This is a long issue but I'll try to be as brief as possible. I have a server at InMotionhosting running CentOS and using WHM/cPanel.
A few weeks ago I started getting a report from "updatenow" that updating failed on the server. I got a really long log file in my Email and the last few lines of the log were:
I fixed this particular error by simply uninstalling all the Percona stuff, I had only tried to test their backup scripts, no big deal. I no longer got this message and the updates apparently went through the next time.
But then I started getting this message:
FIRST:
I also noticed that during this my Spamassassin settings were reset. And also when I logged in to WHM I get this message at the top of the screen:

So can anybody tell me what is going on and what needs updated/changed to stop getting these errors?
Thanks!
A few weeks ago I started getting a report from "updatenow" that updating failed on the server. I got a really long log file in my Email and the last few lines of the log were:
I received one or two of these messages a day, obviously it wasn't being fixed.[20130311.220751] Testing RPM transaction
[20130311.220754] file /usr/lib64/libmysqlclient.so.15.0.0 from install of MySQL50-shared-5.0.96-2.cp1136.x86_64 conflicts with file from package Percona-Server-shared-compat-5.5.20-rel24.1.217.rhel5.x86_64
[20130311.220754] file /usr/lib64/libmysqlclient_r.so.15.0.0 from install of MySQL50-shared-5.0.96-2.cp1136.x86_64 conflicts with file from package Percona-Server-shared-compat-5.5.20-rel24.1.217.rhel5.x86_64
[20130311.220754] W Exit Code: 254
[20130311.220754] ***** FATAL: Test install failed: file /usr/lib64/libmysqlclient.so.15.0.0 from install of MySQL50-shared-5.0.96-2.cp1136.x86_64 conflicts with file from package Percona-Server-shared-compat-5.5.20-rel24.1.217.rhel5.x86_64
[20130311.220754] file /usr/lib64/libmysqlclient_r.so.15.0.0 from install of MySQL50-shared-5.0.96-2.cp1136.x86_64 conflicts with file from package Percona-Server-shared-compat-5.5.20-rel24.1.217.rhel5.x86_64
[20130311.220754] The Administrator will be notified to review this output when this script completes
[20130311.220754] ***** FATAL: Error testing if the RPMs will install: Died at /usr/local/cpanel/scripts/updatenow.static line 12521.
[20130311.220754] see How to Fix RPM Installation Failures in WHM for more information
[20130311.220754] The Administrator will be notified to review this output when this script completes
[20130311.220754] E Detected events which require user notification during updatenow. Will send iContact the log
I fixed this particular error by simply uninstalling all the Percona stuff, I had only tried to test their backup scripts, no big deal. I no longer got this message and the updates apparently went through the next time.
But then I started getting this message:
I ran the script mentioned, and it did not resolved anything. I have a support ticket with InMotion and they were not able to resolve so far either. At the time they attempted to fix it, I got a slew of Email reports as follows:Problems were detected with cPanel-provided files which are RPM controlled.
If you did not make these changes intentionally, you can correct them by running:
> /usr/local/cpanel/scripts/check_cpanel_rpms --fix
The following RPMs are found to be altered from their original install state:
MySQL50-server,5.0.96,2.cp1136,/etc/init.d/mysql
FIRST:
SECOND:fatal,Downgrades to a previous major release are not permitted.
THIRD:An error was detected which prevented updatenow from completing normally.
Please review the enclosed log for further details
----------------------------------------------------------------------------------------------------
[20130409.100127] Detected version '11.36.0.21' from version file.
[20130409.100127] Target version set to '11.34.1.13'
[20130409.100127] E Blocker found: Downgrades to a previous major release are not permitted.
[20130409.100127] ***** FATAL: An attempt to up/downgrade to 11.34.1.13 was blocked. Please review blockers.
[20130409.100127] The Administrator will be notified to review this output when this script completes
[20130409.100127] E Detected events which require user notification during updatenow. Will send iContact the log
FOURTH:Problems were detected with cPanel-provided files which are RPM controlled.
If you did not make these changes intentionally, you can correct them by running:
> /usr/local/cpanel/scripts/check_cpanel_rpms --fix
The following RPMs are found to be altered from their original install state:
MySQL50-server,5.0.96,2.cp1136,/etc/init.d/mysql
Then I guess they just stopped trying, and I have been receiving the same error report daily about the RPM controlled files.Maintenance ended, however it did not exit cleanly (3328). Please check the logs for an indication of what happened
I also noticed that during this my Spamassassin settings were reset. And also when I logged in to WHM I get this message at the top of the screen:

So can anybody tell me what is going on and what needs updated/changed to stop getting these errors?
Thanks!