yum update fails after centos 6.4 to OL conversion

I suggest to try it with a default configuration to eliminate possible repository conflicts.

sudo su - root

cd /etc/yum.repos.d

rename .repo .repo_old *.repo

wget http://public-yum.oracle.com/public-yum-ol6.repo

yum clean all

yum update

What do you get when you type the following:

rpm -qa | grep ntpdate

rpm -qa | grep glibc-headers

I don't know then. It's difficult without having access to the machine and playing with a few commands myself. There is plenty of info on the web and you can Google how to resolve yum duplicates, etc. Perhaps some non standard yum repository messed up the yum database or perhaps you forced some installation, like glibc, that could screw things up. If this is a production system, I would rather install a new machine from scratch, using OL 6.4 and copying some of the configuration, rather than converting CentOS to OL. It can probably be done in a couple of hours, which may take less time than troubleshooting the current issue.