rajewsky-lab / novosparc

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Unable to run sample files #27

Closed YvonneChenCS closed 4 years ago

YvonneChenCS commented 4 years ago

Hi, I think I successfully installed novosparc, but when I tried to run the sample files, I keep getting the following error message:

opt/anaconda3/lib/python3.7/site-packages/pysal/lib/weights/util.py:19: UserWarning: geopandas not available. Some functionality will be disabled. warn('geopandas not available. Some functionality will be disabled.') /opt/anaconda3/lib/python3.7/site-packages/pysal/explore/spaghetti/util.py:13: UserWarning: geopandas/shapely not available. Some functionality will be disabled. warn(err_msg) Traceback (most recent call last): File "reconstruct_bdtnp_with_markers.py", line 5, in import novosparc File "/Users/c/Desktop/novosparc-master/novosparc/init.py", line 17, in from . import analysis File "/Users/c/Desktop/novosparc-master/novosparc/analysis/init.py", line 1, in from ._analysis import morans File "/Users/c/Desktop/novosparc-master/novosparc/analysis/_analysis.py", line 2, in import pysal.lib File "/opt/anaconda3/lib/python3.7/site-packages/pysal/init.py", line 3, in from . import explore File "/opt/anaconda3/lib/python3.7/site-packages/pysal/explore/init.py", line 6, in from . import segregation File "/opt/anaconda3/lib/python3.7/site-packages/pysal/explore/segregation/init.py", line 7, in from . import aspatial File "/opt/anaconda3/lib/python3.7/site-packages/pysal/explore/segregation/aspatial/init.py", line 1, in from .aspatial_indexes import * File "/opt/anaconda3/lib/python3.7/site-packages/pysal/explore/segregation/aspatial/aspatial_indexes.py", line 10, in import geopandas as gpd File "/opt/anaconda3/lib/python3.7/site-packages/geopandas/init.py", line 5, in from geopandas.io.file import read_file # noqa File "/opt/anaconda3/lib/python3.7/site-packages/geopandas/io/file.py", line 6, in import fiona File "/opt/anaconda3/lib/python3.7/site-packages/fiona/init.py", line 83, in from fiona.collection import BytesCollection, Collection File "/opt/anaconda3/lib/python3.7/site-packages/fiona/collection.py", line 9, in from fiona.ogrext import Iterator, ItemsIterator, KeysIterator ImportError: dlopen(/opt/anaconda3/lib/python3.7/site-packages/fiona/ogrext.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libgif.7.dylib Referenced from: /opt/anaconda3/lib/libgdal.20.dylib Reason: image not found

As a side note, I installed nhvosparc through conda. Thank you very much.

enessenel commented 4 years ago

Hi, could you please check which pysal version you have installed and let me know? Upgrading it to version 2.1.0 through conda might help

enessenel commented 4 years ago

pysal dependency is removed so it should function now without the version issues.