Problem when upgrading Zorin 15.3 Pro to Zorin 16.3 (Error:org.debian.apt.TransactionFailed E:Error, pkgProblemResolver::Resolve generated breaks)

Hello, gentlemen of the Zorin OS forum.

Firstly, thank you for the excellent work you do in this forum and for the help you offer.

I am contacting you for the following reason:

Several years ago, I purchased Zorin OS 15.0 Pro (Paid Version) and have enjoyed it for a long time. Currently, I have Zorin OS 15.3 Pro and have gotten a lot of performance and use out of it. Recently, I have tried Zorin OS 16.3 Free version and I also liked it.

So I would like to upgrade to Zorin OS 16.3 Pro, as Zorin OS 15.3 Pro has been outdated for some time now. I have already purchased Zorin OS 16.3 Pro (Paid version) but when I tried to upgrade from Zorin OS 15.3 Pro to Zorin OS 16.3 Pro I encountered a problem.

To do this I have performed the procedure explained in your guide: Upgrade Zorin OS - Zorin Help and when the updater is in step number 4 it informs me that there has been an internal error because it has not been able to complete correctly the check of the update requirements.

The report provided by the system is as follows:

[CHECKING] Started
[CHECKING:Validating Upgrade Attempt] Started
[CHECKING:Validating Upgrade Attempt] Completed
[CHECKING:Checking Filesystem] Started
[CHECKING:Checking Filesystem] Completed
[CHECKING:Creating Necessary Files] Started
[CHECKING:Creating Necessary Files] Completed
[CHECKING:Restarting Apt] Started
[CHECKING:Restarting Apt] Completed
[CHECKING:Simulating Flatpak Transaction] Started
[CHECKING:Simulating Flatpak Transaction] Completed
[CHECKING:Processing Apt Repos] Started
[CHECKING:Processing Apt Repos] Completed
[CHECKING:Updating Apt Repos] Started
[CHECKING:Updating Apt Repos] Completed
[CHECKING:Calculating Upgradeable Packages] Started
[CHECKING:Calculating Upgradeable Packages] Fatal Error: { GDBus.Error:org.debian.apt.TransactionFailed: error-dep-resolution-failed: E:Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. }
[CHECKING:Calculating Upgradeable Packages] Failed
[CHECKING] Failed
[CHECKING:Restoring System] Started
[CHECKING:Restoring System] Completed

I have spent several hours investigating the error and I believe it is due to an incomplete system dependencies issue or problems with packages. I have tried many things on my system to try to correct it, but have been unsuccessful. The closest thing there would be on your forum is the following: Zorin OS Upgrader: Z15.3 Core to Z16.2 Core fails with errors, but this solution didn't work for me either. Finally, after trying many possible solutions to this issue, I have returned the state of my computer back to the way it was before applying all these possible solutions. Before trying all these possible solutions and trying to update the system, just in case, I made a backup. With which I have the computer in the same state as before, I tried to upgrade and address these possible solutions.

In short, I have Zorin OS 15.3 Pro and I want to upgrade to Zorin OS 16.3 Pro, but I can't because of the error described above which is:

[CHECKING:Calculating Upgradeable Packages] Fatal Error: { GDBus.Error:org.debian.apt.TransactionFailed: error-dep-resolution-failed: E:Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. }
[CHECKING:Calculating Upgradeable Packages] Failed
[CHECKING] Failed

I put this other log in case it is of help:

Log time: 2023-06-23 01:05:19.598822
Starting pkgProblemResolver with broken count: 1
Starting 2 pkgProblemResolver with broken count: 1
Investigating (0) packettracer:amd64 < 8.2.1 @iU gK Nb Ib >
Broken packettracer:amd64 Depende on libc6:amd64 < 2.28-0ubuntu1+zorin4 @ii mK > (>= 2.31)
  Removing packettracer:amd64 because I can't find libc6:amd64
Done
ERROR:root:Package docker-desktop has no priority set
ERROR:root:Package scrt-sfx has no priority set
Log time: 2023-06-23 01:07:27.861534
  MarkPurge python-pexpect:amd64 < 4.2.1-1 @ii gK > FU=1
  MarkPurge gir1.2-dbusmenu-glib-0.4:amd64 < 16.04.1+18.04.20171206-0ubuntu2 @ii gK > FU=1
  MarkPurge python-ptyprocess:amd64 < 0.5.2-1 @ii gK > FU=1
  MarkPurge libhtml-template-perl:amd64 < 2.97-1 @ii gK > FU=1
  MarkPurge python-paramiko:amd64 < 2.0.0-1ubuntu1.3 @ii gK > FU=1

I look forward to your help. I remain attentive to your possible solutions.

Thank you very much.

In terminal, can you run

sudo apt --fix-broken install

Relay whether any packages are added, upgraded or removed.

Once that is done, please run:

sudo apt update

Please relay if any repositories are reported as broken or missing a release file for Bionic or for Focal.

What may be happening is - you may have an installed package that does not have any Focal Release Candidate. If we can figure out what that package is - you can decide whether to remove it.
So please run next:

sudo apt upgrade

and relay the results reported in the terminal.

1 Like

Hello @Aravisian excuse me in quoting you here, but your Aksimet system must have detected me as a spammer and blocked me from posting the topic. When really I am not a spammer, so it must have detected me as a false positive.

I mean this:

When you can, please authorize my posting in the review queue manually.

I think your Akismet system has blocked me for attaching the 3 images.

Thank you.

Regards.

1 Like

Hi good morning @Aravisian firstly thank you very much for your help and for your quick response.

Many times I have read posts of yours from the forum, and they have helped me in things and also inspired me to do other things.

Regarding the command: sudo apt --fix-broken install I add the following terminal output image:

1.linux

Referring to the command: sudo apt update I add the following terminal output image:

Ok, ok, perfect :+1: I thought it might be a package conflict issue between versions, it was one of the things I tried for a few hours, but I didn't find the solution.

Regarding the command: sudo apt upgrade I add the following terminal output image:

3.linux

Well, you already have all the results you asked for, and I think 3 pictures are worth a thousand words.

Thank you very much for your help.

I look forward to your help. I remain attentive to your possible solutions.

Thank you very much.

I have marked you as Not Spam.

It looks like all packages are up to date.
So, looking at your added repos:
Nodesource, Anydesk, teamviewer, docker:

Going by the requirements and files - it should be fine. But, I notice that several of their repositories require a repository key.

While you have added the Bionic repo and key, that key may not roll over to Focal.
You may need to remove those apps and repositories - then upgrade Zorin OS. Then re-add the repos for Focal and Reinstall the apps.

1 Like

Hello good morning again @Aravisian

Ok fine, perfect. That way, the forum's Akismet system will no longer block me as spam, and you'll also save yourself some work, since you won't have to authorize any of my posts on your end from the moderator panel's review queue.

Yes, that's right. They require a key to the repository.

Okay, understood.

Ok, I understand. Apart from the applications that you yourself have commented @Aravisian (Nodesource, Anydesk, teamviewer, docker), I understand that I must remove all these applications that appear in the second image:

Hit:1 https://linux.teamviewer.com/deb stable InRelease
Hit:2 https://download.docker.com/linux/ubuntu bionic InRelease                
Hit:3 https://deb.nodesource.com/node_14.x bionic InRelease                    
Hit:4 http://dl.google.com/linux/chrome/deb stable InRelease                   
Hit:5 http://deb.anydesk.com all InRelease                                     
Hit:6 http://ppa.launchpad.net/teejee2008/timeshift/ubuntu bionic InRelease                
Hit:24 https://packages.microsoft.com/repos/ms-teams stable InRelease  

I mean, apart from Nodesource, Anydesk, teamviewer, docker I should also remove: chrome, timeshift and ms-teams.

Is this true?

If so, I will remove them with:

sudo apt remove package_name_to_remove_1 package_name_to_remove_2 and ....etc

You do not need to do this with:

sudo apt purge package_name_to_remove_1 package_name_to_remove_2 and ....etc

Is this other thing I say true?

Finally, I understand that I should delete the following:

Hit:1 https://linux.teamviewer.com/deb stable InRelease
Hit:2 https://download.docker.com/linux/ubuntu bionic InRelease                
Hit:3 https://deb.nodesource.com/node_14.x bionic InRelease                    
Hit:4 http://dl.google.com/linux/chrome/deb stable InRelease                   
Hit:5 http://deb.anydesk.com all InRelease                                     
Hit:6 http://ppa.launchpad.net/teejee2008/timeshift/ubuntu bionic InRelease                
Hit:24 https://packages.microsoft.com/repos/ms-teams stable InRelease  

From the Zorin update repository file as well as the keys that are imported in my system referring to the repositories of these applications that I have mentioned.

Is this last thing true?

Thank you very much for your help.

I do not think those require the additional added step of adding a Key - but please feel free to double check that.

Yes, you can remove without purge.

Since you will reinstall them.

Only the repositories that require the additional step of adding the key.

1 Like

Ok, ok, perfect @Aravisian I will proceed with all of it.

I will remove with: sudo apt remove the commented applications. I will reboot the system to apply the changes and finally, I will try again the update.

I'm going to get to it, and soon I will bring news.

Thank you very much for your help.

1 Like

Hello good again @Aravisian I have performed the following procedures:

  1. uninstall the packages of the applications cited above, with these commands:
sudo apt remove nodejs anydesk teamviewer docker-buildx-plugin docker-ce docker-ce-cli docker-ce-rootless-extras docker-compose-plugin docker-desktop timeshift teams

And I forgot to put the chorme in the first uninstall command, so I did it in another one:

sudo apt remove google-chrome-stable chrome-gnome-shell

I then removed the packages that no longer made sense to have on the machine by removing those applications:

  1. Remove them all from the repositories with:
sudo rm -r  /etc/apt/sources.list.d/anydesk-stable.list
sudo rm -r  /etc/apt/sources.list.d/docker.list
sudo rm -r  /etc/apt/sources.list.d/google-chrome.list
sudo rm -r  /etc/apt/sources.list.d/nodesource.list
sudo rm -r  /etc/apt/sources.list.d/teams.list
sudo rm -r  /etc/apt/sources.list.d/teamviewer.list
sudo rm -r  /etc/apt/sources.list.d/teejee2008-ubuntu-timeshift-bionic.list
  1. I rebooted the machine and launched the following command:
sudo apt update -y && sudo apt upgrade -y && sudo apt dist-upgrade -y && sudo apt clean -y && sudo apt remove -y && sudo apt autoremove -y && sudo apt autoclean -y

To "refresh" and "clean" well before proceeding with the system upgrade:

As you can see in the previous image, the deleted repositories of those applications are no longer shown:

Hit:1 https://linux.teamviewer.com/deb stable InRelease
Hit:2 https://download.docker.com/linux/ubuntu bionic InRelease                
Hit:3 https://deb.nodesource.com/node_14.x bionic InRelease                    
Hit:4 http://dl.google.com/linux/chrome/deb stable InRelease                   
Hit:5 http://deb.anydesk.com all InRelease                                     
Hit:6 http://ppa.launchpad.net/teejee2008/timeshift/ubuntu bionic InRelease                
Hit:24 https://packages.microsoft.com/repos/ms-teams stable InRelease  
  1. Launch again the Zorin updater and K.O. :sob: :sob::

