I'm working with 8 shapefiles at approximately 63 mb in size total and I am trying to use ArcGIS/arcpy's Union to combine them into one single dataset.

Each time I run this, I get the error:

ERROR 999999: Something unexpected caused the tool to fail. Please refer to the error help for potential solutions, or contact Esri Technical Support http://esriurl.com/support.

Invalid Topology [Incomplete void poly.]

Failed to execute (Union).

On this page, as well as on ESRI's website, it is suggested to use arcgis Repair Geometry to fix this issue. I have tried to run check geometry and repair geometry both with ESRI's validation method and with OGC's validation method. OGC found some errors that it reported solved.

This did however not solve the error.

I have also tried to use v.clean in QGIS 3.2, but this messed up some of the shapefiles geometry (I have a backup, luckily).

Is there some other method i could try?

  • Have you tried running the check geometry tool and then joining the output table back to the shapefile to see where the error is? Seeing the bad geometry might help you with identifying why the tool isn't working. It might be that you can then manually repair that single polygon.
    – Dan_h_b
    Jul 23 '18 at 15:24
  • 2
    I've seen this Invalid Topology error be thrown because of memory management issues even when all geometries have been OK. Have you tried doing the Union two-at-a-time? Another suggestion might be to save them as featureclasses in a file geodatabase and trying again.
    – Alexander
    Jul 23 '18 at 15:50
  • Hey @Alexander i was wondering if this was the case - i tried with 7 first, and it worked. Are geodatabase files less memory intensive?
    – Jonas
    Jul 23 '18 at 16:55
  • I'm not sure if there's really any difference, I've just observed that changing the storage format can sometimes help these resource-intensive geoprocessing tools complete. Were you able to fix this issue in the end?
    – Alexander
    Jul 24 '18 at 9:08
  • 1
    The issue was solved yes. It helped splitting the union into several steps, ending with union'ing a "4-stack" and a "4-stack" together.
    – Jonas
    Jul 24 '18 at 15:22

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