The APM 2.6 doesn’t have an internal compass built in, so when there is no external compass connected will display the compass initialization error, this is normal.
If you have the GPS and the MAG ports connected to the GPS and I2C APM’s ports and the GPS is working that means the compass has power, please double check your configuration in mission planner: copter.ardupilot.com/wiki/common … on_Planner
If the connections and configurations are ok, you shouldn’t get a compass initialization error. If you are getting samples but there is not enough points to calibrate, I would recommend you to try to calibrate outdoors following this video: youtube.com/watch?v=-_mjfPlHL9o
Same resolution as you Pureguava, took my NEO-6M apart and the internal 6-pin molex connector had detached from the uBlox chip, that’s an RMA job as I’m not a ninja with the fine solderer yet. Switching to another GPS/compass fixed this issue for me.