The latest version of PHPUnit (3.6.4 at the time of this writing) does not play well with the Zend Framework extensions (Zend_Test_PHPUnit). After asking Matthew Weier O'Phinney about this he answered that they had standardized on PHPUnit-3.4 for ZF1. Having just upgraded to the latest version of PHPUnit on our servers we were no longer able to test our Zend Framework applications. One option was to downgrade PHPUnit, but since we were already using some of the new features this was not going to happen.

He method uses the "installroot" option that can be passed in to the PHPUnit installation process to point it to someplace other than the default PEAR install location. A small change is needed to the "phpunit" executable to have it correctly set the include path. Then it's just a matter of making a symlink to your "/usr/bin" directory pointing to the specific version.