Replace theme() with drupal_render() in search module

$output['suffix']['#markup'] = '</ol>' . drupal_render(array('#theme' => 'pager'));

You can't do this kind of thing with drupal_render() or you'll get fatal errors.

You *must* declare your array and pass it to drupal_render() in two steps as drupal_render() will attempt to modify it by reference.

Eg:

$pager = array('#theme' => 'pager');
drupal_render($pager);

this looks good to me