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HippoMan
Asked: 2022-05-05 16:57:58 +0800 CST

Fixing broken apt **without** destroying my system via "apt autoremove"

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Somehow, my apt system got hosed on my Ubuntu 20.04.4 system, and now there are more than 1,800 packages that are marked as needing to be uninstalled.

This is from the Xubuntu installation, which means I'm running the xfce desktop.

I know that the recommended way to fix this kind of apt problem is to do an apt autoremove followed by reinstalls of the packages. However, if I do that, my system will then be totally unusable after the apt autoremove, due to the fact that most of my system's packages will have been uninstalled.

I'm looking for an alternative way to fix my apt database so that I don't have to destroy my system with the apt autoremove command in order to correct apt.

In order to illustrate the state of apt on my system, here are some of the things I have run ...

% sudo apt-get install -f
[returns a list of the names of the 1,800 packages]

% sudo dpkg configure -a
[no output]

% sudo aptitude search ?broken
[no output]

% sudo cat /var/log/apt/history.log
Start-Date: 2022-05-04  18:01:54
Requested-By: [MYUSERID] (1000)
Upgrade: networkd-dispatcher:amd64 (2.1-2~ubuntu20.04.2, 2.1-2~ubuntu20.04.3), libvirt-daemon-system-systemd:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), openssl:amd64 (1.1.1f-1ubuntu2.12, 1.1.1f-1ubuntu2.13), librbd1:amd64 (15.2.14-0ubuntu0.20.04.2, 15.2.16-0ubuntu0.20.04.1), google-chrome-stable:amd64 (101.0.4951.41-1, 101.0.4951.54-1), libvirt-clients:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), iio-sensor-proxy:amd64 (2.8-1ubuntu1, 2.8-1ubuntu2), libvirt-daemon-driver-storage-rbd:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), libpq5:amd64 (12.9-0ubuntu0.20.04.1, 12.10-0ubuntu0.20.04.1), ubuntu-drivers-common:amd64 (1:0.9.0~0.20.04.6, 1:0.9.0~0.20.04.7), libvirt-daemon-driver-qemu:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), libvirt-daemon-system:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), libssl-dev:amd64 (1.1.1f-1ubuntu2.12, 1.1.1f-1ubuntu2.13), libssl-doc:amd64 (1.1.1f-1ubuntu2.12, 1.1.1f-1ubuntu2.13), libmysqlclient21:amd64 (8.0.28-0ubuntu0.20.04.3, 8.0.29-0ubuntu0.20.04.2), libmysqlclient21:i386 (8.0.28-0ubuntu0.20.04.3, 8.0.29-0ubuntu0.20.04.2), libvirt0:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16), lm-sensors:amd64 (1:3.6.0-2ubuntu1, 1:3.6.0-2ubuntu1.1), libsensors-config:amd64 (1:3.6.0-2ubuntu1, 1:3.6.0-2ubuntu1.1), libssl1.1:amd64 (1.1.1f-1ubuntu2.12, 1.1.1f-1ubuntu2.13), libssl1.1:i386 (1.1.1f-1ubuntu2.12, 1.1.1f-1ubuntu2.13), libsensors5:amd64 (1:3.6.0-2ubuntu1, 1:3.6.0-2ubuntu1.1), libsensors5:i386 (1:3.6.0-2ubuntu1, 1:3.6.0-2ubuntu1.1), librados2:amd64 (15.2.14-0ubuntu0.20.04.2, 15.2.16-0ubuntu0.20.04.1), libvirt-daemon:amd64 (6.0.0-0ubuntu8.15, 6.0.0-0ubuntu8.16)
End-Date: 2022-05-04  18:02:47

% sudo ls -l /etc/apt/sources.list
4 -rw-r--r-- 1 root root 3280 Jan 19 17:24 /etc/apt/sources.list
[note that the file hasn't changed in a few months]

% sudo ls -l /etc/apt/sources.list.d 
total 16
4 -rw-r--r-- 1 root root 190 Jan 19 17:24 google-chrome.list
4 -rw-r--r-- 1 root root 190 Jan 19 17:24 google-chrome.list.save
4 -rw-r--r-- 1 root root  56 Apr 14 11:06 skype-stable.list
4 -rw-r--r-- 1 root root  56 Jan 19 17:24 skype-stable.list.save
[note that none of this has changed recently]

% sudo apt update
Hit:1 http://us.archive.ubuntu.com/ubuntu focal InRelease                                                                                             
Get:2 http://us.archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]                                                                            
Hit:3 http://dl.winehq.org/wine-builds/ubuntu focal InRelease                                                                                         
Get:4 http://us.archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]                                                                          
Get:5 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]                                                                          
Hit:6 http://archive.canonical.com/ubuntu focal InRelease                                                                                             
Hit:7 https://dl.google.com/linux/chrome/deb stable InRelease                                                                 
Get:8 http://us.archive.ubuntu.com/ubuntu focal-updates/main amd64 DEP-11 Metadata [278 kB]
Get:9 http://us.archive.ubuntu.com/ubuntu focal-updates/universe amd64 DEP-11 Metadata [391 kB]      
Get:10 http://us.archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 DEP-11 Metadata [940 B]                     
Get:11 http://us.archive.ubuntu.com/ubuntu focal-backports/main amd64 DEP-11 Metadata [9,568 B]
Get:12 http://us.archive.ubuntu.com/ubuntu focal-backports/universe amd64 DEP-11 Metadata [30.8 kB]
Hit:13 https://repo.skype.com/deb stable InRelease                                              
Get:14 http://security.ubuntu.com/ubuntu focal-security/main amd64 DEP-11 Metadata [40.6 kB]
Get:15 http://security.ubuntu.com/ubuntu focal-security/universe amd64 DEP-11 Metadata [66.3 kB]
Get:16 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 DEP-11 Metadata [2,464 B]
Fetched 1,155 kB in 2s (555 kB/s)                       
Reading package lists... Done
Building dependency tree       
Reading state information... Done
All packages are up to date.

