I have the following slow query information setup in mysql.
SHOW VARIABLES LIKE '%SLOW%';
Variable_name Value
log_slow_queries ON
slow_launch_time 2
slow_query_log ON
slow_query_log_file /var/log/mysql/slow-queries.log
The log file has the following premissions:
-rwxr-xr-x 1 root root 0 Sep 11 14:31 slow-queries.log
The my.cnf file looks like this:
back_log = 2000
slow_query_log = 1
slow_query_log_file = 1
long_query_time = 1
general_log = 1
log-slow-queries=/var/log/mysql/slow-queries.log
From mytop I can see that I have slow queries, but I don't see anything writing to the logs.
As others have suggested, your problem is probably because of the the permissions on the log file.
If mysql runs under the "mysql" user, as it normally does, you can change the file ownership thusly: