Submit Function

gistfile1.php

<?php
  /**
   * Provide the default form form for submitting options.
   */
  function options_submit(&$form, &$form_state, &$options = array()) {
    // We filter the options on only selected ones.
    $options['flags'] = array_filter($options['flags']);
    $options['vocabularies'] = array_filter($options['vocabularies']);
  }