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cPanel: Error: Package system can not be repaired automatically

If, like myself, you have recently upgraded the cPanel control panel system on your Red Hat Enterprise Linux 5.2 server and received the error message “Error: Package system can not be repaired automatically” when upgrading Apache, then it’s probably caused by a problem with either the RedHat Package Manager (RPM) or YUM. To fix it, first ensure that no RPM or yum updates are running:
ps auxwww | grep yum
ps auxwww | grep rpm

If any are running, find out why and kill -9 them if they are zombie processes. Now you just need to rebuild the RPM database:
rm /var/lib/rpm/__db.* -rf
rpm --rebuilddb

This process may take some time (between 1 and 30 minutes depending on your server speed and the number of packages installed). Once it’s completed, you should be able to upgrade without problems.


  1. Becca Becca

    I seem to be having this problem when I try re-building a profile in cPanel (I just want to install GD and Mod Security).

    However I am running Centos 5, so not sure if these commands would work, tried them and received nothing though.

    • Those commands should work on any of the (recently) RedHat Linux variants (such as RedHat Enterprise, CentOS or Fedora). The “ps auxwww | grep yum” and “ps auxwww | grep rpm” commands should return at least one result (the ps command that is currently running) – if you only get one result though, then yum and rpm aren’t running at the moment and so you’re getting a slightly different problem from myself.

      Have you tried looking in the cPanel forums at ? If you search for “Package system can not be repaired automatically”, you may find some useful resources. Unfortunately, I don’t have enough free time myself at the moment to assist other people (I’m spending over 12 hours away from home per day at the moment, so when I get home I just want to eat and sleep). However, if you do need assistance, let me know what sort of server you have (Dedicated or VPS) and which datacenter it is in ( etc) and which version of cPanel and I’ll try and make a recommendation.

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