jsFiddle Demo

This functionality is not possible with an alert. However, you could use a div

function tempAlert(msg,duration)

{

 var el = document.createElement(div);

 el.setAttribute(style,position:absolute;top:40%;left:20%;background-color:white;);

 el.innerHTML = msg;

 setTimeout(function(){

  el.parentNode.removeChild(el);

 },duration);

 document.body.appendChild(el);

}

Use this like this:

tempAlert(close,1000);