60 seconds time out?

[immediate]

When I try to run some actions against a very large table, phpmyadmin keeps giving me 60 seconds time out errors. The action performed will or will not properly finish. However, if I go in mysql command line the actions are correctly performed albeit taking quite some time.

Is there any way I can make phpmyadmin to wait until action is correctly performed? My current phpmyadmin version is 3.5.1. Tried to add set_time_limit() in config.inc.php but it doesn't seem to work. It's weird. Any help would be appreciated.