I’m still a fairly new Linux-user (on Tuxedo OS), and I just ran into an issue that is new to me. If I try to update my system, either via command line or Discover, the apt update command fails. This is the output:

E: Could not get lock /var/lib/apt/lists/lock. It is held by process 1635 (apt-get)
N: Be aware that removing the lock file is not a solution and may break your system.
E: Unable to lock directory /var/lib/apt/lists/

Process 1635 is apt-get update run by root, and persists through restart. I am tempted to try to kill it (kill 1635), but I’m not sure if anything could break from that, so I thought I’d try to ask for help first before I do something stupid.

EDIT:

I have managed to update my system by killing the process, which releases the lock, and then going on to do normal sudo apt update and sudo apt upgrade. For the sake of troubleshooting, I tried to add back my third-party repos one by one, and none of them caused any problem. However, when rebooting the same issue as described above happens again. Software updates is set to “Manually” in the System settings.

In addition, everytime I ran sudo apt upgrade, at the end some update related to initramfs fails. My disk is encrypted using cryptsetup, and as I’ve come to understand, I should be very careful doing anything related to initramfs when that is the case. Here is the output:

Processing triggers for initramfs-tools (0.140ubuntu13.2) ...
update-initramfs: Generating /boot/initrd.img-6.2.0-10018-tuxedo
I: The initramfs will attempt to resume from /dev/dm-2
I: (/dev/mapper/system-swap)
I: Set the RESUME variable to override this.
zstd: error 25 : Write error : No space left on device (cannot write compressed block) 
E: mkinitramfs failure zstd -q -1 -T0 25
update-initramfs: failed for /boot/initrd.img-6.2.0-10018-tuxedo with 1.
dpkg: error processing package initramfs-tools (--configure):
 installed initramfs-tools package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
 initramfs-tools
E: Sub-process /usr/bin/dpkg returned an error code (1)

EDIT 2:

The issue seems to have been narrowed down to a failure of Tuxedo’s driver configuration service that runs at boot. It is this process that calls apt-get (and something I should’ve seen earlier…), and systemctl status reveals some errors:

aug. 08 15:33:56 laptop systemd[1]: Starting Tomte-daemon, finishes tasks that could not be accomplished before...
aug. 08 15:34:06 laptop tuxedo-tomte[1393]: no network found!! some fixes might not be applied correctly
aug. 08 15:34:06 laptop tuxedo-tomte[1393]: systemctlCmd: systemd-run --on-active="30sec" tuxedo-tomte configure all >/dev/null 2>&1

I really appreciate the help from everyone so far. It’s a good experience asking for help here, and I’ve learned a lot from your answers. Makes being a Linux newbie a lot easier. So thank you :)

Since this seems to be a very specific issue related to Tuxedo’s own services, I will contact their support to get their input on what to do next.

  • cyberwolfie@lemmy.mlOP
    1·
    1 year ago

    My sources.list file is pretty clean, with 3 https-sources for the Tuxedo OS mirror repos of the original Ubuntu ones. In the sources.list.d directory, there are some that have been added by me, such as for Signal, Librewolf and VS Codium. In total there are 11 files in here, each with one additional source. All except one is https, and the last one is mirror+file. In the process tree for apt-get, there are 13 subprocesses, while there are 14 sources in total (11+3). Could it be that it hangs on the last one here?

    EDIT: Would this be a viable way to troubleshoot? I backup the sources and just replace them with a blank sources.list file and an empty sources.list.d directory. If that works, I add the repos back one at the time and see which one that fails. Or could I run into unintended trouble if I remove the main repos, even for a short time? I would think that it just wouldn’t find anything and just be happy there are no updates.

    • comicallycluttered@beehaw.org
      2·
      1 year ago

      I don’t think that’s the problem, and I wouldn’t really anything related to sources.list or anything in sources.list.d/.(*)

      It does seem like an auto update thing, so got some quick suggestions.

      Since you mentioned Discover, I’m guessing you’re on KDE Plasma, which is great because it’s what I use and know immediately where to go.

      Go into the main settings and way at the bottom left after all the other sections, there should be a section labeled “Software Update”. The only thing you need to care about is the first option, which will be “Update software: Manually/Automatically”.

      If “Automatically” is checked, try disabling it and then reboot. If that doesn’t, work, there’s a more useful GUI tool, but for some reason it doesn’t show up when searching the application menu (or at least doesn’t for me).

      Quick command line thing here:

      sudo software-properties-kde

      This has a bunch of options which I won’t get into, but in the “Updates” tab, you’ll also see “Automatic updates” with a few more options than the one in Settings. I’d enable “Only notify about available updates” if everything else is enabled.

      You can disable “Check for updates” entirely, but I wouldn’t recommend it. You can change that to “Weekly” or something, so that it isn’t constantly checking, but I don’t know if it starts up on every boot, so might be useless to change that specifically.

