Error updating from 3.0.1.8 - Error: Package ntp-4.2.6p5-10.el6.centos.1.x86_64 (@updates)

[phideauxx]

On my first attempt to update from 3.0.1.8 to 3.0.1.9 it failed with "cannot allocate memory" errors. After rebooting and trying again more recently (now with 3.0.2.1 released) I am seeing a different error message. From looking at others' logs of their working installs everything above this looks normal, up until this "Error: Package: ntp....." below. How do I fix this?

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---> Package yum-utils.noarch 0:1.1.30-37.el6 will be updated
---> Package yum-utils.noarch 0:1.1.30-40.el6 will be an update
--> Running transaction check
---> Package libkadm5.x86_64 0:1.10.3-65.el6 will be installed
---> Package ntpdate.x86_64 0:4.2.6p5-10.el6.centos.1 will be updated
--> Processing Dependency: ntpdate = 4.2.6p5-10.el6.centos.1 for package: ntp-4.2.6p5-10.el6.centos.1.x86_64
--> Finished Dependency Resolution
Error: Package: ntp-4.2.6p5-10.el6.centos.1.x86_64 (@updates)
           Requires: ntpdate = 4.2.6p5-10.el6.centos.1
           Removing: ntpdate-4.2.6p5-10.el6.centos.1.x86_64 (@updates)
               ntpdate = 4.2.6p5-10.el6.centos.1
           Updated By: ntpdate-4.2.6p5-10.el6.centos.2.x86_64 (base)
               ntpdate = 4.2.6p5-10.el6.centos.2
 You could try using --skip-broken to work around the problem
** Found 11 pre-existing rpmdb problem(s), 'yum check' output follows:
GeoIP-GeoLite-data-2016.07-1.el6.noarch has missing requires of GeoIP-GeoLite-data-extra = ('0', '2016.07', '1.el6')
GeoIP-GeoLite-data-2017.01-1.el6.noarch is a duplicate with GeoIP-GeoLite-data-2016.07-1.el6.noarch
kexec-tools-2.0.0-300.el6_8.2.x86_64 is a duplicate with kexec-tools-2.0.0-300.el6_8.1.x86_64
libblkid-2.17.2-12.24.el6_8.3.x86_64 is a duplicate with libblkid-2.17.2-12.24.el6_8.1.x86_64
libtiff-3.9.4-21.el6_8.x86_64 is a duplicate with libtiff-3.9.4-18.el6_8.x86_64
libuuid-2.17.2-12.24.el6_8.3.x86_64 is a duplicate with libuuid-2.17.2-12.24.el6_8.1.x86_64
ntp-4.2.6p5-10.el6.centos.2.x86_64 is a duplicate with ntp-4.2.6p5-10.el6.centos.1.x86_64
ntp-4.2.6p5-10.el6.centos.2.x86_64 has missing requires of ntpdate = ('0', '4.2.6p5', '10.el6.centos.2')
openssl-1.0.1e-48.el6_8.4.x86_64 is a duplicate with openssl-1.0.1e-48.el6_8.3.x86_64
selinux-policy-3.7.19-292.el6_8.3.noarch is a duplicate with selinux-policy-3.7.19-292.el6_8.2.noarch
util-linux-ng-2.17.2-12.24.el6_8.3.x86_64 is a duplicate with util-linux-ng-2.17.2-12.24.el6_8.1.x86_64
Update to Version 3.0.1.9 FAILED.  Updates cancelled.
Please visit http://www.efa-project.org for more information.
sendmail: fatal: root(0): No recipient addresses found in message header
Update to Version 3.0.1.9 FAILED. Updates cancelled.
Please visit http://www.efa-project.org for more information.
/var/EFA/update/EFA-update-script died with exit status 1

[phideauxx]

I found the solution to my problem on another forum.
I had tried

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 yum-complete-transaction

as was suggested by yum output, but that didn't help as it appears it was too late for that since I had tried updating multiple times without running that first it created some duplicate package stuff.

What worked was

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package-cleanup --dupes

to see which packages had duplicates because of previous update failures

Followed by

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package-cleanup --cleandupes

to actually clean up the duplicates.

Then I ran the update again as normal and all proceeded as it should.

Here is a link to where I found this info.
https://serverfault.com/questions/65460 ... ntp-update