On OpenBSD 4.0 amd64, I built 2.6.1.4 with mysql support from sources. Since that didn't work, I used the snort-2.6.0.2.tar.gz distfile from ftp.openbsd.org, no luck there either. (Also in one case, I used the ports files for snort from 4.1 ports to make sure I didn't make any config mistakes.)
Since they all failed, on a fresh install of 4.1 amd64, I downloaded and installed snort-2.6.0.2p1-mysql package directly. But I ran into the same problem. The following is what snort spits out: ERROR: database: mysql_error: Can't connect to local MySQL server through socket '/var/run/mysql/mysql.sock' (2) Fatal Error, Quitting.. When this error occurs, I assure you that MySQL server runs fine (with snort database/tables created properly) and there is no file permission problems. After all, I am able to use mysql output plugin successfully with 2.4.5-mysql package on 4.0. (But I need 2.6.x.x on amd64 due to timestamp problem.) Therefore, if I have not been doing something terribly wrong in my many trials for the last couple of days, I think I'll conclude that mysql output plugin with 2.6.x.x is broken (at least on OpenBSD amd64). Has anybody else noticed the same issue?