when I sa-learn on a folder of spam it takes almost no time and says "learned 1" no matter how many where in the file but when I do an sa-learn of ham, it works fine. Ideas?
What command line did you use? and what format is the mail in?
If you're giving sa-learn a file in mbox format containing multiple emails, you have to use "sa-learn --mbox".
By default sa-learn assumes input files are a single message per file in RFC 822 format.
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