      After rebooting, take a look at what the file /etc/apt/apt.conf.d/20auto-upgrades says.

      It shouldn’t be too long, but depending on what the values might be for Download-Upgradable-Packages and Unattended-Upgrades, that could be the source of the problem.

      Everything in that file should now have a value of “0” except for the first line (Update-Package-Lists which will have a value of “1”).

      (*) Theoretically, your idea about sources lists could maybe be an issue, but I’m not sure. I don’t know if it’s possible that apt-get could be in some kind of loop if there’s a mismatch or duplicates with your repo sources. I’d assume it would error out, but maybe it’s just being weird.

      For now, I’d leave that all alone. If none of the above works, I can give some instructions on dealing with third party repos, but I don’t want to make this comment any longer than it is already.

      • Gellis12@lemmy.caEnglish
        4·
        1 year ago

        Auto update itself isn’t the root problem. The problem is that apt update is hanging and never finishing. It just happens to be getting called automatically as part of an auto update system, but the root issue would still persist even if OP disables auto updates.

        When apt update fails to complete, it’s almost always because of a broken repo somewhere; hence my question about sources.list.

        • comicallycluttered@beehaw.orgEnglish
          3·
          1 year ago

          You may be right.

          I’m wondering why apt-get isn’t erroring out, though. Usually after enough tries, it just quits, at least in my experience.

          Probably best bet, then, is to remove and re-add the third party repos.

      • cyberwolfie@lemmy.mlOP
        1·
        1 year ago

        Ok, so now I have managed to update my system by killing the process, which releases the lock, and then going on to do normal sudo apt updateand sudo apt upgrade. For the sake of troubleshooting, I tried to add back my third-party repos one by one, and none of them caused any problem.

        However, when rebooting, the same problem happens again. In system settings, auto update was already set to “Manually” and offline updates is unchecked. I have not made any modifications to this. I did not have software-properties-kde installed, and it was also not available by running sudo apt install software-properties-kde. It suggested only software-properties-qt instead. So I could not check those settings, but in the 20auto-upgrades file, Update-Package-Lists and Unattended-Upgrades are the only lines present, and both are set to 1.

        In addition, everytime I ran sudo apt upgrade, at the end some update related to initramfs fails. My disk is encrypted using cryptsetup, and as I’ve come to understand, I should be very careful doing anything related to initramfs when that is the case. Here is the output:

        Processing triggers for initramfs-tools (0.140ubuntu13.2) ...
update-initramfs: Generating /boot/initrd.img-6.2.0-10018-tuxedo
I: The initramfs will attempt to resume from /dev/dm-2
I: (/dev/mapper/system-swap)
I: Set the RESUME variable to override this.
zstd: error 25 : Write error : No space left on device (cannot write compressed block) 
E: mkinitramfs failure zstd -q -1 -T0 25
update-initramfs: failed for /boot/initrd.img-6.2.0-10018-tuxedo with 1.
dpkg: error processing package initramfs-tools (--configure):
 installed initramfs-tools package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
 initramfs-tools
E: Sub-process /usr/bin/dpkg returned an error code (1)

        Since this is buried quite a long way down into a thread, I will now also update the main post to include this update.

        • Gellis12@lemmy.caEnglish
          1·
          1 year ago

          zstd: error 25 : Write error : No space left on device (cannot write compressed block)

          What’s the output of df -H?

          Also, this sounds like it’s installing initramfs, which is normally only done when first installing the OS; can we get a list of the packages it’s trying to install/upgrade?

          • cyberwolfie@lemmy.mlOP
            1·
            1 year ago

            This shows up when running sudo apt update after having killed the process that is holding the lock. Where would I find out which packages it is trying to install or upgrade? It does say update-initramfs in the second line there, so I think it’s trying to update?

            Relevant output from df -H:

            /dev/nvme0n1p1           1,1G  945M   24M  98% /boot
/dev/nvme0n1p2           536M  9,3M  527M   2% /boot/efi
            • Gellis12@lemmy.caEnglish
              1·
              1 year ago

              Ok, there’s the problem. Your boot partition is pretty much full. You’re using partitions instead of lvm, so expanding the partition will be next to impossible; so start looking through /boot for stuff that’s safe to delete. It’s weird that you have so much stuff in there, I don’t think I’ve ever seen my boot partition go above 250mb used.

    • Gellis12@lemmy.caEnglish
      2·
      1 year ago

      I’d leave the main sources.list alone, but temporarily move all of the files out of sources.list.d and see if that fixes it.

      • cyberwolfie@lemmy.mlOP
        1·
        1 year ago

        As added as an edit in the original post, I managed to update my system by killing the process, did an upgrade with only the original sources.list and then added back the third-party repos one-by-one. None of the third party repos caused any problem when adding them back. Problem persists upon reboot. There seems to be an issue with updating initramfs at the end of every sudo apt upgrade, but that shouldn’t run on boot, so I don’t think that can be the cause?