Installation issues

[ccruizm]

Good day,

I want to test this wonderful tool. However, I am having issues with the installation. I have created a new conda env with the required packages and got the following error:

ERROR: Command errored out with exit status 1:
     command: /hpc/pmc_stunnenberg/cruiz/miniconda3/envs/novosparc/bin/python3.5 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-i7t40di6/rtree/setup.py'"'"'; __file__='"'"'/tmp/pip-install-i7t40di6/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-i7t40di6/rtree/pip-egg-info
         cwd: /tmp/pip-install-i7t40di6/rtree/
    Complete output (15 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-i7t40di6/rtree/setup.py", line 3, in <module>
        import rtree
      File "/tmp/pip-install-i7t40di6/rtree/rtree/__init__.py", line 1, in <module>
        from .index import Rtree
      File "/tmp/pip-install-i7t40di6/rtree/rtree/index.py", line 6, in <module>
        from . import core
      File "/tmp/pip-install-i7t40di6/rtree/rtree/core.py", line 143, in <module>
        rt.Error_GetLastErrorNum.restype = ctypes.c_int
      File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/novosparc/lib/python3.5/ctypes/__init__.py", line 364, in __getattr__
        func = self.__getitem__(name)
      File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/novosparc/lib/python3.5/ctypes/__init__.py", line 369, in __getitem__
        func = self._FuncPtr((name_or_ordinal, self))
    AttributeError: /hpc/pmc_stunnenberg/cruiz/miniconda3/envs/novosparc/bin/python3.5: undefined symbol: Error_GetLastErrorNum
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I have tested it in two different HPC and both got the same error. What do you think the problem is?

Thanks in advance!

[nukappa]

Hi, thanks for bringing this to our attention, it seems like there's a dependency conflict between libraries from pip and conda. Could you try to install the dependencies with conda first? pysal in particular. We're in the process of wrapping novosparc also in conda, so that should fix those problems.

[ccruizm]

Thanks for your quick reply. I tried installing all dependencies first (including pysal) but still getting the same message error. Any other suggestion I can try?

[dgcha97]

Hi, I think I faced almost same problem, and I solved it by specifying the rtree version. What if you try the command below?: pip install "rtree>=0.8,<0.9"

[enessenel]

Hi Cristian, did installing rtree solved your problem?

[ccruizm]

Hello!

Effectively, specifying the rtree version allows a smooth installation! Thanks @dgcha97 for the suggestion 👍