17.linux

[CHECKING] Started
[CHECKING:Validating Upgrade Attempt] Started
[CHECKING:Validating Upgrade Attempt] Completed
[CHECKING:Checking Filesystem] Started
[CHECKING:Checking Filesystem] Completed
[CHECKING:Creating Necessary Files] Started
[CHECKING:Creating Necessary Files] Completed
[CHECKING:Restarting Apt] Started
[CHECKING:Restarting Apt] Completed
[CHECKING:Simulating Flatpak Transaction] Started
[CHECKING:Simulating Flatpak Transaction] Completed
[CHECKING:Processing Apt Repos] Started
[CHECKING:Processing Apt Repos] Completed
[CHECKING:Updating Apt Repos] Started
[CHECKING:Updating Apt Repos] Completed
[CHECKING:Calculating Upgradeable Packages] Started
[CHECKING:Calculating Upgradeable Packages] Fatal Error: { GDBus.Error:org.debian.apt.TransactionFailed: error-dep-resolution-failed: E:Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. }
[CHECKING:Calculating Upgradeable Packages] Failed
[CHECKING] Failed
[CHECKING:Restoring System] Started
[CHECKING:Restoring System] Completed

I believe that all the procedures I have done are correct, and I don't think I have left anything out.

What do you think of these procedures I have done?

Thank you very much for your help @Aravisian

I agree with you that your removals were on target.

Sadly, it appears our guess as to the cause of the problem was not on target.

You clearly do not show any held packages - we looked at the outputs above for sudo apt update && sudo apt upgrade.

I would have thought Orphaned packages, but I can see you ran apt clean && apt autoremove, as well.

Can you please check /var/log/dist-upgrade/apt.log and search for any missing dependencies?

1 Like

Ok fine, perfect @Aravisian I'm glad I did it correctly.

True, it seems that it was not that. It has not given its fruits :-1: :sob:.... but well we already know that in the computer science many things never work neither to the first, nor to the second... so patience.

True, in fact I have run it again:

sudo apt update && sudo apt upgrade

and nothing:

18.linux

True, in fact I have run it again:

sudo apt clean && sudo apt autoremove

and nothing:

19.linux

  1. Of course, look:

I only get this.

  1. Referring to:
  MarkPurge python-pexpect:amd64 < 4.2.1-1 @ii gK > FU=1
  MarkPurge gir1.2-dbusmenu-glib-0.4:amd64 < 16.04.1+18.04.20171206-0ubuntu2 @ii gK > FU=1
  MarkPurge python-ptyprocess:amd64 < 0.5.2-1 @ii gK > FU=1
  MarkPurge libhtml-template-perl:amd64 < 2.97-1 @ii gK > FU=1
  MarkPurge python-paramiko:amd64 < 2.0.0-1ubuntu1.3 @ii gK > FU=1

These are not currently installed on the system, but I don't think the problem is here.

Do I try installing these anyway? With:

sudo apt install python-pexpect:amd64 gir1.2-dbusmenu-glib-0.4:amd64 python-ptyprocess:amd64 libhtml-template-perl:amd64 python-paramiko:amd64
  1. Referring to:
ERROR:root:Package docker-desktop has no priority set
ERROR:root:Package scrt-sfx has no priority set

I don't think this is the problem due to package priorities not set in the system and now even less in ERROR:root:Package docker-desktop has no priority set having completely removed docker.

  1. Referring to:
Log time: 2023-06-23 01:05:19.598822
Starting pkgProblemResolver with broken count: 1
Starting 2 pkgProblemResolver with broken count: 1
Investigating (0) packettracer:amd64 < 8.2.1 @iU gK Nb Ib >
Broken packettracer:amd64 Depende on libc6:amd64 < 2.28-0ubuntu1+zorin4 @ii mK > (>= 2.31)
  Removing packettracer:amd64 because I can't find libc6:amd64
Done

I think that actually the problem may be here, since:

Investigating (0) packettracer:amd64 < 8.2.1 @iU gK Nb Ib >
Broken packettracer:amd64 Depende on libc6:amd64 < 2.28-0ubuntu1+zorin4 @ii mK > (>= 2.31)
  Removing packettracer:amd64 because I can't find libc6:amd64

And more specifically in: libc6:amd64.

What do you think about it @Aravisian about everything I told you about /var/log/dist-upgrade/apt.log?

