Remove all calls to domAutomationController.setAutomationId.

chrome/test/data/nacl/pnacl_url_loader/pnacl_url_loader.html

 <script>
 window.addEventListener('load', function() {
     init();
   }, false);
 
 function init() {
   var embed = document.createElement('embed');
   embed.addEventListener('message', function(message) {
-      window.domAutomationController.setAutomationId(0);
       window.domAutomationController.send(message.data);
     }, false);
   embed.addEventListener('load', function() {
       embed.postMessage(location.hash.substr(1));
     }, false);
   embed.src = 'pnacl_url_loader.nmf';
   embed.type = 'application/x-pnacl';
   document.body.appendChild(embed);
 }
 </script>