Matthew Turland has put together a guide for getting PHPUnit and Xdebug up and working on one of the latest Ubuntu releases (Karmic) to resolve an upgrade issue with the package install.

This is just a quick post to advise anyone who may be using PHPUnit and Xdebug together on Ubuntu Karmic. If you try to upgrade to PHPUnit 3.4.6 and you’re using the php5-xdebug Ubuntu package (which is Xdebug 2.0.4), you may get output that looks like [this error].

He gives a two ways to overcome the issue - forcing the PEAR installer to ignore dependencies or reinstalling with Xdebug 2.0.5 instead (via the PECL installer) as a shared module.