Oracle VM VirtualBox uninstall/install error-1 running transaction problem prevents me from using VirtualBox

^ As you can see above, this is the error I am receiving while trying to uninstall and reinstall VM VirtualBox. I suspect the reason this is occurring is because of deeper deletions I tried to do of Oracle’s software while trying to remove VirtualBox from my system. I also previously had Virtual Machine Manager and GnomeBoxes installed. VMM is now uninstalled, but Gnome Boxes is still installed (and working).

The reason I want to reinstall VirtualBox is because I have been unable to easily and quickly create a host-only network configuration in Gnome Boxes interface, which I need to do for some of the machines I want to create.

You can also see that in the top right hand corner of the image it says (null)(RPM) I’m not sure what that signifies either.

Any help regarding how to successfully get back to state where I can uninstall and reinstall VirtualBox would be appreciated.

I am currently using Fedora 36 with the Gnome desktop environment and Wayland.

  1. How did you install virtual box? From what repo? or was it compiled & installed manually?
  2. How did you remove the parts you did as deeper deletions. Did you remove things using the package manager (dnf) or manually?

If you removed things manually when they were installed as a package it can cause dnf to barf when it finds things that are not consistent.

I have always installed VirtualBox from the rpmfusion repo using dnf and it just works. I also removed it the same way (using dnf).

If you installed it from the rpmfusion repo then it is likely that the command sudo dnf reinstall VirtualBox* or maybe sudo dnf install VirtualBox* will reinstall everything needed. Removal is the same sudo dnf remove VirtualBox*

# dnf install VirtualBox*
Last metadata expiration check: 1:02:02 ago on Thu 28 Jul 2022 02:05:35 PM CDT.
Dependencies resolved.
======================================================================================================================================================
 Package                                  Architecture              Version                           Repository                                 Size
======================================================================================================================================================
Installing:
 VirtualBox                               x86_64                    6.1.34-4.fc36                     rpmfusion-free-updates                     21 M
 VirtualBox-devel                         x86_64                    6.1.34-4.fc36                     rpmfusion-free-updates                    6.6 M
 VirtualBox-kmodsrc                       noarch                    6.1.34-4.fc36                     rpmfusion-free-updates                    874 k
 VirtualBox-server                        x86_64                    6.1.34-4.fc36                     rpmfusion-free-updates                     18 M
 VirtualBox-webservice                    x86_64                    6.1.34-4.fc36                     rpmfusion-free-updates                    6.9 M
Installing dependencies:
 akmod-VirtualBox                         x86_64                    6.1.34-3.fc36                     rpmfusion-free-updates                     19 k
 gsoap                                    x86_64                    2.8.117-3.fc36                    fedora                                    713 k
 liblzf                                   x86_64                    3.6-23.fc36                       fedora                                     27 k
 python3-VirtualBox                       x86_64                    6.1.34-4.fc36                     rpmfusion-free-updates                    209 k

Transaction Summary
======================================================================================================================================================
Install  9 Packages

Total download size: 55 M
Installed size: 182 M
Is this ok [y/N]: n

Thanks for the response, originally, virtualbox I believe was installed manually from Oracle’s website. I originally removed it using the package manager, but there were still virtualbox files with virtualbox in the title that remained in /etc I believe. I manually went through and removed anything associated with virtualbox there and in the filing system in general.

sudo dnf install VirtualBox* returns quite a few errors, I’m assuming one set of these files needs to be removed or swaped? Not sure how to easily do that for all of them though:

