Shapely OSError: Could not find lib c or load any of its variants []

Question

I'm just trying to use the demo code. I run the following in Jupyter Notebook:

from shapely.geometry import shape

Which gives me the following:

OSError                                   Traceback (most recent call last)
<ipython-input-4-cf5b4d0962ea> in <module>()
----> 1 from shapely.geometry import shape

/Users/hkwik/anaconda/lib/python2.7/site-packages/shapely/geometry/__init__.py in <module>()
      2 """
      3 
----> 4 from .base import CAP_STYLE, JOIN_STYLE
      5 from .geo import box, shape, asShape, mapping
      6 from .point import Point, asPoint

/Users/hkwik/anaconda/lib/python2.7/site-packages/shapely/geometry/base.py in <module>()
      7 from ctypes import pointer, c_size_t, c_char_p, c_void_p
      8 
----> 9 from shapely.coords import CoordinateSequence
     10 from shapely.ftools import wraps
     11 from shapely.geos import lgeos, ReadingError

/Users/hkwik/anaconda/lib/python2.7/site-packages/shapely/coords.py in <module>()
      6 from ctypes import byref, c_double, c_uint
      7 
----> 8 from shapely.geos import lgeos
      9 from shapely.topology import Validating
     10 

/Users/hkwik/anaconda/lib/python2.7/site-packages/shapely/geos.py in <module>()
     81         _lgeos = load_dll('geos_c', fallbacks=alt_paths)
     82 
---> 83     free = load_dll('c').free
     84     free.argtypes = [c_void_p]
     85     free.restype = None

/Users/hkwik/anaconda/lib/python2.7/site-packages/shapely/geos.py in load_dll(libname, fallbacks, mode)
     59         raise OSError(
     60             "Could not find lib {0} or load any of its variants {1}.".format(
---> 61                 libname, fallbacks or []))
     62 
     63 _lgeos = None

OSError: Could not find lib c or load any of its variants [].

However, if I run from the interpreter, everything is fine.

Any idea what's going on?

Californium

Have you attempted any solutions yet? It looks like an OSX exclusive problem, there are two issues on Github regarding this: github.com/carsonfarmer/python_geospatial/issues/… & github.com/Toblerity/Shapely/issues/394#issuecomment-235163776 – Mote

Do you use virtual environment? How have you installed jupyter? Standard? – Timberhead

Have to say that @Mote comment looks like it is the answer - did you try it @Huey? – Zincate

Possible duplicate #19742906 Need to install libgeos-c1 libgeos-3.4.2 libgeos-dev packages – Fedora

Possible duplicate of Could not find library geos_c or load any of its variants – Fedora

Answer 1

I simply uninstalled Shapely and re-installed it to fix the issue.

python -m pip uninstall shapely

python -m pip install shapely

Darg

The wonders of technology never cease to amaze me. – Oceania

Doing pip3 install shapely --upgrade is another solution which worked for me. – Symbolist

Answer 2

You may try to reset the environment variable DYLD_FALLBACK_LIBRARY_PATH:

export DYLD_FALLBACK_LIBRARY_PATH=$(HOME)/lib:/usr/local/lib:/lib:/usr/lib

Source

Error

In my env the DYLD_FALLBACK_LIBRARY_PATH was set to $(HOME)/anaconda/lib. After changing it everything works well. – Error

Answer 3

Try this may help you:

pip install --upgrade --force-reinstall shapely

Polygynist

Answer 4

For macOS users:

brew install geos
pip3 install shapely --upgrade

Haileyhailfellowwellmet

Answer 5

The way I fixed it:

apk add geos libc-dev musl-dev
pip install Shapely

Particularly

Answer 6

For me, only works after installing Shapely from the shapely lib and executing the following command from Anaconda Prompt:

pip install Shapely-1.7.1-cp37-cp37m-win_amd64.whl --force-reinstall

This forces a re-install of shapely.

Bema

Answer 7

I had to do a conda update --all to fix this.

Aleda

Answer 8

@user2977865 and @anothernode are correct in their approach but it may not work for everyone. By default, shapely will look for libraries in the DYLD_PATH.

I had it set to DYLD_LIBRARY_PATH=/usr/local/lib/:/usr/local/mysql/lib/

But these libraries are placed in /usr/lib.

So I had to modify it as follows:

export DYLD_LIBRARY_PATH=/usr/lib/:/usr/local/mysql/lib/

Bonus note: Ensure that your environment variables have been set by restarting terminal and clearing cache of any IDEs you might be using.

Surprising

Answer 9

I had a very similar issue running code in aws lambda with the error message:

 OSError: Could not find lib c or load any of its variants ['libc.musl-x86_64.so.1'].

I added musl-dev to my container installation and adapted the symlink:

ln -s /usr/lib/x86_64-linux-musl/libc.so /lib/libc.musl-x86_64.so.1

Masqat