% sudo grep -r "^deb" /etc/apt/ --include=*.list
/etc/apt/sources.list.d/google-chrome.list:deb [arch=amd64] https://dl.google.com/linux/chrome/deb/ stable main
/etc/apt/sources.list.d/skype-stable.list:deb [arch=amd64] https://repo.skype.com/deb stable main
/etc/apt/sources.list.d.save/alex-p-ubuntu-aegisub-focal.list:deb http://ppa.launchpad.net/alex-p/aegisub/ubuntu focal main
/etc/apt/sources.list.d.save/teamviewer.list:deb https://linux.teamviewer.com/deb stable main
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal main restricted
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal main restricted
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal-updates main restricted
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal-updates main restricted
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal universe
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal-updates universe
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal-updates universe
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal multiverse
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal multiverse
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal-updates multiverse
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal-updates multiverse
/etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ focal-backports main restricted universe multiverse
/etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/ focal-backports main restricted universe multiverse
/etc/apt/sources.list:deb http://archive.canonical.com/ubuntu focal partner
/etc/apt/sources.list:deb-src http://archive.canonical.com/ubuntu focal partner
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu focal-security main restricted
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu focal-security universe
/etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu focal-security universe
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu focal-security multiverse
/etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu focal-security multiverse
/etc/apt/sources.list:deb http://dl.winehq.org/wine-builds/ubuntu/ focal main

I had a similar problem in the past which I fixed as described in the "Answers" section of the following post: apt forgot about more than 1,000 packages, and I'm unable to reinstall ... it's the Answer which begins with "I figured out how to fix this problem ..."

However, this seems like a hack-y way to fix this, and I'm not sure how reliable it will be if I run it now.

Can anyone suggest any other way to fix this problem without sudo apt autoremove and without that hack-y method that I used in the past?

Thank you very much in advance.

PS: I take daily backups of my system. Are there perhaps any files or directories I can restore from my latest backup which would contain the non-broken versions of the apt database?

PPS: I tried installing xubuntu-desktop as discussed in the comments below. Sadly, it didn't help ...

% sudo apt install xubuntu-desktop
Reading package lists... Done
Building dependency tree       
Reading state information... Done
xubuntu-desktop is already the newest version (2.233).
xubuntu-desktop set to manually installed.
The following packages were automatically installed and are no longer required:
[list of 1,800 package names, followed by ...]
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

And all those packages remain marked as requiring uninstallation.

apt

1 Answers

  1. Best Answer

    I fixed the problem.

    After reinstalling xubuntu-desktop and xubuntu-core, my problem persisted. Therefore, I assume that the problem is not due to simply one missing installation at the top of the dependency tree, but rather, that the entire apt database had probably somehow gotten corrupted.

    So, I gave up on shortcuts, I crossed my fingers, and I ended up biting the bullet and doing a slight variation of what I did in the past, as described in my Answer here: apt forgot about more than 1,000 packages, and I'm unable to reinstall

    This time, I only did the install of each package, not the initial remove before each install, and it worked. Here are the steps I took ...

    Step 1:

    % sudo apt-get install -f >apt-installs

    After running this, the apt-installs file contained this data ...

    Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
[names of more than 1,800 packages]
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.

    Step 2:

    I edited this apt-installs file to remove the top 4 lines and the bottom 2 lines, and I reformatted it so that there is one package name per line.

    Step 3:

    I prepended the string fixit to the beginning of each line.

    Step 4:

    I created a shell function called fixit to install the specified package, and I put that function at the top of the apt-installs file. Now, here's what the first dozen or so lines of apt-installs look like ...

    fixit() {
  [[ $# -lt 1 ]] && return 0
  package="${1}"
  shift
  echo "### fixing ${package}"
  apt-get -y install "${package}"
  echo ''
}
fixit accerciser
fixit accountsservice
fixit acpi-support
fixit acpid
fixit adb
[more than 1,800 similar lines]

    Step 5:

    I ran this:

    % sudo bash apt-installs

    This ran for around 30 minutes and reinstalled each of the packages. As can be seen in the fixit function, no remove was done before each install.

    Step 6:

    I then ran these two commands ...

    % sudo apt-get purge aptitude
% sudo apt-get install aptitude

    This got aptitude back in sync with the apt database.

    Everything seems back to normal now.

    I'm guessing that if I knew what apt-related files/directories to reinstall from my recent backup, I could have fixed the problem that way, as well. However, I don't know enough about the lower-level internals of apt, and I couldn't quickly figure out what items would need to be restored.

    For future reference, I'd like to know this information about how to restore the apt database, because it will make it easier to fix this kind of problem if it occurs again.

    And many thanks to user535733!

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