yum duplicate package
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Repair duplicate rpm package is not an easy task. In this post we will learn on how to repair duplicate rpm in Centos system. Before this we have learn how to recover wrongly set permission on Centos 7.

Recently I have encounter problem with duplicate rpm issue in one of my server using Centos. The problem was caused by sudden server reboot during yum update. This cause server to have multiple duplicate rpm across the system.

We cannot continue to run the yum update because stuck at the following error example below;

1:ea-php73-php-pdo-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-pdo-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-pgsql-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-pgsql-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-posix-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-posix-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-process-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-process-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-pspell-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-pspell-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-soap-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-soap-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-sockets-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-sockets-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-xml-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-xml-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-xmlrpc-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-xmlrpc-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-php-zip-7.3.13-1.el7.cloudlinux.1.x86_64 is a duplicate with 1:ea-php73-php-zip-7.3.11-1.el7.cloudlinux.x86_64
1:ea-php73-runtime-7.3.13-1.el7.cloudlinux.x86_64 is a duplicate with 1:ea-php73-runtime-7.3.11-1.el7.cloudlinux.x86_64

To check the list of the duplication use command below;

# package-cleanup --dupes

Use below command to write to file what is the list of the duplicate files;

#package-cleanup --dupes | tail -n +3 > duplicate.txt

Using ‘cat’ command to read the list.

The idea is to remove the lowest version of the package from rpm database (rpmdb).
Then reinstall back the highest version of the package.

The command should be like;

rpm -e --justdb --nodeps PKGNAME
yum -y reinstall PKGNAME

Example ;

rpm -e --justdb --nodeps ea-nghttp2-1.39.2-1.el7.cloudlinux.1.x86_64
yum -y reinstall ea-nghttp2

It is the best to check the command before real operation;

cat duplicate.txt | 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)}'

Also can write the command to file;

cat duplicate.txt | 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)}' > reinstall.txt

The content of the reinstall.txt file will be similar like ;

rpm -e --justdb --nodeps ea-php73-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73
rpm -e --justdb --nodeps ea-php73-php-bcmath-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-bcmath
rpm -e --justdb --nodeps ea-php73-php-bz2-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-bz2
rpm -e --justdb --nodeps ea-php73-php-cli-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-cli
rpm -e --justdb --nodeps ea-php73-php-common-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-common
rpm -e --justdb --nodeps ea-php73-php-curl-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-curl
rpm -e --justdb --nodeps ea-php73-php-dba-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-dba
rpm -e --justdb --nodeps ea-php73-php-devel-7.3.11-1.el7.cloudlinux.x86_64
yum -y reinstall ea-php73-php-devel

Download duplicate.txt and reinstall.txt if required. reinstall.txt is useful if we want to install high priority package manually. Manual install is the most recommended way if there are not to many duplicate and you are not an expert system admin.
Wrongly remove package can render your server unbootable of problem with multilib issue.

If you know what are you doing then you can just run below command to repair duplicate rpm.

cat duplicate.txt | 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

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