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The violations in JPG are viols between cell blockages and special nets (power/ground). Usually special nets are routed using other tools, and NR will not touch them, so not check DRC for them.
The issue you encounterred seems to be cell problem, not routing problem.
Hi Greatrebel,
The warning messages means if a top level pin is not logical, that is, it is placed, then it must have some geometries defined.
You may output the def file, the check the PIN Y for something like:
---
+ PIN Y
+ LAYER Mx (x1 y1) (x2 y2)
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