I had R.java file in my android application. But I don't know, It is delete some how. To create it again I clean my project and also Rebuild my project by clicking on Build Project. I do not know what is the problem. It is not getting created again. Generally It gets created automatically whenever I build project.
If you are facing this problem after updating ADT, you should install that Android Build Tools . In my case installing Build Tools and restarting eclipse solved this problem.