The code in:

https://github.com/theseer/phpdox/blob/master/phpdox#L62

(new TheSeer\phpDox\Factory())->getCLI()->run(
    new TheSeer\phpDox\CLIOptions($_SERVER['argv'])
);

Doesn't work on a PHP 5.3.10 installation.My other installation with 5.5.14 works without problems.

Either correct the dependancy or correct the code:

$factory = new TheSeer\phpDox\Factory();
$factory->getCLI()->run(
    new TheSeer\phpDox\CLIOptions($_SERVER['argv'])
);

Would make it compatible with 5.3.3 I would chose this option as still quite some 5.3.* installations are out there.