Upgrading a Linux system is always a non-trivial task. In the following, I’ll list the phenomena and problems I met during upgrading Debian from Bullseye to Bookworm.

Basic information

Debian 12 Bookworm was released on 2023-06-10. Up to now, it includes the following key updates:

  • Linux kernel 6.1 series
  • Cryptsetup 2.6
  • GNU Compiler Collection 12.2
  • The GNU C Library 2.36
  • LLVM/Clang toolchain 13.0.1, 14.0 (default), and 15.0.6
  • Emacs 28.2
  • CMake 3.25.1: However, this is not enough for C++20.
  • GNU Octave 7.3.0
  • Python 3.11
  • Ruby 3.1
  • Julia 1.5.3
  • LibreOffice 7.5.3.2

After sudo apt upgrade

Cannot load module /usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)
/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so does not export GTK+ IM module API: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)
Processing triggers for libgtk2.0-0:amd64 (2.24.33-2) ...
Cannot load module /usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/immodules/im-fcitx.so: GModule (/usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)
/usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/immodules/im-fcitx.so does not export GTK+ IM module API: GModule (/usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)

During sudo apt dist-upgrade

  • The following packages were removed but some other packages still had dependencies on them. However, after dist-upgrade was finished, the following packages were reinstalled automatically.

    Removing texlive-bibtex-extra (2020.20210202-3) ...
Removing texlive-fonts-extra (2020.20210202-3) ...
dpkg: texlive-extra-utils: dependency problems, but removing anyway as you requested:
 doxygen-latex depends on texlive-extra-utils.
    
Removing texlive-extra-utils (2020.20210202-3) ...
dpkg: texlive-font-utils: dependency problems, but removing anyway as you requested:
 latex-cjk-common depends on texlive-font-utils (>= 2007.dfsg.2-1).
 doxygen-latex depends on texlive-font-utils.
    
Removing texlive-font-utils (2020.20210202-3) ...
dpkg: texlive-binaries
    
Removing texlive-latex-base (2020.20210202-3)
    
dpkg: texlive-latex-extra: dependency problems, but removing anyway as you requested:
    
dpkg: texlive-pictures: dependency problems, but removing anyway as you requested:

After sudo apt dist-upgrade

Anki

The GUI interface of Anki (2.1.49) does not show anything.

Solution: upgrade to Anki 24.04.1 with Qt6. Install Debian packages qt6-base-dev and qt6-base-dev-tools to acquire Qt6.

Emacs

  • LaTeX fragments previewed in Org mode become extremely large. Changing the scale factor from 2.5 to 1.5 solves the problem. The configuration is stored in the variable org-format-latex-options:

    (custom-set-variables
 '(org-format-latex-options
   '(:foreground default :background default :scale 1.5 :html-foreground "Black" :html-background "Transparent" :html-scale 1.0 :matchers
                 ("begin" "$1" "$" "$$" "\\(" "\\["))))

  • Mixed installation of Org mode error

    Org mode version 9.5.5 (release_9.5.5 @ mixed installation! /usr/share/emacs/28.2/lisp/org/ and /usr/share/emacs/site-lisp/elpa/org-9.4/)

    The former version /usr/share/emacs/28.2/lisp/org/ has actually been installed via the Debian package elpa-org, which further depends on the package org-mode. From this we can see that org-mode has been integrated into Emacs itself instead of an external package.

    Solution

    • Remove /usr/share/emacs/site-lisp/elpa/org-9.4/, which is obviously obsolete.
    • Install the Debian package elpa-org-contrib, which contains ox-freemind and ox-taskjuggler. I have been using them to export Org mode contents to Freeplane mind map as well as TaskJuggler for project management. Both of them are enabled in the variable org-export-backends. The package elpa-org-contrib is installed to the folder /usr/share/emacs/site-lisp/elpa/org-contrib-0.4.

  • Each time when I export Org mode contents including LaTeX source code blocks, there will be an prompt about whether each of them should be executed.

    Solution: add the header arguments :eval never-export :exports code to the source code block will prevent such prompts.

  • CMake file cannot be automatically formatted by the package cmake-format anymore.

    cmake-format errors:
Traceback (most recent call last):
  File "/home/jihuan/.local/bin/cmake-format", line 5, in <module>
    from cmakelang.format.__main__ import main
ModuleNotFoundError: No module named 'cmakelang'

    This is because the Emacs cmake-format package relies on the Python package cmakelang. However, Python has been upgraded from 3.7 to 3.11 during the system upgrade, which means all previously installed Python packages via pip should be reinstalled.

Python

As mentioned above, all Python packages should be reinstalled.

  • If there is a corresponding Debian package in apt, install that package system-wide.
    • cmake-format
  • If there is no such as Debian package, create a virtual environment and install the package within it.

Jekyll

Cannot build blog anymore with the error:

bundle: cannot execute: required file not found

The cause is after system upgrade, ruby-rubygems is upgraded from version 2.7 to 3.3.15 and all gems should be reinstalled.

  • bundler
  • jekyll
  • minima: blog style
  • kramdown: markdown support
gem install bundler jekyll minima kramdown

Change to the folder of the blog, run bundle install.

Texlive based LaTeX

ntheorem does not work with hyperref anymore.

Solution: the package option thref for ntheorem should not be used.

GNU Octave

Compatibility issue of octave::interpreter::eval_string related functions, when a function without return value is called from C++ via libinterp.

KDE Plasma desktop

The fast key “Meta” for triggering the Application launcher cannot be disabled in “Shortcuts”.

Solution: remove Application launcher applet and use “Ctrl+mouse right button” to trigger it when showing the desktop.

PulseAudio

Debian Bookworm uses pipewire by default, which replaces previous pulseaudio.

If pulseaudio is needed, it can be switched back like this.

systemctl unmask pulseaudio
systemctl --now disable pipewire-pulse
systemctl --now enable pulseaudio.service pulseaudio.socket
systemctl --user restart pulseaudio.service

Wacom tablet

When switching to my predefined fast keys for some applications such as xournal, there is the “invalid offset” error.

Invalid offset into Wacom Button Actions property.

Cause: Button 9 on the Pen Stylus is not available on Debian Bookworm. This can be checked by executing

xsetwacom -s get <device-id/device-full-name> all | grep Button

Solution: all settings related to Button 9 on the Pen Stylus should be removed from my Wacom scripts.

Video player

VLC and mplayer cannot play mkv or mp4. VLC reported the following error.

VLC could not decode the format "h264" (H264 - MPEG-4 AVC (part10))

Solution: install the Debian package mediastreamer2-plugin-openh264.