The process failed similarly on two machines, with many duplicated packages and dependency errors or conflicts. On both machines,
rpm -q suggests that two different OS versions are present:
When I now run "yum update" on one of them it begins with[root@www ~]# uname -a
Linux http://www.uoxray.uoregon.edu 2.6.32-358.18.1.el6.i686 #1 SMP Wed Aug 28 14:27:42 UTC 2013 i686 i686 i386 GNU/Linux
[root@www ~]# rpm -q centos-release
centos-release-6-4.el6.centos.10.i686
centos-release-6-5.el6.centos.11.2.i686
[root@www ~]#
and ends with a long list of duplicated packages. I'll be happy to post that list if it would help.--> Running transaction check
---> Package ca-certificates.noarch 0:2010.63-3.el6_1.5 will be updated
---> Package ca-certificates.noarch 0:2013.1.95-65.1.el6_5 will be an update
--> Processing Dependency: p11-kit-trust >= 0.18.4-2 for package: ca-certificates-2013.1.95-65.1.el6_5.noarch
---> Package openssl.i686 0:1.0.1e-16.el6_5 will be updated
---> Package openssl.i686 0:1.0.1e-16.el6_5.1 will be an update
--> Running transaction check
---> Package p11-kit-trust.i686 0:0.18.5-2.el6 will be installed
--> Processing Conflict: p11-kit-trust-0.18.5-2.el6.i686 conflicts nss < 3.14.3-33
--> Finished Dependency Resolution
Error: p11-kit-trust conflicts with nss-3.14.3-4.el6_4.i686
You could try using --skip-broken to work around the problem
The results of getinfo.sh are posted at http://molbio.uoregon.edu/~remington/basedata.aZMU37
I've looked through some old posts that reveal similar problems and this looks like a difficult issue to fix, so any hints would be much appreciated!