Plesk update completes with a Warning: Information on some packages might not be actual: inconsistencies were detected in the system's package manager database

Symptoms

• Plesk Obsidian running on a Debian-based Linux operating system (most commonly Ubuntu 22)

• Plesk update completes with an error that is similar to the following:

  CONFIG_TEXT: Setting up grub-efi-amd64-signed (1.187.6+2.06-2ubuntu14.4) ...
  Installing grub to /boot/efi.
  Installing for x86_64-efi platform.
  grub-install: warning: Internal error.
  grub-install: error: failed to register the EFI boot entry: Operation not permitted.
  dpkg: error processing package grub-efi-amd64-signed (--configure):
  installed grub-efi-amd64-signed package post-installation script subprocess returned error exit status 1
  Setting up pp18.0.56-bootstrapper (18.0-v.ubuntu.22.04+p18.0.56.3+t231031.1251) ...
  Errors were encountered while processing:
  grub-efi-amd64-signed
  needrestart is being skipped since dpkg has failed
  E: Sub-process /usr/bin/dpkg returned an error code (1)
  Launching component and product checkers...
  Downloading file report-update: 0%
  Downloading file report-update: 100% was finished.
  Downloading file pool/PSA_18.0.56_13119/examiners/py_launcher.sh: 0%
  Downloading file pool/PSA_18.0.56_13119/examiners/py_launcher.sh: 100% was finished.
  
  ERROR: An error occurred on attempt to install packages.
  Attention! Your software might be inoperable.

  CONFIG_TEXT: Some problems occurred with the System Updates tool on your server example.com. Please resolve them manually

• The following error is also present in Tools & Settings > System Updates:

  PLESK_WARN: Warning: Information on some packages might not be actual: inconsistencies were detected in the system's package manager database. Please resolve this issue manually.

• The log file /var/log/plesk/systemupdatestool.logcontains errors that are similar to the following:
  

  CONFIG_TEXT: 2023-10-10 06:26:33 INFO: pum is called with arguments: ['--list', '--repo-info', '--json']
  2023-10-10 06:27:11 ERROR: Apt cache fetch failed: 2023-10-10 06:27:11
  ERROR: 2023-10-10 06:27:11 ERROR: Exited with returncode 1

  CONFIG_TEXT: The following packages are only half configured, probably due to problems configuring them the first time.
  The configuration should be retried using dpkg --configure <package> or the configure menu option in dselect:
  grub-efi-amd64-signed GRand Unified Bootloader, version 2 (EFI-AMD64 version,

• Running the dpkg --audit command results in the following output:
  

  # dpkg --audit
  The following packages are only half configured, probably due to problems
  configuring them the first time. The configuration should be retried using
  dpkg --configure <package> or the configure menu option in dselect:
  grub-efi-amd64-signed GRand Unified Bootloader, version 2 (EFI-AMD64 version,

   

Cause

There is a known glitch in the upgrade to grub-efi-amd64-signed and grub-efi-amd64-bin packages, where they both need to be upgraded, but they depend on each other and neither one of them wants to go first. This in turn creates issues with the package installers for Debian-based operating systems to hang and that prevents further package updates and upgrades form happening.

Resolution

Due to the importance of the related grub packages in connection with the server booting process, the recommended course of action is to contact your server provider or Linux administrator to solve the issue with system packages.

As an alternative solution to this issue, you may execute the following steps:

Warning: In certain conditions, these steps may make your server unable to boot, due to which you should take precautions and execute the steps below at your own risk

1. Log into your server via SSH

2. Execute the following command in order to get the updates for all system packages:

# apt update

3. Execute the following command in order to reinstall only the grub-efi-amd64-signed package:

# apt --only-upgrade install grub-efi-amd64-signed

4. Execute the following command in order to make sure the grub-efi-amd64-bin package is installed

# apt install grub-efi-amd64-bin

5. Now that the dependencies are resolved, execute the following command in order to upgrade all system packages:

# apt upgrade

6. The final step is to perform an update of all Plesk packages by executing the following command:

# plesk installer update

Additional information

apt - grub-efi-amd64-signed dependency issue in Ubuntu 22.04LTS - Ask Ubuntu

Fixing grub-efi-amd64-signed dependency issue in Ubuntu 22.04LTS | DeviceTests

System updates warning in Plesk: Information on some packages might not be actual: inconsistencies were detected in the system's package manager database. Please resolve this issue manually