jquery fadeIn not working

Unless the element is hidden, no fade will occur, you need something like this:

$(".warning").hide().fadeIn(4000);

You can give it a try here, also $() is deprecated in 1.4+, you should use $(document) or the shorter version, like this:

$(function() {
  $(".warning").hide().fadeIn(4000);
});

The alternative is to give the element a display: none initially but this breaks for JS-disabled users, or if JavaScript errors occur preventing the fade, so you may want to steer clear of this approach.