cPanel: Error: Package system can not be repaired automatically

June 7th, 2009 by Richy B. Leave a reply »

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.

This post is over 6 months old.

This means that, despite my best intentions, it may no longer be accurate.

This blog holds over 12 years of archived content - during that time, I may have changed my opinion of something, technology will have advanced (and old "best standards" may no longer be the case), my technology "know how" has improved etc etc - it would probably take me a considerable amount of time to update all the archival entries: and defeat the point of keeping them anyway.

Please take these posts for what they are: a brief look into my past, my history, my journey and "caveat emptor".


  1. Becca says:

    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.

    • Richy C. says:

      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.

%d bloggers like this: