[Plugin: Theme-Check] Invalid warnings

I’m getting a bunch of warnings from theme check that don’t appear to be true:

REQUIRED: Could not find wp_list_comments. See: wp_list_comments
 <?php wp_list_comments( $args ); ?>
REQUIRED: Could not find wp_link_pages. See: wp_link_pages
 <?php wp_link_pages( $args ); ?>
REQUIRED: Could not find wp_head. See: wp_head
 <?php wp_head(); ?>
REQUIRED: Could not find register_sidebar() or register_sidebars(). See: register_sidebar
 <?php register_sidebar( $args ); ?>
REQUIRED: Could not find dynamic_sidebar. See: dynamic_sidebar
 <?php dynamic_sidebar( $index ); ?>
REQUIRED: Could not find comments_template. See: comments_template
 <?php comments_template( $file, $separate_comments ); ?>
REQUIRED: Could not find comment_form. See: comment_form
 <?php comment_form(); ?>
REQUIRED: Could not find body_class call in body tag. See: body_class
 <?php body_class( $class ); ?>
REQUIRED: Could not find add_theme_support( 'automatic-feed-links' ). See: add_theme_support
 <?php add_theme_support( $feature ); ?>

Here are a couple of greps from my theme to show what I’m talking about:

comments.php:                                                   <?php wp_list_comments (array ('callback' => array ($ewlFramework, 'commentCallback'))); ?>

content-front-page.php:                                                         wp_link_pages (array ('before' => '<div class="page-link"><span>' . __ ('Pages', EWL_FRAMEWORK_TEXTDOMAIN) . ':</span>', 'after' => '</div>'));
content-single.php:                                                             wp_link_pages (array ('before' => '<div class="page-link"><span>' . __ ('Pages', EWL_FRAMEWORK_TEXTDOMAIN) . ':</span>', 'after' => '</div>'));
content.php:                                                            wp_link_pages (array ('before' => '<div class="page-link"><span>' . __ ('Pages', EWL_FRAMEWORK_TEXTDOMAIN) . ':</span>', 'after' => '</div>'));

header.php:     <?php wp_head (); ?>

framework/Framework.php:                if (function_exists ('register_sidebar')) {
framework/Framework.php:                        register_sidebar (array (
framework/Framework.php:                                register_sidebar (array (

http://wordpress.org/extend/plugins/theme-check/