Agfdhyk

I am having trouble importing a specific package using reticulate within R (Feather Spray, version 3.5.1) and RStudio (version 1.1.456) on my MacBook Pro running High Sierra. The Python module I'm working with is called RDKit (https://github.com/rdkit/rdkit). The package works fine on the same computer when importing from the Python command line (or Spyder for that matter) as follows:

>>> import rdkit

import rdkit # directory /Users/pleeferguson/apps/rdkit/rdkit

# /Users/pleeferguson/apps/rdkit/rdkit/__init__.pyc matches /Users/pleeferguson/apps/rdkit/rdkit/__init__.py

import rdkit # precompiled from /Users/pleeferguson/apps/rdkit/rdkit/__init__.pyc

dlopen("/Users/pleeferguson/apps/rdkit/rdkit/rdBase.so", 2);

import rdkit.rdBase # dynamically loaded from /Users/pleeferguson/apps/rdkit/rdkit/rdBase.so

>>>

When I try to import RDKit within RStudio using reticulate, it fails as follows:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")

> library(reticulate)

> rdkit <- import_from_path("rdkit", "/Users/pleeferguson/apps/rdkit/rdkit")

Error in py_module_import(module, convert = convert) : 

  ImportError: No module named rdBase

> 

I also tried to import the module directly within R from the terminal (outside of RStudio), where I received a more informative error message:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")

> library(reticulate)

> rdkit <- import("rdkit")

Error in py_module_import(module, convert = convert) : 

  ImportError: dlopen(/Users/pleeferguson/apps/rdkit/rdkit/rdBase.so, 2): Library not loaded: @rpath/libRDKitRDBoost.1.dylib

  Referenced from: /Users/pleeferguson/apps/rdkit/rdkit/rdBase.so

  Reason: image not found



Detailed traceback: 

  File "/Users/pleeferguson/apps/rdkit/rdkit/__init__.py", line 2, in <module>

    from .rdBase import rdkitVersion as __version__

>

I've verified that there is indeed a symlink named libRDKitRDBoost.1.dylib at the right place and pointing to the correct dylib file (it does exist within the lib directory of the RDKit package).

Also, I have no trouble importing other packages (e.g. pandas) within RStudio using reticulate:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")

> library(reticulate)

> pd <- import("pandas", as = "pd")

> 

On my other MacBook Pro with an earlier version of both R (Sincere Pumpkin Patch) and RDKit (2015 build), the rdkit package loads just fine (and is functional) from within RStudio, using reticulate.

Any ideas what might be happening here? I don't think it is an RStudio issue, as I've tried installing the newest daily build of RStudio but get the same behavior. Also, the fact that I can't get the package to import from R within the terminal (outside of RStudio) tells me it must be something else.