To put it concisely, there is no action included in those updates that can instruct the deletion of /var/log/dpkg.log and /var/log/apt/history.log.
@ajo001 has done an amazing job of sorting through this with you and each step of the way, we are seeing indications of the same thing as above:
What this most looks like to me is a mild hardware failure that led to file or disk corruption.
While I would not call it "common", it is "common enough" across all operating systems. The majority of us have experienced corruptions from downloads or during installations across a wide variety of O.S.'s and across Web browsers over the years.
@Mr_Magoo , you did point out during the troubleshooting that Saved Snapshots exist.
If that is available, it may save you a lot of headache in restoring your system to a state prior to the updates.
Otherwise, I would recommend a fresh re-install of your copy of Zorin OS.
That is exactly what I would do in your situation. As @ajo001 pointed out, you are tunneling down a rabbit hole that each attempt can actually result in more cascading problems.
@Aravisian@Mr_Magoo,
I wonder if the contents of this script that was run may have something to do with the problem at hand? It seems a bit on the heavy-handed side to run such a comprehensive update/upgrade process that I believe is already mostly automated by the system.
It is mostly redundant, actually.
It includes several commands to upgrade.
It refreshes Snap and Flatpak, though I could swear I previously saw Mr Magoo say he removed Flatpak and Snap from his system.
The full command script is harmless, though and I do not see a way it could tangle or corrupt system files.
Ah, I see. No worries and glad it doesn't tangle things up as you said. I just thought that the purge command was a little erroneous, I didn't know what would be purged if nothing was specifically identified for the purge process.
I also noticed the multiple versions of upgrade requests. I just don't know which one, if any, would be the one we would normally run. I do remember being told at one point or another, that a certain version of the upgrade command would pull upgrades from a place other than those which are strictly for Zorin OS updates, vice Ubuntu, etc. If that makes any sense at all, haha. Still waking up though...
Thought there might have been a connection having to do with a purge command that had no argument for what to purge.
There's also that autoremove instance in there and it stood out to me because I rarely use it and thought if the script were run as often as I think it is on OP's system, that could be a reasonable explanation for missing dependencies or supplementary packages.
Yes, I have removed Snap and Flatpak. Those commands are a hold-over from when I still had Snap and Flatpak installed. Now they just return "Command not found", so I leave them in, so others who still have Snap and Flatpak installed know they can use them.
If you mean you didn't run the autoremove part of the script, or the purge part of it, the way I understand scripts is that it runs all included commands when run. So each time you run the script, however often, you're commanding the package manager to purge something, as well as autoremove things, for which the package manager usually prompts the user's confirmation.
In other words, like you alluded to above, if you just let the software updater program take care of things, it pauses and waits for you to confirm that you want to autoremove redundant or residual packages it thinks you no longer need for some reason.
No, the original update was triggered by the Software Updater, not the script. I used the script after that to see if there was any update for clutter, which there wasn't.
The script can't take any action without user intervention... there are no -y flags used. If there are no updates, it goes through to completion and ends on its own. If there are updates, it requires user intervention to proceed. Likewise, if there is nothing to purge, it goes through to completion and ends on its own. If there is something to purge, it requires user intervention to proceed.
Software Updater just popped up with new updates...
Desktop icon support for GNOME Shell
Changes for gnome-shell-extension-zorin-desktop-icons versions:
Installed version: 0.18.2
Available version: 0.18.3
Version 0.18.3:
Added Clutter GObject Introspection package as a dependency
GObject introspection data for the Clutter 1.0 library
Changes for gir1.2-clutter-1.0 versions:
Installed version: None
Available version: 1.26.4+dfsg-1
GObject introspection data for the Cogl 1.0 library
Changes for gir1.2-cogl-1.0 versions:
Installed version: None
Available version: 1.22.6-1
GObject introspection data for the CoglPango 1.0 library
Changes for gir1.2-coglpango-1.0 versions:
Installed version: None
Available version: 1.22.6-1
I'm going to install them, then I'll report back.
[EDIT]
Software Updater crashed the first time it tried to install the updates. I waited a minute for the system to settle, then restarted Software Updater, it installed the updates, and my desktop icons are back.
I'm going to reboot, then I'll report back.
[EDIT 2]
All is working well after a reboot. Problem solved.
Generally, you run apt purge followed by the package name.
Running purge alone, without specifying a package, would merely purge any Residual files from previously removed programs. It is safe to do, just not commonly done.
. Sorry about that!