Duplicate Package - update / upgrade - Centos - centos

Question

When I try running yum update on a CentOS 6.3 box, I am getting errors, and says to run yum check. The output of yum check is:
➜ ~ yum check
Loaded plugins: fastestmirror
glibc-2.12-1.107.el6_4.5.x86_64 is a duplicate with glibc-2.12-1.107.el6_4.4.x86_64
glibc-common-2.12-1.107.el6_4.5.x86_64 is a duplicate with glibc-common-2.12-1.107.el6_4.4.x86_64
glibc-devel-2.12-1.107.el6_4.5.x86_64 is a duplicate with glibc-devel-2.12-1.107.el6_4.4.x86_64
glibc-devel-2.12-1.107.el6_4.5.x86_64 has missing requires of glibc-headers = ('0', '2.12', '1.107.el6_4.5')
iputils-20071127-17.el6_4.2.x86_64 is a duplicate with iputils-20071127-17.el6_4.x86_64
nspr-4.9.5-2.el6_4.x86_64 is a duplicate with nspr-4.9.2-1.el6.x86_64
nss-3.14.3-4.el6_4.x86_64 is a duplicate with nss-3.14.0.0-12.el6.x86_64
nss-softokn-3.14.3-3.el6_4.x86_64 is a duplicate with nss-softokn-3.12.9-11.el6.x86_64
nss-util-3.14.3-3.el6_4.x86_64 is a duplicate with nss-util-3.14.0.0-2.el6.x86_64
tzdata-2013g-1.el6.noarch is a duplicate with tzdata-2013c-2.el6.noarch
2:xinetd-2.3.14-39.el6_4.x86_64 is a duplicate with 2:xinetd-2.3.14-38.el6.x86_64
Error: check all
Any idea how to fix these packages? I tried yum reinstall xinetd tzdata nss-util nss-softokn nss nspr iputils glibc glibc-common glibc-devel but got:
Error: Multilib version problems found. This often means that the
root
cause is something else and multilib version checking is just
pointing out that there is a problem.

Answer 1

For me it looks like you rebooted your computer (or it crashed) while you where in the process of upgrading packages. So new packages where installed, but old packages where not removed.
First look if you have any uncomplete transactions with: yum-complete-transaction
If this doesn't help then take a look at the package-cleanup tool which is part of the yum-utils package.
package-cleanup --dupes lists duplicate packages
package-cleanup --cleandupes removes duplicate packages
But be carefull with the command and create a backup before removing duplicates.

Answer 2

This is the way I did fix one CentOS 7 server with 471 dupes.
First I had to install yum utils:
yum install yum-utils
Have tried yum-complete-transaction and other stuff without luck, I gave up the transaction with:
yum-complete-transaction --cleanup-only
Then I got a sorted list of duplicated packages so I could identify older versions to remove filtering even and odd lines later:
package-cleanup --dupes | sort -u > dupes.out
Then I got a uninstall list from this sorted file this way:
cat dupes.out | grep -v 'Loaded plugins:' | sort -u | awk 'NR % 2 == 1' > uninstall.in
Then I removed from rpm database the old versions:
for f in `cat uninstall.in`; do rpm -e --nodeps -f --justdb $f; done
Finally I could continue on regular system upgrade:
yum upgrade
Some things to pay attention:
On this case, I have carefully reviewed the "package-cleanup --dupes" output to make sure how to generate the uninstall list.
I have tried a "reinstall the newer" approach inverting the list (awk 'NR % 2 == 0') but there where lots of packages not available anymore at that version (server was left this way for an year).
I thought about removing from rpmdb the newer packages, so upgrade later should reinstall everything, but after checking on filesystem installed files, it was clear for me that new versions were in place, with only older rpm entries still in rpmdb. Maybe your case is different.

Answer 3

I was able to remove all duplicates by using yum shell:
I first ordered it to remove all packages using remove foo-package-*
Then order it to install previous version by specifying the exact version install foo-package-3.14.1-5.i386 foo-package-3.14.1-5.x86_64
Committing the transaction by run
After that, the duplicates were gone and I could update the system to current packages without problem and without introducing any new duplicates.
This works even for system packages like nss or yum.

Answer 4

Try running:
yum reinstall [package-new.version]
It is mean, if you get the output of yum check is:
# yum check
Loaded plugins: fastestmirror
nss-3.14.3-4.el6_4.x86_64 is a duplicate with nss-3.14.0.0-12.el6.x86_64
Do reinstall:
yum reinstall nss-3.14.3-4.el6_4.x86_64

Answer 5

A minor upgrade was interrupted by SSH disconnection. After handholding a few packages while trying to get other fixes to work, I ended up fixing the rest like so:
sudo yum reinstall --skip-broken $(/usr/bin/package-cleanup --dupes -q |sort)

Answer 6

First install yum utils and run cleanup afterwards to remove old duplicated packages
yum install yum-utils &&
package-cleanup –-cleandupes -y
hint:
sometimes you need to run package-cleanup –-cleandupes few times

Answer 7

A couple of months ago I also ran into this problem after upgrading my fedora.
I also tried the package-cleanup utility and it started removing required libs rendering my workstation unworkable. Luckily I could reinstall Fedora not deleting my home partition.
Yesterday the same problem occured and I fixed it removing the older version of the duplicate.
For example:
I got these duplicates:
oxygen-icon-theme-4.8.3-1.fc16.noarch is a duplicate with oxygen-icon-theme-4.8.2-1.fc16.noarch
sane-backends-libs-1.0.22-10.fc16.i686 is a duplicate with sane-backends-libs-1.0.22-8.fc16.i686
What I did is I used the yum remove sane-backends-libs-1.0.22-8.fc16.i686 and afterwards a yum update.
Everything is now working fine.
from http://forums.fedoraforum.org/showthread.php?t=268328

Answer 8

In my case nothing above has worked.
So after having the Duplicates list, I copied it to a Text Editor ...
And i did
yum upgrade {package name}
As I edited the whole list, I did it continuously ...
Example: yum upgrade sudo nano came mariadb, etc ...

Answer 9

what worked for me is :
1) getting the list of duplicated packages : package-cleanup --dupes
2) deleting manually old duplicates : rpm -e --justdb --nodeps {old-version-duplicated-package}
3) yum update