Geodjango Exception when importing django.contrib.gis.gdal: OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name

Question

I have followed the tutorial for installing Geodjango on my Ubuntu 14.04. I am using Django 1.10 and Python 3.5, postgres-9.6 and postgis 2.3.

I have checked here and here, but found no solution. In a newly installed ubuntu 14.04 Virtual Machine, it worked.

But in my installation, when I tried making migrations, I got: OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name

Investigating a bit further, I tried simply:

from django.contrib.gis import gdal

And got:

Traceback (most recent call last):   
File "<stdin>", line 1, in <module>   
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/__init__.py", line 49, in <module>
    from django.contrib.gis.gdal.driver import Driver  # NOQA   
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/driver.py", line 5, in <module>
    from django.contrib.gis.gdal.prototypes import ds as vcapi, raster as rcapi   
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/prototypes/ds.py", line 9, in <module>
    from django.contrib.gis.gdal.libgdal import GDAL_VERSION, lgdal   
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/libgdal.py", line 48, in <module>
    lgdal = CDLL(lib_path)   
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/ctypes/__init__.py", line 347, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name

Is there any suggestions on how I could repair my setup?

UPDATE

It seems to be a problema with my conda environment. When I started using a pip virtualenv, the problem did not arise anymore. I am not answering the question, because I could not find the solution, only a workaround. But rebuilding the environment with pip virtualenv works.

Answer 1

Have you built SQLite from source? Then, you forgot to enable Column metadata. Recompile SQLite with

CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1" ./configure
make
sudo make install

Have fun using the cutting edge SQLite.

Reference - https://www.sqlite.org/compile.html#enable_column_metadata

Answer 2

I was having this issue as well and the specifying

GDAL_LIBRARY_PATH = <HOME>/anaconda3/envs/<env_name>/lib/libgdal.so

(in project.settings or os.environ.setdefault) led to

libicui18n.so.56: cannot open shared object file: No such file or directory. 

The fix that worked for me was to upgrade icu:

conda install -c conda-forge icu=58

Upgrading icu lead to some changes in other package versions as well (qt downgraded from 5.6.2-4 to 5.6.2-3, the rest upgraded).

Answer 3

In conda environment: conda install -c conda-forge gdal=2.2.1

In django settings.py: GDAL_LIBRARY_PATH = '<HOME>/anaconda3/envs/<env_name>/lib/libgdal.so'

Answer 4

I simply run under my conda environment:

conda install gdal

Guy de Carufel's solution did not work for me, though he pointed to a correct direction, thanks