Conflict With Rogue RPM

In this example, MySQL causes the installation process to fail:

[20130128.230346] Testing RPM transaction
[20130128.230348] error: Failed dependencies:
[20130128.230348] MySQL conflicts with *mysql-5.0.77-4.el5_4.2.i386*
[20130128.230348] W Exit Code: 254
[20130128.230348] ***** FATAL: Test install failed: error: Failed dependencies:
[20130128.230348] MySQL conflicts with mysql-5.0.77-4.el5_4.2.i386
[20130128.230348] The Administrator will be notified to review this output when this script completes
[20130128.230348] E Error testing if the RPMs will install: Died at /usr/local/cpanel/scripts/updatenow.static line 12517.
[20130128.230348] E Detected events which require user notification during updatenow. Will send iContact the log

Notice the version of MySQL in the update log. We can look closer at it with the following command: rpm -qa|grep mysql-5

# rpm -qa|grep mysql-5
mysql-5.0.77-4.el5_4.2

Then, we can compare that RPM to the other MySQL RPMs in the repository:

MySQL-server-5.5.28-2.cp.1132
MySQL-devel-5.5.28-2.cp.1132
MySQL-client-5.5.28-2.cp.1132
MySQL-test-5.5.28-2.cp.1132
MySQL-shared-5.5.28-2.cp.1132

The solution to this conflict is to remove the rogue RPM file and run the cPanel update process again.

Source: http://docs.cpanel.net/twiki/bin/view/AllDocumentation/InstallationGuide/RPMTroubleshoot

In order to resolve this cPanel support suggested running:

rpm -e --nodeps --justdb mysql-5.0.45-7.el5.i386
If done correctly, it will just drop you back to the prompt.  Then try your update again.
 

What the above command does is not actually erase any RPM or dependencies from your server. It just hides the installed RPM from the RPM database so that the cPanel updater doesn't see it and won't have a conflict with it when it goes to install the proper version of MySQL that it wants to install.


Source: http://blog.zweck.net/