I'm responsible for a couple of CPanel/WHM managed dedicated servers.
We keep them updated, and try to do as little customization as possible outside of what cPanel knows about. We enabled mod_proxy_fcgi and PHP-FPM, so we can use Apache 2.4 MPM Event for our fairly high traffic web site. It's a unfortunate that CPanel doesn't have this configuration available out of the box, but that's for another blog post.
Today early in the morning we got a message from our lfd daemon (a service installed by a free ConfigServer Security & Firewall CPanel plugin installed by our hosting provider):
The following list of files have FAILED the md5sum comparison test. This means that the file has been changed in some way. This could be a result of an OS update or application upgrade. If the change is unexpected it should be investigated:
The funny thing is, nothing upgraded any RPM files in this time window, our /var/log/yum.log didn't mention any upgrades to ghostscript package that provides the /usr/bin/gs binary (/usr/bin/ghostscript is a symlink to gs), we have disabled automatic updates that can be initiated by the cpanel upcp --cron sciprt, but the system us regulagrly kept up to date manually with yum update.
I've reinstalled the package with yum reinstall ghostscript (ghostscript-8.70-19.el6.x86_64 was reinstalled)
and the binary size and md5sum changed like this:
size: 19152 bytes
size: 6760 bytes
This is what actually happened: Our managed hosting provider had apparently changed our setup to upgrade our system packages automatically (probably with best intentions due to recent gnutls issue). And prelinking seems to be enabled on our system, so when upcp (CPanel automatic upgrade cron script that runs periodically) executed /usr/local/cpanel/scripts/rpmup to upgrade system packages, it also did the prelinking step, adding extra prelinking stuff to our /usr/bin/gs binary.
Similar issue described here: