Since the beginning of time, cPanel has had logs that it simply does not rotate properly. Why this has been an ongoing problem that has never been fixed is beyond me, but it CAN be fixed and we'll go through what is needed to accomplish this.

The most important logs that are missed are the Apache system logs that are located in /usr/local/apache/logs. SSH into your server as root.

pico /etc/logrotate.d/httpd
(on some servers this file is called apache)

The first line should read:

/usr/local/apache/logs/*log {

Also you need to change the line that reads:

/bin/kill -HUP `cat /var/run/httpd.pid 2>/dev/null` 2> /dev/null || true

to:

/bin/kill -HUP `cat /usr/local/apache/logs/httpd.pid 2>/dev/null` 2> /dev/null || true
(the above line should all be on ONE LINE!)

The next log file that needs to be dealt with is /var/log/xferlog.  This is your FTP transfer log.

pico /etc/logrotate.d/ftp

This will create a new file.  If you are running ProFTP, paste the following snippet into this file:

/var/log/xferlog {
postrotate /bin/kill -HUP `cat /var/run/pure-ftpd.pid 2> /dev/null` 2> /dev/null || true
endscript
missingok
}

The next item we need to deal with is for any sites for which you have installed SSL certificates for.  If you have not installed any SSL certificates, then you can skip this section.  Any domain that you have installed an SSL certificate for gets a log file for tracking SSL traffic and it is located in /var/log.  These are pretty simple to add.

pico /etc/logrotate.conf

Add an entry styled like the one below for each secure domain you have on your server at the end of the file:

/var/log/securedomain.tld {
weekly
rotate 1
}

Take a look in /var/log to make sure that you have the proper filename i that first line.  It will match exactly as you have it set up in WHM.

One other stray log that cPanel ignores is /var/log/chkservd.log.  Add this section to the same file (/etc/logrotate.conf) that you were just editing:

/var/log/chkservd.log {
weekly
rotate 1
}

To add insult to injury, cPanel is not rotating its own logs either.  Place this in the same file we have been editing:

/usr/local/cpanel/logs/stats_log {
weekly
rotate 1
}

/usr/local/cpanel/logs/access_log {
weekly
rotate 1
}

/usr/local/cpanel/logs/error_log {
weekly
rotate 1
}

That is all the logs in my systems that I found that were not getting rotated.  Armed with this information you should be able to rotate nearly any log, but if you do find some more, please drop me a line so I can update the article.