I read the FAQ and saw something about using a different user to run sa-learn and that it might cause issues WRT to Bayes. Is this correct ?
Yes, this is correct, unless you over-ride the bayes_path and file mode.
I'm running sa-learn as "root" and spamd as "spamd" (UID 196).
Unless spamd and root have the same home directory, by default your training will not be used by spamd.
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