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@Gordon
Ahh - I think if the part has USB but USB isn't used, we should make sure it doesn't get defined. Do the EFM32 headers define it then?
For the timers, the best thing might be to include the software PWM support (copy it from the top part of AnalogOutput in STM32) and to enable soft PWM on a pin. Hopefully you'll be able to see quite easily if you're scheduling the timers correctly.
Also
digitalPulse(the jshardware implementation probably wants copying too - ideally it needs taking out to a shared file) - that's a good way to test as it should schedule a one-shot timer for a fixed time period.