Error: after update flake about python3.11-tkinter

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[SOLVED] HOWTO: Fix fatal error: tommath.h during qemu_full build on NixOS

Hi everyone,

I managed to solve this build issue, and I wanted to share the full solution. A big thank you to those who suggested the problem might be related to qemu—that was the key. The troubleshooting process was a bit long, so I’ve used an AI to help me write up a clear and detailed explanation for anyone else who runs into this.

The Problem

When trying to update my NixOS system with sudo nixos-rebuild switch --flake .#nixos, the build process would fail with the following error:

error: builder for '/nix/store/zdi06d8rz9wbsn8hg4dd7k7l6qrhv5zw-python3.11-tkinter-3.11.13.drv' failed with exit code 1;
       ...
       /build/python3.11-tkinter-3.11.13/tk8.6.13/unix/../generic/tk.h:76:11: fatal error: tommath.h: No such file or directory
          76 | # include <tommath.h>
             |           ^~~~~~~~~~~
       compilation terminated.

As the log shows, the core issue was the failure to build the python3.11-tkinter package, caused by the missing header file tommath.h. This pointed to a missing dependency bug within Nixpkgs.

Diagnosis Steps

Since I hadn’t explicitly installed tkinter, I needed to find out which package in my configuration.nix was pulling in this broken dependency.

Step 1: Dependency Tracing

Using the nix-store -q --referrers command, I started tracing the dependency chain. I found that matplotlib depended on tkinter, and other packages depended on matplotlib. This manual tracing became too complex.

Step 2: Identifying the Main Culprit (qemu_full)

I shifted my approach to inspecting my configuration.nix directly. The qemu_full package stood out as a large application with many potential dependencies and was identified as the prime suspect.

Step 3: Discovering the First Root Cause (QEMU Docs)

My investigation revealed that qemu_full, by default, builds its own documentation. This created the first problematic dependency chain:

  • The documentation build uses the sphinx tool.
  • sphinx (or one of its extensions) requires matplotlib for plotting.
  • matplotlib requires tkinter for its GUI backend.

Chain 1: qemu_full → Documentation Build → sphinx → matplotlib → tkinter (the broken package)

Step 4: Discovering the Second Root Cause (Ceph Support)

After disabling the documentation build, the error persisted! The new build log, however, pointed to another failing package: ceph.

  • The qemu_full package also enables support for Ceph (a distributed storage system) by default.
  • The ceph package itself has a complex Python environment, which includes data science libraries.
  • These libraries also depend on matplotlib, which in turn depends on tkinter.

Chain 2: qemu_full → Ceph Support → ceph package → ceph’s Python Environment → matplotlib → tkinter

Root Cause Analysis

The direct cause of the error is a bug in the python3.11-tkinter package definition in Nixpkgs. However, this broken package was being pulled into my system configuration by qemu_full through two distinct and optional features:

  1. The documentation build process.
  2. The default-enabled support for the Ceph distributed storage system.

To fix the build, both of these dependency chains had to be broken.

The Final Solution

The solution is to work around the tkinter bug by overriding the qemu_full package in configuration.nix to disable both of these optional features.

Go to your /etc/nixos/configuration.nix file and edit the environment.systemPackages section as follows:

// In your /etc/nixos/configuration.nix

environment.systemPackages = with pkgs; [
  # ... other packages you have ...
  
  # qemu_full  // REMOVE OR COMMENT OUT THIS LINE
  
  # And add this instead:
  (pkgs.qemu_full.override { 
    enableDocs = false; 
    cephSupport = false; 
  })

  # ... other packages ...
];

After applying this change, save the file and rebuild your system with sudo nixos-rebuild switch.

Explanation of the Fix
  • enableDocs = false;: This disables the QEMU documentation build, breaking the first dependency chain related to sphinx.
  • cephSupport = false;: This disables support for the Ceph storage system, breaking the second dependency chain.

By doing this, the core qemu_full package can be built successfully without pulling in the problematic optional dependencies. The main functionality of the simulator for typical use cases is not affected.

I hope this guide helps others who run into the same issue!

Search Keywords:
NixOS, build failed, qemu, qemu_full, tkinter, fatal error, tommath.h, matplotlib, ceph, nixos-rebuild, dependency issue.

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