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dnf conflicts with file from package


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When I try and run sudo dnf update I get a bunch of errors that state

... conflicts with file from package ...

So in researching the wonderful world of the web I found a suggestion to check for duplicates and if running the following command produces any results, you are in a bad way.

sudo dnf repoquery --duplicated

[[email protected] ~]$ sudo dnf repoquery --duplicated
Extra Packages for Enterprise Linux 8 - x86_64                                                                                                                                                    0.0  B/s |   0  B     00:00
Docker CE Stable - x86_64                                                                                                                                                                         0.0  B/s |   0  B     00:00
Failed to synchronize cache for repo 'epel', ignoring this repo.
Failed to synchronize cache for repo 'docker-ce-stable', ignoring this repo.
Last metadata expiration check: 0:39:17 ago on Tue 03 Nov 2020 11:49:50 AM EST.
kernel-devel-0:3.10.0-1127.10.1.el7.x86_64
kernel-devel-0:3.10.0-1127.13.1.el7.x86_64
kernel-devel-0:3.10.0-1127.18.2.el7.x86_64
kernel-devel-0:3.10.0-1127.19.1.el7.x86_64
kernel-devel-0:3.10.0-1127.el7.x86_64
[[email protected] ~]$ 

 So as you can see, I'm in a bad way.  Since I'm running this server on proxmox, I went to the GUI and backed up this virtual before I run the next command which "could" render the server inaccessible (so I need the ability to restore)

sudo dnf --disableplugin=protected_packages remove $(sudo dnf repoquery --duplicated --latest-limit -1 -q)

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Total                                                                                                                                                                                             1.3 MB/s | 755 MB     09:36
Running transaction check
Error: transaction check vs depsolve:
(flatpak-selinux = 1.6.2-3.el8_2 if selinux-policy-targeted) is needed by flatpak-1.6.2-3.el8_2.x86_64
rpmlib(RichDependencies) <= 4.12.0-1 is needed by flatpak-1.6.2-3.el8_2.x86_64
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'.
[[email protected] ~]$ 

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sudo dnf remove --duplicates

Tried again: 

sudo dnf install 'dnf-command(config-manager)' --allowerasing

Running transaction check
Error: transaction check vs depsolve:
(flatpak-selinux = 1.6.2-3.el8_2 if selinux-policy-targeted) is needed by flatpak-1.6.2-3.el8_2.x86_64
rpmlib(RichDependencies) <= 4.12.0-1 is needed by flatpak-1.6.2-3.el8_2.x86_64
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'.
[[email protected] ~]$    

 

-rw-r--r-- 1 root root  173 Jul 12  2019 google-chrome.repo
-rw-r--r-- 1 root root 1203 Dec 18  2019 epel-testing.repo
-rw-r--r-- 1 root root 1266 Dec 18  2019 epel-testing-modular.repo
-rw-r--r-- 1 root root 1104 Dec 18  2019 epel.repo
-rw-r--r-- 1 root root 1249 Dec 18  2019 epel-playground.repo
-rw-r--r-- 1 root root 1167 Dec 18  2019 epel-modular.repo
-rw-r--r-- 1 root root  928 Jun  2 21:02 CentOS-Media.repo
-rw-r--r-- 1 root root  338 Jun  2 21:02 CentOS-fasttrack.repo
-rw-r--r-- 1 root root  756 Jun  2 21:02 CentOS-Extras.repo
-rw-r--r-- 1 root root  668 Jun  2 21:02 CentOS-Debuginfo.repo
-rw-r--r-- 1 root root 1043 Jun  2 21:02 CentOS-CR.repo
-rw-r--r-- 1 root root  712 Jun  2 21:02 CentOS-Base.repo
-rw-r--r-- 1 root root  731 Jun  2 21:02 CentOS-AppStream.repo
-rw-r--r-- 1 root root 1075 Nov  3 15:15 epel.repo.rpmsave
-rw-r--r-- 1 root root  798 Nov  3 15:21 CentOS-centosplus.repo
-rw-r--r-- 1 root root  738 Nov  3 15:24 CentOS-HA.repo
-rw-r--r-- 1 root root  736 Nov  3 15:25 CentOS-PowerTools.repo
-rw-r--r-- 1 root root 1382 Nov  3 15:25 CentOS-Sources.repo
-rw-r--r-- 1 root root  743 Nov  3 15:27 CentOS-Devel.repo

Official Centos Repos

[Base] – The packages that make up Centos, as it is released on the ISOs. It is enabled by default

[Updates] – Updated packages to [Base] released after the Centos ISOs. This will be Security, BugFix, or Enhancements to the [Base] software. It is enabled by default

[Addons] – Contains packages required in order to build the main Distribution or packages produced by SRPMS built in the main Distribution, but not included in the main Red Hat package tree (mysql-server in Centos-3.x falls into this category). Packages contained in the addons repository should be considered essentially a part of the core distribution, but may not be in the upstream Package tree. It is enabled by default

[Contrib] – Packages contributed by the Centos Users, which do not overlap with any of the core Distribution packages. These packages have not been tested by the Centos developers, and may not track upstream version releases very closely. It is disabled by default

[Centosplus] – Packages contributed by Centos developers and the users. These packages might replace rpm’s included in the core distribution. You should understand the implications of enabling and using packages from this repository. It is disabled by default

[csgfs] – Packages that make up the Cluster Suite and Global File System. It is disabled by default

[Extras] – Packages built and maintained by the Centos developers that add functionality to the core distribution. These packages have undergone some basic testing, should track upstream release versions fairly closely and will never replace any core distribution package. It is enabled by default

[Testing] – Packages that are being tested prior to release, you should not use this repository except for a specific reason. It is disabled by default

You can have a look at the packages here:
http://dev.centos.org/centos/6/
http://dev.centos.org/centos/7/

Base Repository:

Updates Repository:

Addons Repository:

Contrib Repository:

Centosplus Repository:

CSGFS:

Extras:

Testing:

Section 2

Then tried 

sudo rpm --rebuilddb

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