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The PHP Filter module has been removed from Drupal Core and moved to a contributed module at http://drupal.org/project/php .
If your contributed modules allows a Drupal user to execute php via the interface you should update it. The method of checking depends on the existing an instance of ModuleHandler on your object:
$this->moduleHandler->moduleExists('php') && user_access('use PHP for settings')before allowing the code to be entered.
$this->moduleHandler->moduleExists('php')before allowing the code to be executed.
If your object does not have an instance of ModuleHandler available, it can be accessed statically: