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/usr/share/php/PHP/Invoker/TimeoutException.php is in php-invoker 1.1.4-3.

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<?php
/*
 * This file is part of the PHP_Invoker package.
 *
 * (c) Sebastian Bergmann <sebastian@phpunit.de>
 *
 * For the full copyright and license information, please view the LICENSE
 * file that was distributed with this source code.
 */

/**
 * @since      Class available since Release 1.0.0
 */
class PHP_Invoker_TimeoutException extends RuntimeException
{
}