Working with 2.0.0.6 I received similar error messages for three genomaps. No visible errors in genomaps.
Attached the print screen....
Thanks in advance,
Carlos
I have discovered the reason why the intersection cannot be determined. The script is trying to generate SVG code for a relationship line. However the centre of the object at one end of the relationship is placed within the boundary of the second object, and so no line can be drawn.
I will remove this message at the next release.