ERROR while importing GeoPandas in Python3 (Ubuntu); "Unable to open EPSG support file gcs.csv. (...)"

[swiss-knight]

Expected behavior and actual behavior.

I met the following error while importing geopandas in python3 on Ubuntu 18.04:

>>> import geopandas as gpd
ERROR 4: Unable to open EPSG support file gcs.csv. 
         Try setting the GDAL_DATA environment variable to point 
         to the directory containing EPSG csv files.

Notice; I installed GDAL using release 3.1.0 from github and the following procedure after having unzip the tar in a folder /opt/gdal-3.1.0:

cd /opt/gdal-3.1.0

./autogen.sh

./configure --enable-shared --with-python=python3 \
--with-proj=/usr/local CXXFLAGS="-Wall -std=c++11"

make

sudo checkinstall

sudo ldconfig

Checkinstall listed a few swig/python files that would not be embed in the dist package:

Some of the files created by the installation are inside the build
directory: /opt/gdal-3.1.0

You probably don't want them to be included in the package,
especially if they are inside your home directory.
Do you want me to list them?  [n]: y

/opt/gdal-3.1.0/swig/python/GDAL.egg-info/dependency_links.txt
/opt/gdal-3.1.0/swig/python/GDAL.egg-info/PKG-INFO
/opt/gdal-3.1.0/swig/python/GDAL.egg-info/requires.txt
/opt/gdal-3.1.0/swig/python/GDAL.egg-info/SOURCES.txt
/opt/gdal-3.1.0/swig/python/GDAL.egg-info/top_level.txt
/opt/gdal-3.1.0/swig/python/record.txt

Should I exclude them from the package? (Saying yes is a good idea)  [y]:  y

After what, I installed gdal in Python3 using pip:

sudo -h pip3 install -U gdal
It went fine, without any errors.

Environment

OS: Ubuntu 18.04.

Python3: Python 3.6.9 (default, Apr 18 2020, 01:56:04)

gdalinfo --version: GDAL 3.1.0, released 2020/05/03

geopandas:

>>> import geopandas as gpd
>>> gpd.__version__
'0.7.0'

gdal (python):

>>> from osgeo import gdal
>>> gdal.__version__
'3.1.0'
>>> gdal.__file__
'/usr/local/lib/python3.6/dist-packages/osgeo/gdal.py'

This may be useful (these files are certainly unrelated to the current installation):

$ sudo find /usr -iname gcs.csv
./share/gdal/2.4/gcs.csv
./share/epsg_csv/gcs.csv
./local/lib/python3.6/dist-packages/rasterio/gdal_data/gcs.csv
./local/lib/python3.6/dist-packages/fiona/gdal_data/gcs.csv

And this led to no results:

$ sudo find /opt -iname gcs.csv

I wonder what this file is and if there is something that should have been done during the installation for it to be aware of this file gcs.csv?

[rouault]

Looks like you have a mix of GDAL versions in your environemnt. gcs.csv is no longer used since GDAL 3.0.