Thank you very much for your help @Aravisian

P.S.: If in the following hours I do not give an answer, it is because I will not be able to be in front of the computer that has the issue for a few hours. Anyway, post your answer and when I get it, in a few hours. Then we continue :+1:

This appears to have been logged toward the end of June.

It says it removed the package, thereby correcting the held package. So, I am not as confident that is the issue. Plus, you have run sudo apt --fix-broken install which would have corrected that if it had not been corrected previously.

I find it odd that it could not find libc6:amd64.
What is your terminal output for

ldd --version

I would return to this:

These may not be purged, only marked for purge. They may not be fully installed, but orphaned.
And orphaned packages can cause the issue. So, this is where I would try solving first. Search out any of the above package components and remove them. Do not remove python - just those as exactly named above or their direct files.
While you are at it, you can try searching for any residual files for packettracer, just in case.

1 Like

Yes, that's right.

Well, I have acted in the 3 different proposed focuses.

  1. Well, I have performed the following procedure for one stop:
sudo apt purge packettracer:amd64
sudo apt --fix-broken install
sudo apt update -y && sudo apt upgrade -y && sudo apt dist-upgrade -y && sudo apt clean -y && sudo apt remove -y && sudo apt autoremove -y && sudo apt autoclean -y

As you can see (I have used purge, as I will not use this package and application anymore in the future):

21.linux

22.linux

Yes it has been successfully removed packettracer:amd64

And I rebooted the machine and tried again to update and nothing:

17.linux

  1. Referring to:

The system displays the following:

23.linux

  1. Referring to:

Okay.

Well, I have launched the following command:

sudo apt purge python-pexpect:amd64 gir1.2-dbusmenu-glib-0.4:amd64 python-ptyprocess:amd64 libhtml-template-perl:amd64 python-paramiko:amd64

To try to remove any of those packages if they were actually installed, and it turns out that none of them are installed. As you can see:

I then launched this:

25.linux

And none of them have found any similar matches or with the completions described in the commands in the dpkg of the system.

I then launched this:

And none of them are referenced or related to packettracer

Moving on.

Thanks, @Aravisian

Greetings.

I am honestly stumped.

Since this deals with a recently released and long anticipated feature: Zorin OS Direct Upgrade; I am going to elevate this to the ZorinGroup in case this is a present bug in the new package that needs addressing.

1 Like

Hello good morning again @Aravisian

Yes, I don't know where to catch or attack the problem either. As I said before opening this topic I already did several tests and tried several things, some of them similar to what we have done in this topic and none of them worked either.

Yes, right it all came out just this past June 28, 2023, which is about 3 and a half months ago as seen in this article: The Zorin OS Upgrader Has Arrived - Zorin It is a short time.

Ok, perfect agreement. Now for my part I have some small doubts on how to proceed in this topic from now on:

  1. Will you yourself @Aravisian continues to lead, answer and attend this topic?

  2. Or is someone from ZorinGroup going to intervene directly in this topic from now on?

  3. For my part do you think I can provide you with some more information about this incident so that when you escalate it to ZorinGroup they have more information about this whole issue/problem?

I look forward to hearing from you.

Thanks, @Aravisian

The ZorinGroup consists of the Two Developers. Artyom and Kyrill Zorin.
They are tasked with the Zorin Operating System Development, Direct upgrade tool development, Zorin Grid development, bug reports and staying on top of critical system updates.
They also provide Zorin OS Pro installation support directly, meaning that they respond and address user issues installing Zorin OS Pro.

This means that it may take some time for them to

  • see the notification for this issue (I sent it in shortly after I made my post above stating I would do so).
  • address any other priority concerns first
  • research this issue and look over their Direct Upgrade Tool code to be prepared for the topic
  • formulate a response

Other Ladies and Gentlemen of the forum may view this public thread and any of us might post a suggestion at any time that may be helpful.
It is also possible that the ZorinGroup may present a response to the moderators that they can relay on the forum.

