio4r (1.2.1)
nokogiri (1.6.8)
notiffany (0.1.1)
pkg-config (1.1.7)
power_assert (0.2.6)
pry (0.10.4)
psych (2.0.17)
rack (2.0.1, 1.6.4)
rack-test (0.6.3)
rails (5.0.0, 4.2.5)
rails-deprecated_sanitizer (1.0.3)
rails-dom-testing (2.0.1, 1.0.7)
rails-html-sanitizer (1.0.3)
railties (5.0.0, 4.2.5)
rake (11.3.0, 11.2.2, 10.4.2)
rb-fsevent (0.9.7)
rb-inotify (0.9.7)
rdoc (4.2.2, 4.2.1)
request_store (1.3.1)
ruby-progressbar (1.8.1)
ruby_dep (1.4.0)
rubygems-bundler (1.4.4)
rvm (1.11.3.9)
sass (3.4.22)
sass-rails (5.0.6)
sdoc (0.4.1)
shellany (0.0.1)
slop (3.6.0)
spring (1.7.2, 1.1.3)
sprockets (3.7.0)
sprockets-rails (3.2.0, 3.1.1)
sqlite3 (1.3.11, 1.3.9)
test-unit (3.1.5)
thor (0.19.1)
thread_safe (0.3.5)
tilt (2.0.5)
turbolinks (5.0.1)
turbolinks-source (5.0.0)
tzinfo (1.2.2)
uglifier (3.0.2)
web-console (3.3.1, 2.3.0)
websocket-driver (0.6.4)
websocket-extensions (0.1.2)