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Import Error: Libncurses, Libspatialite? #46

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Per48edjes opened this issue Oct 15, 2018 · 1 comment
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Import Error: Libncurses, Libspatialite? #46

Per48edjes opened this issue Oct 15, 2018 · 1 comment

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@Per48edjes
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Hi all, opening up a new issue since it seems I've cleared the gdal and multiple channel snafus (by making a new environment, setting conda-forge as the default, and fresh-installing geopandas). Apologies in advance if this should be folded in elsewhere! (Also, full disclosure, I'm pretty green when it comes to working with Conda.)

Issue:

Here's a link to my issue on SO, but I'll reproduce the necessary bits below!

ImportError                               Traceback (most recent call last)
<ipython-input-1-e48a390bcc03> in <module>()
      7 import matplotlib.pyplot as plt
      8 from matplotlib.ticker import FuncFormatter, MultipleLocator, AutoMinorLocator
----> 9 import geopandas as gpd
     10 
     11 

//anaconda/lib/python3.6/site-packages/geopandas/__init__.py in <module>()
      2 from geopandas.geodataframe import GeoDataFrame
      3 
----> 4 from geopandas.io.file import read_file
      5 from geopandas.io.sql import read_postgis
      6 from geopandas.tools import sjoin

//anaconda/lib/python3.6/site-packages/geopandas/io/file.py in <module>()
      1 import os
      2 
----> 3 import fiona
      4 import numpy as np
      5 import six

//anaconda/lib/python3.6/site-packages/fiona/__init__.py in <module>()
     67 from six import string_types
     68 
---> 69 from fiona.collection import Collection, BytesCollection, vsi_path
     70 from fiona._drivers import driver_count, GDALEnv
     71 from fiona.drvsupport import supported_drivers

//anaconda/lib/python3.6/site-packages/fiona/collection.py in <module>()
      7 
      8 from fiona import compat
----> 9 from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
     10 from fiona.ogrext import Session, WritingSession
     11 from fiona.ogrext import (

ImportError: dlopen(//anaconda/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libncurses.6.dylib
  Referenced from: //anaconda/lib/libspatialite.7.dylib
  Reason: image not found

