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My theme is currently activated and showing only the background image and the "home" link. I believe the issue lies within header.php, but I can't quite figure out what. Any ideas? (Also, is there a php validator I could run my code through, or would a WP theme's code be too WP specific?)

<!DOCTYPE html>

    <meta http-equiv="Content-Type" content="<?php bloginfo('html_type'); ?>; charset=<?php bloginfo('charset'); ?>" />
    <meta name="generator" content="Wordpress <?php bloginfo('version'); ?>" />
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
    <title><?php bloginfo('name'); ?> <?php wp_title(); ?></title>
    <link rel="pingback" href="<?php bloginfo('pingback url'); ?>" />
    <link rel="alternate" type="application/rss+xml" title="RSS 2.0" href="<?php bloginfo('rss2_url'); ?>" />
    <link rel="stylesheet" href="<?php bloginfo('stylesheet_url'); ?>" />
    <link rel="shortcut icon" href="<?php bloginfo('template_directory'); ?>/img/favicon.ico" />
    <?php wp_head(); ?>

    <div id="header">
        <div class="logo">
            <a href="<?php bloginfo('url'); ?>"><img src="images/logo.png" alt="return to the home page" id="logo" /></a>
        </div><!-- end logo -->
        <div id="nav">
                <li><a href="<?php bloginfo('url'); ?>">Home</a></li>
                <?php wp_lists_pages('title_li=&include=9,5,60,62,64'); ?>
        </div><!-- end nav -->
    </div><!-- end header -->
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up vote 1 down vote accepted

wp_lists_pages is not a valid function, it's wp_list_pages (no s at end of list).

enable debugging in your wp-config.php file to see php errors

Edit: additional ifo

To answer your other question most advanced editors will check the syntax in your code and will flag errors. With a function spelling error you would need an advanced IDE like PhpStorm to check core WordPress functions and do code completion while you type.

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Wow three answers all at once... I'm deleting mine and adding to yours. – Chris_O May 17 '12 at 19:32
perfect, thank you! – user1255049 May 17 '12 at 19:34

Your php is simply outputting html, so start there. Try the W3C html/css validator at http://validator.w3.org/ and check "Show Source" under More Options.

Use Firebug with Firefox, or use the developer tools in Chrome or Safari or IE to see what's loading on your site.

Could be an html error, or javascript. Those tools are very good to use.

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