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What the problem was: duplicate points After inspecting your data, I could identify the problem: you have a lot of duplicate points as well as a few points that are "almost" duplicates (extremely close to each other). From originally 954 features in the point layer you provided, only 229 (ca. 24%) are really unique points (thus not duplicates or ...


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I solved pip-installing the last rtree version downloaded from https://www.lfd.uci.edu/~gohlke/pythonlibs/#rtree,


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