The Magic DRC checks report these 3 violations

Violation Message "Deep N-well spacing < 6.3um (dnwell.3) "found 47 Times.
Violation Message "Deep N-well spacing to N-well < 4.5um (nwell.7) "found 288 Times.
Violation Message "N-well overlap of Deep N-well < 0.4um outside, 1.03um inside (nwell.5a, 7) "found 55 Times.
 DRC Checks on GDS Failed, Reason: Total # of DRC violations is 390

in a region which doesn't make sense to me. The violating areas start out in my PNP array, but veer way off from any relevant part of the design. When I check my layout with

drc(full)

(I select all area and do

DRC Update

) I don't get any violations. I read some of `open_pdks/sky130A/libs.tech/magic/sky130A-GDS.tech`and saw that it mentions

Generally, this covers rules not found in sky130A.tech

. In any case, I don't understand why I would need any deep nwell for parasitic PNPs.

I would appreciate it if you could post this example; I have a flattened version of your layout (or some version of it) but that doesn't trigger the error. None of this makes any sense without a deep nwell. . .

Yes yes yes. Seeing that too

Okay, I can reproduce the error. GDS layer numbers got crossed somewhere. Should be an easy fix.

cool! thanks

I have pushed the correction. You can either pull or fix the line by hand.