Line 650 in PEAR\Config.php does
$this->_registry['default'] = &new PEAR_Registry( $this->configuration['default']['php_dir'] );
This will raise an
E_DEPRECATED message depending on whether you have enabled error_reporting to include that level. The error handlers of
ZendPHPUnit will convert those to
Because PHP will raise
E_DEPRECATED already at compile time, the only way to suppress these errors is in php.ini. My assumption is, that your PHPUnit you run from CLI is using a different php.ini than that your Zend Studio and in that php.ini the error level is not low enough to raise
If you can provide a reproducable example, we might be able to make more sense of it. In any case, try to update your PEAR installation to the latest version.