Most times I prefer to perform manual updates with YUM or automated ones using cron to launch YUM rather than use the desktop PackageKit. These can interfere with or be interfered with by the PackageKit software manager.
The typical symptoms of this are a warning message when doing a manual update that YUM is waiting for the lock file.The lock file is created by PackageKit so that only one process can access the YUM and RPM databases at a time.
To resolve this problem you need to disable automatic update checks for PackageKit.
Edit the file, /etc/yum/pluginconf.d/refresh-packagekit.conf and change “enabled=1″ to “enabled=0″ and you should be good to go.
It is also easy to remove PackageKit using the command below.
yum -y remove PackageKit
Be sure to use the spelling exactly as shown with the uppercase letters.