jruby環境でgem install ruby-debug-baseとすると下記のようなエラーが出てくると思います。

Building native extensions.  This could take a while...
WARNING: JRuby does not support native extensions or the `mkmf' library.
         Check wiki.jruby.org for alternatives.
extconf.rb:16: undefined method `create_makefile' for main:Object (NoMethodError)
ERROR:  Error installing ruby-debug-base:
        ERROR: Failed to build gem native extension.

"C:/Program Files/NetBeans 6.8/ruby2/jruby-1.4.0/bin/jruby.exe" extconf.rb

Gem files will remain installed in C:/Program Files/NetBeans 6.8/ruby2/jruby-1.4.0/lib/ruby/gems/1.8/gems/linecache-0.43 for inspection.
Results logged to C:/Program Files/NetBeans 6.8/ruby2/jruby-1.4.0/lib/ruby/gems/1.8/gems/linecache-0.43/ext/gem_make.out

メッセージの通りJRubyは、NativeExtension をサポートしていないようです。

RubyDebugging - NetBeans Wiki


Automatic instalation for JRuby is not supported yet. You need to install two gems to get it working following steps below:

1. Manually download the ruby-debug-base- from debug-commons to a local directory.
2. Install the Gem into your JRuby Gem repository:

jruby -S gem install -l ruby-debug-base-

3. Now install ruby-debug-ide with:

jruby -S gem install --ignore-dependencies -v 0.4.6 ruby-debug-ide

See Troubleshooting section if you encounter problems.