The Direct Upgrade tool is new on Zorin OS. I am not an Expert with this tool and all its intricacies. It is entirely possible that any member may posit a solution at any time - simply by knowing the things that I don't.

Yes, you can submit details into one condensed post that I will then tag that post as the one to get their attention.
Details include

  • your Full Computer make, year and model and specs (CPU, GPU, RAM. etc.).
  • You have provided a list above with your added third party repositories - but you can resend that in one condensed post if you like so that they do not need to scroll up and down the thread.
  • Whether you are dual booting and if so or not - whether Secure Boot is disabled in BIOS / EFI Settings.
  • A full copy of the error that halts the Direct Upgrade
  • Any additional modifications you made to your system that are noteworthy - For example, I have in the past changed Zorin OS Lite from using SystemD to Sysvinit - which was kind of a big deal. If you modified anything in Root other than default.
  • If you are using any additional Grub parameters that you have manually added.
1 Like

Hello good morning again @Aravisian

Firstly, I apologize for the delay in responding to you. My sincerest apologies.

Well, I have been sick for several weeks, I have had family and personal problems. Also, work has taken up a lot of my time, so with all this I have not been able to dedicate myself to it.

Now I was reviewing pending issues of mine and I saw this one.

Let's continue…

Ok, I understand.

Ok, perfect, understood.

Ok, perfect, got it :+1:.

Ok, perfect, understood :+1:. On my side, there is no hurry. I didn't bring you the information you asked for (I'll bring it to you soon).

Is there any news about this notification you told me @Aravisian about Artyom and Kyrill Zorin?

Ok, all this understood as well. Thank you for this information and clarification.

Thank you for this information and clarification.

OK.

ASUS.

ASUSPRO ADVANCED B551LA.

Intel® Core™ i7 4558U/Intel vPro CPU Processor.

Integrated Intel® HD Graphic 5100

DDR3L 1600 MHz SDRAM, 2 x DIMM socket for expansion up to 16 GB SDRAM.

I think that with all this, in this part of the data, it is enough.

Yes, that's right, that's right. Ok, no problem, this is it:

Hit:1 https://linux.teamviewer.com/deb stable InRelease
Hit:2 https://download.docker.com/linux/ubuntu bionic InRelease                
Hit:3 https://deb.nodesource.com/node_14.x bionic InRelease                    
Hit:4 http://dl.google.com/linux/chrome/deb stable InRelease                   
Hit:5 http://deb.anydesk.com all InRelease                                     
Hit:6 http://ppa.launchpad.net/teejee2008/timeshift/ubuntu bionic InRelease                
Hit:24 https://packages.microsoft.com/repos/ms-teams stable InRelease

I believe that I have not left anything out and that I have put the most important of what you have asked me.

No, on this machine where I have the problem, there is no dual boot. I just have Zorin on this machine and that's it.

Secure Boot is currently disabled in BIOS on this machine.

Well, I brought it up at the time, but the most recent log of having gone through this process is:

In principle, as far as I can remember, nothing noteworthy.

No, nothing at all modified in GRUB.

Well @Aravisian, I hope all this information is enough and necessary.

If you find anything missing, let me know.

Let me know how to proceed with this issue as soon as you can.

I look forward to hearing from you.

Thanks for everything, @Aravisian

PS: I wish you a happy new year.

Hello good morning @Aravisian

Sorry to post/write in this topic again without first waiting for your reply, but....

With all the information I brought you in the previous post of mine, I understand that it is enough about everything you asked me at the time.

Is all this correct?

Thank you very much for your help and apologies.

I look forward to hearing from you.

Thanks for everything, @Aravisian

I am sorry, it is my turn to be late to reply.

Have you checked your sources.list and sources.list.d to ensure that no repositories are added that can conflict?
Launch Software& Updates and ensure you are on Main Server.
Then; run

sudo apt update && sudo apt full-upgrade

on Zorin OS 15. Monitor the terminal for any 404 or other errors. If no errors, open
the Zorin Upgrader and test if able to upgrade to Zorin OS 16.

1 Like

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