I see this problem with 3.1.10.2:
% at midnight
Cannot open lockfile /var/spool/cron/atjobs/.SEQ: Permission denied
However, contrary to the original poster, atd is running on my system.
The rpoblem for me is that atjobs/.SEQ is owned by root:
% sudo ls -l /var/spool/cron/atjobs/.SEQ
-rw------- 1 root root 0 2008-10-22 10:17 /var/spool/cron/atjobs/.SEQ
On a stable system, it is owned by daemon.daemon. Changing ownership
back to daemon.daemon allows at to work again.
Andrew
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