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(Copied from MM message, I am not sure if I have time to fix it myself later so leaving it here for the record, thanks!)
When trying the latest instructions on freshly installed Ubuntu 25.10 or even 24.04 LTS for sel4test (https://docs.sel4.systems/projects/buildsystem/host-dependencies.html) when one gets to ninja step there is a missing "python3-protobuf" error which if followed installs python3-protobuf-2.5.0 that then causes lots of issues as it is really old one. :-) This is on the latest Ubuntu, so some others may hit this issue as I think Ubuntu comes with later protobuf version. This can be easily fixed by forcing the right protobyf in your python venv by "pip install --upgrade "protobuf>=4.21.0,<6.0.0"" for example. Just FYI.
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