The apt get update itself isn’t a problem,
but if you run apt get upgrade it can be, as it updates the OS’s kernel, and current navigator/BlueOS releases are based on a previous kernel.
sudo SKIP_WARNING=1 rpi-update 1340be4
should downgrade to the BlueOS current supported kernel
Thank you @RaulTrombin it does work I could recover direct access to the PWM’s through the python API.
Now I have a follow up question (maybe it warants another topic): setting the PWM seems to mess up with ardusub: I’m trying to read the mavlink attitude message, and also publish the PWM’s; to no avail.
How would you do that? I’ve tried to set the servos through mavlink rather than through the python api; but it seems that MAV_CMD_DO_SET_SERVO only allows setting one servo at a time every 1/50Hz, which is a bit slow.
Navigator libraries do access the hardware sensors directly, so it’s recommended to use them with ardusub disabled.
When the navigator libraries’ init() function is called, for example, it resets and configures the sensors, so it could break any ardusub routines in progress.
Thank you for the explanation @RaulTrombin , good to know!
Since I do want some of the ardupilot machinery for now (in particular the estimator) I ended up using pymavlink’s rc_channels_override_send function. (in hindsight, sticking to mavlink to talk to the navigator makes sense)