I'm trying to Clip the contents of a GPKG file (https://geodata.nationaalgeoregister.nl/brpgewaspercelen/extract/2020-definitief/brpgewaspercelen.zip). I select the feature from a different layer, with data originating in a GDB file, as to reduce the output to the area of interest.

However every time I perform this opperation I'm met with:

WARNING 000117: Warning empty output generated.

I simply added the GPKG file from the add data button. The other layer has no problems, as I used that a milion times before when doing operations like this, but then on data from other GDB files.

Both the GPKG file and data that came from a GDB are polygon's and have the same coordinate system (GCS Amersfoort).

Screenshot showing the input of the Clip tool.

Screenshot of the two layers (halfway through loading the .gpkg file data), in purple are the features I use to clip. One in the top right corner and one in the middle on the bottom. enter image description here

  • Yes it definetly should not be empty. There should be a couple of thousand, if not 10thousands results @BERA
    – Luuklag
    Oct 12, 2020 at 11:38
  • I assume you are trying to clip features, but it's not 100% clear. Are you trying to clip features or trying to clip a raster (.gpkg can include both, I think? Are you using the correct clip tool. Perhaps edit your question to include a picture of the tool with all parameters filled in. Nov 5, 2021 at 1:14
  • @SonofaBeach I updated the question with a new link. I am indeed trying to clip the features that are present in de .gpkg file, using a layer I have in my map.
    – Luuklag
    Nov 5, 2021 at 8:01
  • @SonofaBeach also addressed the other points you've raised with edits.
    – Luuklag
    Nov 5, 2021 at 8:43
  • 1
    @BERA ArcGis Pro was able to handle the geopackages, from there I was able to convert them to gdb files.
    – Luuklag
    Nov 12, 2021 at 13:46

2 Answers 2


I managed to install a version of ArGIS Pro today, and in that I was able to export the file as a geodatabase using the tool: Feature Class to Geodatabase.

The resulting gdb was opened fine by ArcMap and I could do my desired Clipping on that.


Try this workflow:

  1. Use the feature class to feature class geoprocessing tool in ArcMap to create a copy of the input and clip features.
  2. Save the output of the conversion into a new GDB along with the clip feature.
  3. Run the clip tool again.


  • This also results in empty layers.
    – Luuklag
    Nov 9, 2021 at 7:10

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