ImportError: libicui18n.so.56 and/or libicui18n.so.58 when importing fiona (geopandas)

[plelong]

Hi,
I'm using anaconda on Ubuntu 16.04 (xenial Xerus) on EC2.
After installing anaconda I install geopandas with:
conda install geopandas --channel conda-forge
That works great but I then go to a jupyter notebook and try to import geopandas but get :

`ImportError                               Traceback (most recent call last)
<ipython-input-1-c9ee6bd24dbc> in <module>()
----> 1 import geopandas

/home/ubuntu/anaconda3/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

/home/ubuntu/anaconda3/lib/python3.6/site-packages/geopandas/io/file.py in <module>()
      1 import os
      2 
----> 3 import fiona
      4 import numpy as np
      5 from shapely.geometry import mapping

/home/ubuntu/anaconda3/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

/home/ubuntu/anaconda3/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: libicui18n.so.56: cannot open shared object file: No such file or directory`

This has to do with the fiona package that requires libicui18n.so.56. When I type
conda search icu --channel conda-forge
I do get that it is the 54 version which is installed (with a *) and I therefore use
conda install icu=56.1 --channel conda-forge
and that installs a entire set of packages (and downgrade python from 3.6 and 3.5) when this is done, my import error gives me:
ImportError: libicui18n.so.58: cannot open shared object file: No such file or directory
It seems like fiona is requiring both 56 and 58 version of icu. When I switch to 58 then 56 is missing ...
Do you have any idea of what is going wrong there and what I could do to fix this?
Thanks,

[ocefpaf]

It looks like you have the usual "multiple channes" problem. Please take a look at http://conda-forge.github.io/docs/conda-forge_gotchas.html#using-multiple-channels and let us know if that fixes it for you. (Closing this for now but feel free to ask further questions here in case you are in doubt.)

[plelong]

I tried to fix it using
conda config --add channels new_channel before running conda install geopandas
and I do get
cat .condarc
channels:
- conda-forge
- defaults
But when importing geopandas in a jupyter notebook I still get an error on fiona:
ImportError: libicui18n.so.56: cannot open shared object file: No such file or directory

Do you any other idea of what that might be ? let me know if you need some more info on my system

[plelong]

Update: creating a new conda env seems to solve the issue. I will let you know if this is not the case.

[pkmn99]

I have exact the same problem. Creating a new environment works, but i really hope there could be a fix without creating a new env. The new environment takes a lot space (2GB) ...

[ocefpaf]

The new environment takes a lot space (2GB)

There is no way around it because those extra packages are the ones you need to be compatible with the package you are requesting from conda-forge. That is why I recommend people to use miniconda and create envs. Miniconda is lightweight and won't bring any extra package that will be replaced by conda-forge later, unlike the anaconda distro which will be probably 99% replaced. And then, with envs, you will get symlinks to the packages you download avoiding the space waste when creating multiple envs.

[pkmn99]

Yes, I am using anaconda. The duplicated packages in Anaconda indeed take my disk space. Glad to know these features of miniconda. Thanks ocefpaf!

[ivanhigueram]

Hello,
Thanks for sharing how you solved the issue. I am right now having the same problem installing and calling geopandas. I have create a new virtual environment using: conda create -n env python=3.5 anaconda. Nonetheless, the ImportError persists. There is another road to take to solve this problem?

[ocefpaf]

Nonetheless, the ImportError persists. There is another road to take to solve this problem?

It should, you installed the whole anaconda distro there 😄

Please read http://conda-forge.github.io/docs/conda-forge_gotchas.html#using-multiple-channels with care and note that the reason for isolating into envs and preferring the conda-forge channels when using conda-forge packages is to avoid conflicts with the anaconda distribution.

[kyle-sama]

So I read the multiple channels link.
I have the two channels:
channels:

• conda-forge
• defaults
  I created a new environment
  conda create -n env whatever
  install my libraries
  conda install geopandas, ipykernel, basemap

and I still get the error. What the heck am I doing wrong?

[ocefpaf]

@kyle-sama seems like you did everything right 😕

Can you send the results of conda info and conda list for tht env?

[clementlefevre]

Hi,
Similar problem :

Fiona==1.7.9
geopandas==0.3.0

Using a python 3.5 env and install geopandas using conda install geopandas, i can import the ´geopandas´ package from the python console but not from ipython/jupyter notebook.

/home/ramon/anaconda2/lib/python2.7/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: libicui18n.so.56: cannot open shared object file: No such file or directory

conda info:
(env) ramon@ramon-ThinkPad-X220:~$ conda info
Current conda install:

               platform : linux-64
          conda version : 4.3.29
       conda is private : False
      conda-env version : 4.3.29
    conda-build version : 2.0.2
         python version : 2.7.12.final.0
       requests version : 2.18.4
       root environment : /home/ramon/anaconda2  (writable)
    default environment : /home/ramon/anaconda2/envs/env
       envs directories : /home/ramon/anaconda2/envs
                          /home/ramon/.conda/envs
          package cache : /home/ramon/anaconda2/pkgs
                          /home/ramon/.conda/pkgs
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : /home/ramon/.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.29 requests/2.18.4 CPython/2.7.12 Linux/4.4.0-98-generic debian/stretch/sid glibc/2.23    
                UID:GID : 1000:1000
´

[ocefpaf]

I am locking this thread b/c people keep finding it with Google but they are not really reading everything in here. First I recommend to go to conda-forge's docs to understand the issue. https://conda-forge.org/docs/conda-forge_gotchas.html

Then try what is recommended in the docs:

conda create --yes --name TEST geopandas
source activate TEST
python -c "import geopandas; print(geopandas.__version__)"

that proves the package works in the right conditions. Any other third party channel mixing and/or pre-installed packages in an env, like the Anaconda distribution, is not guaranteed to work!