Critical issue after full-upgrade

Support & Help Requests
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#14

Hi question. Re-installed 05 Aug 2023 and had issue similar to above where I manually re-installed the packages shown. Long story short is there a way to make Apt aware (believe it is sources) of the packages that are shown in dpkg and Synaptic or would it be better to re-install after the final release of the .3. No problem if re-install is better as use calc sheet and just go down the line in Synaptic. System does recognize the PPA's in sources.list.d. Never had problem till now and no updates are shown.
Thanks

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#15

Hi, @mendy :slight_smile:

I'm afraid that I'm having some difficulty understanding what you're asking. Having said that, let me quote some excerpts from the following web page that I believe are relevant in this context:

From that web page, the excerpts that seem to me to be the most relevant are the following ones (my apologies if you know all of this already):

" (...)

Advanced Packaging Tool – APT

The apt command is a powerful command-line tool, which works with Ubuntu’s Advanced Packaging Tool (APT). The commands contained within apt provide the means for installing new software packages, upgrading existing software packages, updating the package list index, and even upgrading the entire Ubuntu system.
(...)

  • Update the package index
    The APT package index is essentially a database of available packages from the repositories defined in the /etc/apt/sources.list file and in the /etc/apt/sources.list.d directory. To update the local package index with the latest changes made in the repositories, type the following:
    sudo apt update

Actions of the apt command, such as installation and removal of packages, are logged in the /var/log/dpkg.log log file.

For further information about the use of APT, read the comprehensive APT User’s Guide, or type apt help
(...)

dpkg

dpkg is a package manager for Debian-based systems. It can install, remove, and build packages, but unlike other package management systems, it cannot automatically download and install packages – or their dependencies. APT and Aptitude are newer, and layer additional features on top of dpkg. This section covers using dpkg to manage locally installed packages:

  • To list all packages in the system’s package database, installed and uninstalled, from a terminal prompt type:
    dpkg -l

(...)"

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#16

dpkg -l correctly shows all my installed packages (2236 total). Had error and manually in Synaptic upgraded the packages in the error message. Now while I have 2236 installed packages in dpkg and /etc/apt/sources.list is the contents of Software & Updates and /etc/apt/sources.list.d has my packages installed via PPA. apt list --installed shows a little over 400 was less not sure why more now but question is there a way to sync the dpkg installed to the apt installed for update purposes. Like I mentioned not a problem to reinstall after final release just concerned no updates shown as usually are almost every day. Thanks Probably still not explaining correctly, this was third re-install with everything working (IE: never had clock in Indicator Applet Complete). Second fixed issue with edit menus and a couple of other issues.

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#17

Thanks for the clarification, @mendy :slight_smile:

Could you please tell what is the output of the following commands? I'm including the outputs for my installation here as well:

$ sudo dpkg-query -l | grep '^ii ' | wc -l
2212

$ sudo dpkg -l | grep '^ii ' | wc -l
2212

$ sudo apt list --installed | wc -l

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

2213
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#18

Hi here is requested information:
Output of commands

mendy@mendy:~$ sudo dpkg-query -l | grep '^ii ' | wc -l
[sudo] password for mendy: 
2236
mendy@mendy:~$ sudo dpkg -l | grep '^ii ' | wc -l
2236
mendy@mendy:~$ sudo apt list --installed | wc -l

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

2237
mendy@mendy:~$

Then these commands end up with different #
sudo apt list --installed and apt list --installed both show the same packages, when selecting all and pasting into pluma =418 lines. ????

#19

OK, @mendy. So, the outputs of all the 3 commands that end in "| wc -l" (which counts the lines of the output) that you ran at my request are consistent among themselves, showing equal or very similar results. That is good! :slight_smile:

Regarding your other question:

That's probably the effect of the Bug #1922276 ("Select All (Shift+Ctrl+A) followed by Copy (Shift+Ctrl+C) copies only visible part of terminal output") that still affects Ubuntu MATE 22.04 LTS ("Jammy Jellyfish"):

@Norbert_X mentioned that Bug (and another one) in the following post, here in the "Ubuntu MATE Community" discussion forums, last year (in June 2022):

Other than that, I'm assuming that you've already (re)configured the "Default" Profile in "MATE Terminal" to change the default lines of "Scrollback" from the default of only showing the (last) 512 lines to "Unlimited" or, at least, to a large value. Right? :slight_smile:

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#20

Not Right :pensive:
Oh well after looking at terminal after your change found the select all issue.
Thank you and sorry to others here about partially hijacking post.

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#21

I didn't expect it to be release critical (it impacts upgrades; not new installs which is what the release is for). That document tracks the ISO release.

