Fix Fedora Multilib Version Problem (YUM / DNF)

So here is the Fedora fix for the multilib problem. I had run yum update in terminal when my laptop shutdown abnormally, causing the update to be interrupted. After rebooting and running the update again, I ran across this problem: 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

The Problem

After rebooting and running the update again, I got:

Protected multilib versions:
p11-kit-0.18.4-1.fc19.i686 != p11-kit-0.18.3-1.fc19.x86_64

This typically happens because:

Duplicate packages are installed
Different architectures (i686 vs x86_64) are out of sync
A previous update was interrupted

1. You have an upgrade for p11-kit which is missing some
dependency that another package requires. Yum is trying to
solve this by installing an older version of p11-kit of the
different architecture. If you exclude the bad architecture
yum will tell you what the root cause is (which package
requires what). You can try redoing the upgrade with
–exclude p11-kit.otherarch … this should give you an error
message showing the root cause of the problem.

2. You have multiple architectures of p11-kit installed, but
yum can only see an upgrade for one of those architectures.
If you don’t want/need both architectures anymore then you
can remove the one with the missing update and everything
will work.

3. You have duplicate versions of p11-kit installed already.
You can use “yum check” to get yum show these errors.

…you can also use –setopt=protected_multilib=false to remove
this checking, however this is almost never the correct thing to
do as something else is very likely to go wrong (often causing
much more problems).

Protected multilib versions: p11-kit-0.18.4-1.fc19.i686 != p11-kit-0.18.3-1.fc19.x86_64

This error was due to duplicate packages, so I was unable to run update again. After bit of research I came across the following solution.

1. Open Terminal and run following command

Start by syncing all packages to correct versions:

#Note: distro sync can be used to upgrade/downgrade the distribution
yum distro-sync

#Note: distro sync can be used to upgrade/downgrade the distribution
yum distro-sync

2. If the issue persists, try the following

yum check

yum check

It gave the list of packages that caused the problem, Something like

bluez-libs-4.101-8.fc19.x86_64 is a duplicate with bluez-libs-4.101-6.fc19.x86_64
2:cheese-libs-3.8.2-4.fc19.x86_64 is a duplicate with 2:cheese-libs-3.8.2-3.fc19.x86_64
clutter-1.14.4-4.fc19.x86_64 is a duplicate with clutter-1.14.4-2.fc19.x86_64
fuse-libs-2.9.2-4.fc19.x86_64 is a duplicate with fuse-libs-2.9.2-3.fc19.x86_64
glusterfs-3.4.0-0.6.beta3.fc19.x86_64 is a duplicate with glusterfs-3.4.0-0.5.beta2.fc19.x86_64
glusterfs-api-3.4.0-0.6.beta3.fc19.x86_64 is a duplicate with glusterfs-api-3.4.0-0.5.beta2.fc19.x86_64
1:grub2-tools-2.00-23.fc19.x86_64 is a duplicate with 1:grub2-tools-2.00-22.fc19.x86_64
gvfs-1.16.3-2.fc19.x86_64 is a duplicate with gvfs-1.16.3-1.fc19.x86_64
1:java-1.7.0-openjdk-1.7.0.25-2.3.10.4.fc19.x86_64 is a duplicate with 1:java-1.7.0-openjdk-1.7.0.25-2.3.10.3.fc19.x86_64
2:libcacard-1.4.2-4.fc19.x86_64 is a duplicate with 2:libcacard-1.4.2-3.fc19.x86_64
libpwquality-1.2.2-1.fc19.x86_64 is a duplicate with libpwquality-1.2.1-2.fc19.x86_64
libsss_idmap-1.10.0-12.fc19.beta2.x86_64 is a duplicate with libsss_idmap-1.10.0-11.fc19.beta2.x86_64
os-prober-1.58-3.fc19.x86_64 is a duplicate with os-prober-1.58-1.fc19.x86_64
p11-kit-0.18.4-1.fc19.x86_64 is a duplicate with p11-kit-0.18.3-1.fc19.x86_64
policycoreutils-2.1.14-46.4.fc19.x86_64 is a duplicate with policycoreutils-2.1.14-45.fc19.x86_64
poppler-0.22.1-4.fc19.x86_64 is a duplicate with poppler-0.22.1-3.fc19.x86_64
2:qemu-common-1.4.2-4.fc19.x86_64 is a duplicate with 2:qemu-common-1.4.2-3.fc19.x86_64
2:qemu-img-1.4.2-4.fc19.x86_64 is a duplicate with 2:qemu-img-1.4.2-3.fc19.x86_64
sane-backends-1.0.23-11.fc19.x86_64 is a duplicate with sane-backends-1.0.23-10.fc19.x86_64
sane-backends-libs-1.0.23-11.fc19.x86_64 is a duplicate with sane-backends-libs-1.0.23-10.fc19.x86_64
selinux-policy-3.12.1-57.fc19.noarch is a duplicate with selinux-policy-3.12.1-54.fc19.noarch
spice-glib-0.20-1.fc19.x86_64 is a duplicate with spice-glib-0.19-1.fc19.x86_64
Error: check all

3. Now remove the packages that caused the conflict.

For example consider the package:

spice-glib-0.20-1.fc19.x86_64 is a duplicate with spice-glib-0.19-1.fc19.x86_64

now you can remove the second one that is of older version using

yum remove spice-glib-0.19-1.fc19.x86_64

yum remove spice-glib-0.19-1.fc19.x86_64

do this for all package

4. Clean Cache and Update

Once duplicates are removed:

yum clean all
yum update

yum clean all
yum update

At this point, your system should update normally.

Important Notes

Avoid using:

--setopt=protected_multilib=false

This disables safety checks and can break your system further.

Always remove the older version, not the newer one.
Interrupted updates are the most common cause, so try to avoid shutting down during upgrades.

Update:

If you’re using newer versions of Fedora, replace yum with:

dnf distro-sync
dnf check
dnf remove <package>

Final Thoughts

This issue looks scary at first, but it usually comes down to duplicate or mismatched packages.

Once you clean those up, Fedora works perfectly again.

If you have a cleaner or automated approach, feel free to improve this workflow.