Thanks for your help. I just discovered Batocera, and besides some issues I still need fixed I am really pleased with it.
So the problem is some glsl presets (crt-royale in this case, but there are others) are trying to load glsl shader files that are not included in the distro.
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Failed to open /recalbox/share_init/shaders/shaders_glsl/crt/shaders/crt-royale/src/crt-royale-bloom-approx-fake-bloom-intel.glsl: No such file or directory
[ERROR] Failed to load GLSL shader: /recalbox/share_init/shaders/shaders_glsl/crt/shaders/crt-royale/src/crt-royale-bloom-approx-fake-bloom-intel.glsl.
[WARN] [GL]: Stock GLSL shaders will be used.
[INFO] Resetting shader to defaults ...
[WARN] [GL]: Failed to set multipass shader. Falling back to stock.
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Not sure if there was a better way to do this but to fix I replaced the shaders in
usr/share/batocera/datainit/shaders/shaders_glsl
with the ones from the libretro repo https://github.com/libretro/glsl-shaders
and ran /recalbox/scripts/recalbox-save-overlay.sh
Any chance to have up to date shaders for the next release ?