> 1.Getting the following messages:
>  spamd[28788]: Still running as root: user not specified, not found, or set
> to root.  Fall back to nobody.
> 
>     How do I fix this?

start spamd with the option -u whatever-user-you-want

> 2.What config files does it actually read in order to run in a sitewide
> mode?  /etc/mail/spamassin ?

I am not sure what you mean.

My sitewide conf file is /etc/mail/spamassassin/local.cf (it may have
changed in newer version of SA).
 
> 3.I believe it is working because I see it has created some
> /home/user/spamtrap files and dumped SPAM into those.  Is there a way to
> consolidate these files into a single file?  I would like all spam to either
> go in one directory or one big file. Eventually I may give users control
> over things, but for now I don't want to.

It depends on your MDA.

If you use procmail, you could have, in /etc/procmailrc, a receipt like:

:0:
* ^X-Spam-Status: Yes
/var/mail/spamtrap

to put all the spam in a single /var/mail/spamtrap file, or:

:0:
* ^X-Spam-Status: Yes
/var/mail/spamtrap
$DEFAULT-spam

to put the spam in a file /var/mail/<username>-spam file per user.

And for future use, I wrote some scripts that quarantine spam and
deliver a summary to users, so they can recover spam through email
http://www.cs.ait.ac.th/laboratory/email/quarantine.shtml

> 4.Recommended procedure for taking the redhat-rc-script.sh and making it a
> startup script?

I don't use Linux.

Olivier

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