Do not know why it is not working ...

The HTML:
<script src="http://code.jquery.com/jquery-1.9.1.js"></script>
<script src="http://example.com/scripts/loader.js"></script>

The PHP:
if ($something == $somethingelse) {
    echo ("<div id=\"errorMessage\">Some error message</div>);
}

The loader.js
function include (filename) {

	var js = document.createElement('script');

	js.setAttribute('type', 'text/javascript');
	js.setAttribute('src', filename);
	js.setAttribute('defer', 'defer');
	document.getElementsByTagName('HEAD')[0].appendChild(js);

	var cur_file = {};
	cur_file[window.location.href] = 1;

	if (!window.php_js) window.php_js = {};
	if (!window.php_js.includes) window.php_js.includes = cur_file;
	if (!window.php_js.includes[filename]) {
		window.php_js.includes[filename] = 1;
	} else {
		window.php_js.includes[filename]++;
	}

	return window.php_js.includes[filename];

}

include('http://example.com/scripts/PopUpMessages.js');

$(document).ready(function() {
	$("#errorMessage").PopUpMessages({
		textColor: '#ffffff',
		backgroundColor: '#ff5555',
		borderColor: '#800000'
	});
});

The PopUpMessages.js
(function($) {

	$.fn.PopUpMessages = function(options) {

		var defaults = {
			fadeInTime: '1000',
			fadeOutTime: '1000',
			textColor: '#333333',
			backgroundColor: '#ffdd55',
			borderColor: '#aa8800'
		};

		var options = $.extend(defaults, options);

		$(this).fadeIn(options.fadeInTime);

	};

})(jQuery);