Error while using sjoin in GeoPandas

Question

I have a problem with GeoPandas sjoin, I work with Ubuntu and I want to use:

opolskieadresy = geopandas.sjoin(smallopolskie, adresy, how="inner", op='intersects') 

and i'm getting error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/gis/.local/lib/python3.8/site-packages/geopandas/tools/sjoin.py", line 88, in sjoin
    sindex = right_df.sindex
  File "/home/gis/.local/lib/python3.8/site-packages/geopandas/base.py", line 593, in sindex
    self._generate_sindex()
  File "/home/gis/.local/lib/python3.8/site-packages/geopandas/base.py", line 98, in _generate_sindex
    sindex_cls = get_sindex_class()
  File "/home/gis/.local/lib/python3.8/site-packages/geopandas/sindex.py", line 42, in get_sindex_class
    raise ImportError(
ImportError: Spatial indexes require either `rtree` or `pygeos`. See installation instructions at https://geopandas.org/install.html

When I try to install rtree: sudo pip3 install rtee I'm getting:

Collecting rtree
  Using cached Rtree-0.9.4.tar.gz (62 kB)
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ib_695_y/rtree/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ib_695_y/rtree/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-ib_695_y/rtree/pip-egg-info
         cwd: /tmp/pip-install-ib_695_y/rtree/
    Complete output (15 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-ib_695_y/rtree/setup.py", line 3, in <module>
        import rtree
      File "/tmp/pip-install-ib_695_y/rtree/rtree/__init__.py", line 1, in <module>
        from .index import Rtree
      File "/tmp/pip-install-ib_695_y/rtree/rtree/index.py", line 6, in <module>
        from . import core
      File "/tmp/pip-install-ib_695_y/rtree/rtree/core.py", line 143, in <module>
        rt.Error_GetLastErrorNum.restype = ctypes.c_int
      File "/usr/lib/python3.8/ctypes/__init__.py", line 386, in __getattr__
        func = self.__getitem__(name)
      File "/usr/lib/python3.8/ctypes/__init__.py", line 391, in __getitem__
        func = self._FuncPtr((name_or_ordinal, self))
    AttributeError: /usr/bin/python3: undefined symbol: Error_GetLastErrorNum
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Answer 1

Solution:

First:

sudo apt install libspatialindex-dev

Then:

sudo pip3 install rtree

Answer 2

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

Answer 3

in my case, the only thing that helped:

> # install and import condalab, run twice.

!pip install -q condacolab -q

import condacolab

condacolab.install()

> # install geopandas, this could take long

!conda install geopandas

import geopandas as gpd

Answer 4

Install libspatialindex fixed it for me (I installed geopandas with pip).
You can try the following:

conda install -c conda-forge libspatialindex=1.9.3

If you install geopandas from conda directly, I think it should run without problem.