Warning messages don't go to STDOUT, and the redirection you're using only redirects STDOUT to a file. This is typically a good thing, since it's nice to be able to have all of your prints, for example, be saved in a file while your warnings are not.

You can either use the shell to redirect such warnings to a file, as others have explained, or in your code you can set up a signal handler for warnings:

open WARN, '> warnings.txt' or die ("Cannot write warnings.txt: $!");
local $SIG{__WARN__} = sub { print WARN @_,"\n" };
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Or, even easier IMO, redirect STDERR, so that everything written there (which includes warnings) will be written to a file.

open WARN, '> warnings.txt' or die ("Cannot write warnings.txt: $!");
*STDERR = *WARN;
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