How do I fix duplicated packages issue

Issue

Sometimes after incorrect updates duplicated packages appear in the system

In some occasions you may have an error such as "is a duplicate with". In such case, you will need to remove the duplicates from yum.

For example:

<...>
alt-python27-2.7.13-3.el6.x86_64 is a duplicate with alt-python27-2.7.11-7.el6.x86_64
alt-python27-2.7.13-4.el6.x86_64 is a duplicate with alt-python27-2.7.13-3.el6.x86_64
alt-python27-libs-2.7.13-3.el6.x86_64 is a duplicate with alt-python27-libs-2.7.11-7.el6.x86_64
alt-python27-libs-2.7.13-4.el6.x86_64 is a duplicate with alt-python27-libs-2.7.13-3.el6.x86_64
<...>

Environment

CloudLinux OS 6(h)/7(h)/8

Solution

Make sure that you have yum-utils installed before you continue:

yum install yum-utils -y

We can check the full list of dupes by running:

package-cleanup --dupes | tail -n +3

Number of dupes:

package-cleanup --dupes | tail -n +3 | wc -l

The following command will scan for dupes, but it will also remove the older of each pair to correct the issue:

package-cleanup --cleandupes

An alternative way to remove the duplicates (in case the above command did not help):

package-cleanup --dupes | tail -n +3 | sort --version-sort | awk 'NR % 2 {print "rpm -e --justdb --nodeps " $1 } !(NR % 2) {match($0, "-[0-9]");print "yum -y reinstall " substr($0,0,RSTART-1)}' | sh

Depending on your situation, you may get the following error:

Warning: Some duplicates were not removed because they are required by installed packages.
You can try --cleandupes without --removenewestdupes, or review them with --dupes and remove manually.

To resolve this, execute the following command:

package-cleanup --cleandupes --removenewestdupes

If this command still shows errors, you can try to reinstall the packages. Replace packagename with the actual packagename you want to reinstall.

yum reinstall <packagename>

In some rare cases, you can face a different error during the yum update:

Running transaction check
To diagnose the problem, try running: 'rpm -Va --nofiles --nodigest'.
You probably have corrupted RPMDB, running 'rpm --rebuilddb' might fix the issue.
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.

In such case, try to use "yum update -v" (verbose flag) to see the actual error:

Running transaction check
Error: transaction check vs depsolve:
kernel-core-uname-r = 4.18.0-477.10.1.lve.el8.x86_64 is needed by (installed) kernel-1:4.18.0-477.10.1.lve.el8.x86_64
kernel-modules-uname-r = 4.18.0-477.10.1.lve.el8.x86_64 is needed by (installed) kernel-1:4.18.0-477.10.1.lve.el8.x86_64

The root cause is the kernel duplicate packages which are not counted by the package-cleanup utility as duplicates, for example:

# rpm -qa | grep kernel-4.18.0-477.10.1.lve.el8.x86_64
kernel-4.18.0-477.10.1.lve.el8.x86_64
kernel-4.18.0-477.10.1.lve.el8.x86_64

In such cases, you can remove it manually using:

# rpm -e --nodeps --allmatches kernel-4.18.0-477.10.1.lve.el8

And reinstall if needed, using:

# yum install kernel