The lack of the PXE bug fix (fixed in casper 1.470.3) is a shame, the current 22.04.3 ISO switched back to the older casper without the fix (the newer casper installed on BIOS, uEFI & Secure-uEFI that I saw; alas it wasn't tested in a PXE setup impacted by bug)

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#22

I'm surprised that this is marked "not release critical". Sure, in the absolute sense, one can install the OS successfully. But if an update appears the next day, then the OS is going to get borked by the removal of required system packages. Obviously not desirable.

I wanted to repeat what I said in my earlier message in this discussion. The talk seems to focus on dist-upgrade. However, I was just doing a routine update via Update Manager, and encountered this problem. So the problem is much more pervasive than dist-upgrade. It will affect everyone doing any type of update.

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#23

Easy to reproduce the issue about FULL-UPGRADE:

  • Install 22.04.1
  • Manually upgrade upto the 3th August 2023
  • Reboot
  • Then wipe the system with sudo apt full-upgrade
#24

I have successfully restored my system to a backup. Latest backup I had was 6 months old :pensive: Learned my lesson to backup more frequently.

I now want to bring this system up to a date before this problem occurred on August 4, 2023. I don't see an option in apt to limit updates to a latest date, e.g., apply all updates on or before August 1, 2023. Is this possible?

Thanks.

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#25

I would just apply a full-upgrade, and even if some essential packages get removed (aka bug) the metapackages can be re-installed in a second or two. I wrote about it here as I let the damage occur on my primary box (to confirm it would be easy to fix).

If I'd suffered the damage you described earlier, I'd likely have done a non-destructive re-install too; as I re-install some of my systems weekly instead of performing normal package upgrades as it achieves the package upgrade (I use daily ISOs and not released images) at the same time accomplishing a QA-test of the newer daily ISO.

Do note the non-destructive re-install is great where no third party packages are involved, OR specific ones built to be 'future proof' are involved, but experiences can differ depending on what third-party packages are used; if you're not familiar with what I'm describing you can look at an answer I wrote here

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#26

I just updated an Ubuntu MATE VM, which is separate from the native install I discussed earlier in this discussion. The update of the VM installation completed without issue - nothing got deleted. I'm typing this on Friday, August 10, 2023, so I'm concluding that something got fixed to address this problem. I'm going to wait a little longer to try an update on the native install that I just recovered. I'd like to avoid repeating messing it up.

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#27

Thanks a lot for your tests and further analysis!

#28

I provided a link to linux.org where I talked about the issue, later in that thread I mentioned

Hopefully though, you're correct, in the that issue has been fixed. :slight_smile:

Alas the message from Julian Andres Klode on the bug report comment #16

refer currently to a package only in -proposed.

 apt | 2.4.9           | jammy-updates   | source, amd64, arm64, armhf, i386, ppc64el, riscv64, s390x
 apt | 2.4.10          | jammy-proposed  | source, amd64, arm64, armhf, i386, ppc64el, riscv64, s390x

but maybe I'm wrong, regardless we'll get there :slight_smile:

4 Likes
#29

Hello just updating my situation not totally related to above. At time I installed UM22.04.2 via usb (not aware that .3 was in progress) and ended up with upgrading something like 148 pkgs.. Then no updates were showing in GUI upgrader. Did another install with same usb and this time only 2 .dap upgrades were held back. This was on 08 Aug 2023. Then every day checking with GUI updater Computer is up to date. Well today 13 Aug 2023 updater pointed out two ( the dap that were held back). Think my issue was related to items here:
https://ubuntu.com/server/docs/about-apt-upgrade-and-phased-updates
Clumsily initally upgraded all those packages. Checking on the two *dap in latest installation on what would happen if I removed them it would have wiped most of my system.
Just update (of what I found)edit

#30

Last Saturday, it was the first time ever I tried to run full-upgrade command. It was on a 10ys old wife's computer running Ubuntu MATE 22.04, wiping core packages and destroying the system :joy: Because it was totally unexpected, I really did not know what to do. So I took advantage of the situation and bought a new SSD, removed the old slow HDD and reinstalled the system. Now the computer is much more usable, so thank you for this issue :stuck_out_tongue_winking_eye:

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#31

Welcome @ratatoskr to the community!

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#32

After one week since my first alert, back at home. Good news, the issue about full-upgrade is gone. Last week, a simulation with full-upgrade will wipe the system. Today, same simulation on same system, nothing will be wipe. On the other hand, I don't understand why main stream sites about Ubuntu didn't communicate about this issue, for example, tell to people to not update.

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#33

Hopefully final update from me on this issue. I finally decided to upgrade my Ubuntu MATE bootable installation on my primary system; because of this issue, I was cautious to do a dry-run first, and ensure that nothing was going to be deleted. I'm happy to report that it succeeded with no issues. It did hold back about 8 packages. I searched about these hold backs, and found suggestions to just be patient, that these hold backs are a result of phased updates.

Today, I did another update, and 6 of the 8 where upgraded. So, I'm going to take a backup, and assume this issue is resolved. My thanks to all who provided assistance and guidance here.

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