Environment (conda list): 
$ conda list

# Name                    Version                   Build  Channel
anaconda                  custom           py36ha4fed55_0
appnope                   0.1.0                 py36_1000    conda-forge
backcall                  0.1.0                      py_0    conda-forge
blas                      1.0                         mkl
bleach                    3.0.2                      py_0    conda-forge
boost-cpp                 1.67.0               h3a22d5f_0    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2018.8.24            ha4d7672_0    conda-forge
cairo                     1.14.12              he6fea26_5    conda-forge
certifi                   2018.8.24             py36_1001    conda-forge
clangdev                  6.0.1                 default_1    conda-forge
click                     7.0                        py_0    conda-forge
click-plugins             1.0.4                      py_0    conda-forge
cligj                     0.5.0                      py_0    conda-forge
curl                      7.61.1               h74213dd_2    conda-forge
cycler                    0.10.0                     py_1    conda-forge
decorator                 4.3.0                      py_0    conda-forge
descartes                 1.1.0                      py_2    conda-forge
entrypoints               0.2.3                 py36_1002    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fiona                     1.7.13           py36hb00a9d7_3    conda-forge
fontconfig                2.13.1               hce039c3_0    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
freexl                    1.0.5                h470a237_2    conda-forge
gdal                      2.2.4            py36hb00a9d7_9    conda-forge
geopandas                 0.4.0                      py_1    conda-forge
geos                      3.6.2                hfc679d8_3    conda-forge
geotiff                   1.4.2                h700e5ad_4    conda-forge
gettext                   0.19.8.1             h1f1d5ed_1    conda-forge
giflib                    5.1.4                h470a237_1    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
hdf4                      4.2.13               h951d187_2    conda-forge
hdf5                      1.10.2               hc401514_2    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
intel-openmp              2019.0                      118
ipykernel                 5.1.0              pyh24bf2e0_0    conda-forge
ipython                   7.0.1           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.13.1                py36_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
json-c                    0.12.1               h470a237_1    conda-forge
jsonschema                2.6.0                 py36_1002    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kealib                    1.4.9                h0bee7d0_2    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.16.1               hbb41f41_0    conda-forge
libcurl                   7.61.1               hbdb9355_2    conda-forge
libcxx                    6.0.1                         0    conda-forge
libdap4                   3.19.1               h18059cb_1    conda-forge
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgdal                   2.2.4                hdb23ba1_9    conda-forge
libgfortran               3.0.1                h93005f0_2
libiconv                  1.15                 h470a237_3    conda-forge
libkml                    1.3.0                hccc92b1_8    conda-forge
libnetcdf                 4.6.1                h039f2a5_8    conda-forge
libpng                    1.6.35               ha92aebf_2    conda-forge
libpq                     10.5                 hf16a0db_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libspatialindex           1.8.5                hfc679d8_3    conda-forge
libspatialite             4.3.0a              h3b29d86_23    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libtiff                   4.0.9                he6b73bb_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
llvm-meta                 6.0.1                         0    conda-forge
llvmdev                   6.0.1                h2d50403_2    conda-forge
markupsafe                1.0              py36h470a237_1    conda-forge
matplotlib                3.0.0            py36h45c993b_1    conda-forge
mistune                   0.8.4            py36h470a237_0    conda-forge
mkl                       2019.0                      118
mkl_fft                   1.0.6                    py36_0    conda-forge
mkl_random                1.0.1                    py36_0    conda-forge
munch                     2.3.2                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
notebook                  5.7.0                 py36_1000    conda-forge
numpy                     1.15.2           py36h6a91979_1
numpy-base                1.15.2           py36h8a80b8c_1
openblas                  0.3.3                ha44fe06_1    conda-forge
openjpeg                  2.3.0                h316dc23_3    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
pandas                    0.23.4           py36hf8a1672_0    conda-forge
pandoc                    2.3.1                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.3.1                      py_0    conda-forge
pcre                      8.41                 hfc679d8_3    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
poppler                   0.67.0               h4d7e492_3    conda-forge
poppler-data              0.4.9                         0    conda-forge
postgresql                10.5                 ha408888_0    conda-forge
proj4                     4.9.3                h470a237_8    conda-forge
prometheus_client         0.4.2                      py_0    conda-forge
prompt_toolkit            2.0.6                      py_0    conda-forge
psycopg2                  2.7.5            py36hdffb7b8_2    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pyparsing                 2.2.2                      py_0    conda-forge
pyproj                    1.9.5.1          py36h508ed2a_5    conda-forge
pysal                     1.14.4.post2             py36_1    conda-forge
python                    3.6.6                h5001a0f_0    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pytz                      2018.5                     py_0    conda-forge
pyzmq                     17.1.2           py36hae99301_1    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
rtree                     0.8.3                 py36_1000    conda-forge
scipy                     1.1.0            py36h28f7352_1
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.4.3                   py36_0    conda-forge
shapely                   1.6.4            py36h164cb2d_1    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
six                       1.11.0                py36_1001    conda-forge
sqlalchemy                1.2.12           py36h470a237_0    conda-forge
sqlite                    3.25.2               hb1c47c0_0    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tk                        8.6.8                ha92aebf_0    conda-forge
tornado                   5.1.1            py36h470a237_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.32.1                   py36_0    conda-forge
xerces-c                  3.2.0                h5d6a6da_2    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_5    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ): 
$ conda info

     active environment : new_env
    active env location : //anaconda/envs/new_env
            shell level : 1
       user config file : /Users/ravidayabhai/.condarc
 populated config files : /Users/ravidayabhai/.condarc
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.6.6.final.0
       base environment : //anaconda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : //anaconda/pkgs
                          /Users/ravidayabhai/.conda/pkgs
       envs directories : //anaconda/envs
                          /Users/ravidayabhai/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.11 requests/2.19.1 CPython/3.6.6 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 502:20
             netrc file : None
           offline mode : False

Any help would be most appreciated! 🙏
@ocefpaf ocefpaf mentioned this issue Oct 16, 2018
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@ocefpaf
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ocefpaf commented Oct 16, 2018

Things as working on Linux for me with:

conda create --name TEST --channel conda-forge python=3.6 geopandas --yes
conda activate TEST
python -c "import geopandas; print(geopandas.__version__)"

However, I don't have a Mac to test it so I'm issuing a re-render in fiona to ensure we have a package with latest pinning. See #46

PS: closing this b/c it is not a geopandas issue. We can track this at the PR I mentioned above.

@ocefpaf ocefpaf closed this as completed Oct 16, 2018
@forman forman mentioned this issue Dec 19, 2018
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@ocefpaf @Per48edjes