I have seen spikes with Here 2 over I2C but never timeouts like this. Have you checked that the I2C lines are not too long and not close to other wiring? Does it happen when you move the cables in a way?
In general they recommend to use the Here 2 over UAVCAN but I think this issue should tracked down nevertheless.
Some more data points that would be interesting:
- Does it happen on other hardware, e.g. not with a Pixracer but something else?
- Does anything else in the log file have these pauses?
- Does it happen with other Here 2 hardware, or do you only have one?
- Does it still happen with a fast (more expensive) SD card? (There could be some other effects be happening.)
Could you upload that log to http://logs.px4.io please, so I can have a look? Thx.