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you can't really.. the browser sets its own timeout restrictions. I'd suggest emailing the user when the ftp operation is complete... potentially with a log of what happened. I'd also suggest only doing the email with log on larger amounts of data, the threshold between this would be determined by the impatience of your users and the speed of the connections involved..
is there maybe a way to count the number of seconds that pass while the ftp_put function is running and output something to the buffer to hold the browser from timing out?
I believe PHP hangs while it sends the data. So no. Is your page timing out instead of the browser? Because that's a different thing.. set_time_limit() can tell php to allow more time for the script to execute.