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In ~/.spamassassin/user_prefs add a line containing:
loadplugin HitFreqsRuleTiming HitFreqsRuleTiming.pm
Run spamassassin on an email.
Find timing.log in your current directory, containing the number of seconds each rule took to run, in the 2nd and 3rd columncolumns.
Warning: Enabling this will almost certainly slow down SpamAssassin. Possibly a lot (I haven't checked).