The fix, for people running version Komodo 4.0 or 4.1, is to tell the debugger not to use the alarm() function internally. Make sure the value of the
PERLDB_OPTS environment variable includes
alarm=0. You can set this either before Komodo is launched, or in
Preferences|Environment.
If anyone's wondering why, it's because I use the alarm() function to poll for a break command from the debugger client (usually Komodo) to see if I should set $DB::single to 1.
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