Thanks for a great package!
I've had some problems I've managed to fix by tweaking the extend_val parameter of parseWorkspace.
I would sometimes get an error "try to extend the coordinates for ellipse gate!". I think this emerged from line 320 in gate.cpp. I didn't understand it at first, but it was urging me to adjust the extend_val parameter as the actual coordinates of the gate that caused the error, were smaller than the extend_val.
I also had different values in gate counts from flowCore and FlowJo, and the gates in plots (from plotGate) would suddenly snap out as a straight line to the edge.
I fixed it by setting extend_val to -Inf and haven't had these problems since. I can't find a performance penalty or other side effects, but I guess there is a small performance penalty. Maybe this problem was specific for me. Just thought I'd share as this has been bugging me for some time. If there is a recommended way, I'd be happy to learn!