Yum Remove duplicate packages

During mayor upgrades on several systems I came along the bad situation with duplicate packages..

This helped me solve the issue of having duplicate packages installed. I only needed to add another flag to have:

rpm -e --justdb --nodeps <package-old_version>

Below you will find the steps to semi automate this, but beware, Your millage may vary, make sure you check the output that are put into the files.

Bottom of output from:

yum --assumeno upgrade
Warning: RPMDB altered outside of yum.
** Found 247 pre-existing rpmdb problem(s), 'yum check' output follows:
#(truncated)
chkconfig-1.7.4-1.el7.x86_64 is a duplicate with chkconfig-1.7.2-1.el7.x86_64
1:gmp-6.0.0-15.el7.x86_64 is a duplicate with 1:gmp-6.0.0-12.el7_1.x86_64
gobject-introspection-1.50.0-1.el7.x86_64 is a duplicate with gobject-introspection-1.42.0-1.el7.x86_64
grep-2.20-3.el7.x86_64 is a duplicate with grep-2.20-2.el7.x86_64
gzip-1.5-9.el7.x86_64 is a duplicate with gzip-1.5-8.el7.x86_64
pcre-8.32-17.el7.x86_64 is a duplicate with pcre-8.32-15.el7_2.1.x86_64
4:perl-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-5.16.3-291.el7.x86_64
4:perl-libs-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-libs-5.16.3-291.el7.x86_64
4:perl-macros-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-macros-5.16.3-291.el7.x86_64
shared-mime-info-1.8-3.el7.x86_64 is a duplicate with shared-mime-info-1.1-9.el7.x86_64
2:tar-1.26-32.el7.x86_64 is a duplicate with 2:tar-1.26-31.el7.x86_64

Put above package names (starting from packages listed) into:

vi yum-fix.txt

Suggested to run from yum, but doesn’t seem to help. maybe it does a bit..

yum-complete-transaction --cleanup-only
cat yum-fix.txt|grep "is a duplicate with" > yum-fix_dupe.txt
cat yum-fix.txt|grep -v "is a duplicate with" > yum-fix_manually.txt

Parse output of some packages that start with a number and colon:

cat yum-fix_dupe.txt |awk '{print $6}'|awk -F":" '{if ((length($1) != 1) && (length($1) != 2)) print $1}' > yum-fix_dupe2.txt
cat yum-fix_dupe.txt |awk '{print $6}'|awk -F":" '{if ((length($1) == 1) || (length($1) == 2)) print $2}' >> yum-fix_dupe2.txt

Remove old package version from rpm db:

for i in $(cat yum-fix_dupe2.txt);do rpm -e --justdb --nodeps $i;done

Remove last 2 columns from output, and put on same line:

cat yum-fix_dupe2.txt | awk -F"-[0-9]" '{print $1}' |tr '\n' ' ' > yum-fix_dupe2-reinstall.txt

Reinstall packages:

yum reinstall $(cat yum-fix_dupe2-reinstall.txt)

Don’t forget to go back and manually fix the non-duplicates above could have fixed them.. try yum upgrade to see if any more errors):

cat yum-fix_manually.txt
yum --assumeno upgrade

Ronny Roethof

Ronny Roethof
Your bio goes here. It shouldn't be super long but a good two sentences or two should suffice.

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Published on April 06, 2016