Install 10 Packages

Total size: 55 M
Installed size: 182 M
Is this ok [y/N]: y
Downloading Packages:
[SKIPPED] gsoap-2.8.117-3.fc36.x86_64.rpm: Already downloaded
[SKIPPED] liblzf-3.6-23.fc36.x86_64.rpm: Already downloaded
[SKIPPED] sdl12-compat-0.0.1~git.20211125.4e4527a-4.fc36.x86_64.rpm: Already downloaded
[SKIPPED] akmod-VirtualBox-6.1.34-3.fc36.x86_64.rpm: Already downloaded
[SKIPPED] python3-VirtualBox-6.1.34-4.fc36.x86_64.rpm: Already downloaded
[SKIPPED] VirtualBox-6.1.34-4.fc36.x86_64.rpm: Already downloaded
[SKIPPED] VirtualBox-devel-6.1.34-4.fc36.x86_64.rpm: Already downloaded
[SKIPPED] VirtualBox-kmodsrc-6.1.34-4.fc36.noarch.rpm: Already downloaded
[SKIPPED] VirtualBox-server-6.1.34-4.fc36.x86_64.rpm: Already downloaded
[SKIPPED] VirtualBox-webservice-6.1.34-4.fc36.x86_64.rpm: Already downloaded
Running transaction check
Transaction check succeeded.
Running transaction test
Error: Transaction test error:
file /usr/bin/VBox from install of VirtualBox-server-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/bin/VBoxTunctl from install of VirtualBox-server-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/bin/rdesktop-vrdp from install of VirtualBox-server-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/bin/vbox-img from install of VirtualBox-server-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/bin/vboximg-mount from install of VirtualBox-server-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/lib/python3.10/site-packages/vboxapi/init.py from install of python3-VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/lib/python3.10/site-packages/vboxapi/pycache/VirtualBox_constants.cpython-310.opt-1.pyc from install of python3-VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/lib/python3.10/site-packages/vboxapi/pycache/VirtualBox_constants.cpython-310.pyc from install of python3-VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/lib/python3.10/site-packages/vboxapi/pycache/init.cpython-310.opt-1.pyc from install of python3-VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/lib/python3.10/site-packages/vboxapi/pycache/init.cpython-310.pyc from install of python3-VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/applications/virtualbox.desktop from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/128x128/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/16x16/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/20x20/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/32x32/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/40x40/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/48x48/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/icons/hicolor/64x64/apps/virtualbox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64
file /usr/share/pixmaps/VBox.png from install of VirtualBox-6.1.34-4.fc36.x86_64 conflicts with file from package VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64

Please run, and post here the output of
dnf list installed *VirtualBox*

Every package it names that contains 150636-fedora36 came from a non-fedora repo and should be removed to allow installing the ones from rpmfusion. (Ok, rpmfusion is technically not a fedora repo either, but it does contain packages that are specifically designed and tested to be fedora compatible.)

See below:

VirtualBox-6.1.x86_64-------------6.1.34_150636_fedora36-2-------------@@System

According to the error list you posted, you have

VirtualBox-6.1-6.1.34_150636_fedora36-2.x86_64

installed, and the VirtualBox package causes most of those errors.

Please run sudo dnf remove VirtualBox-6.1 and let us know if that works or not, and if there is anything else it wants to remove before you say “yes”.

Also let us see the output of dnf repolist

The following is the result of sudo dnf remove VirtualBox-6.1

The result of dnf repolist

This tells you exactly what failed. Is that one of the things you deleted?
Screenshot from 2022-07-28 16-35-52

Did you remove /usr/lib/virtualbox directory?

You might need to reinstall that package before you can remove it.

Yes, that is one of the directories I deleted. I’m trying to see how that can be reinstalled. Not sure how exactly to reinstall that one part.

As I said…

^ Yes I realize what you said, what I am saying is I’m not sure how to reinstall that particular package. I’m researching options at the moment, I’m also looking at my backups to see if there’s a way of restoring it from there. That’s the only option I can really think of.

Did you download the rpm then install it?
Did you install it from a web site?

If you downloaded it and have not deleted the .rpm file, then the simplest way to do a reinstall is to cd to the directory where that file is located, then sudo dnf upgrade ./VirtualBox-6.1-6.1.36_152435_fedora36-1.x86_64.rpm where the full file name goes after the ./ (I used the current file in that command, and not the one you actually have installed) If you have the older rpm file then use ‘reinstall’, but if you have to download it again then use ‘upgrade’.

If you have already deleted the rpm file then simply download it again and do the same with the new file.

The current rpm file can be found here
https://www.virtualbox.org/wiki/Linux_Downloads
and is named
VirtualBox-6.1-6.1.36_152435_fedora36-1.x86_64.rpm

Once it has been reinstalled/upgraded then you should be able to remove it.

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I installed the current rpm file at the link for Fedora 36, and then did the command you listed:

I got the result below, and I uninstalled it from the graphical interface. Then I reinstalled and everything works perfectly fine. I really appreciate your help (and patience in dealing with me) quite a lot. I’ve learned my lesson too. Even if I want something fully removed from my machine in the future, the answer is probably not to go around deleting related directories/files esp. in root:

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