I'm trying to run Python in RStudio. I have installed Python 3.8.5 via pyenv, and created a virtual environment with pyenv virtualenv (which I call venv-Rstudio) in my RStudio project folder. Based on the instructions given here, I think I have correctly managed to indicate to RStudio which Python environment to use:
>Sys.setenv(RETICULATE_PYTHON="/Users/my_username/.pyenv/versions/venv-Rstudio/bin/python")
> py_discover_config()
python: /Users/my_username/.pyenv/versions/3.8.5/envs/venv-Rstudio/bin/python
libpython: [NOT FOUND]
pythonhome: /Users/my_username/.pyenv/versions/3.8.5:/Users/my_username/.pyenv/versions/3.8.5
version: 3.8.5 (default, Oct 1 2020, 21:50:37) [Clang 12.0.0 (clang-1200.0.32.2)]
numpy: /Users/my_username/.pyenv/versions/3.8.5/envs/venv-Rstudio/lib/python3.8/site-packages/numpy
numpy_version: 1.18.5
When trying to call Python, I get the following error:
> py_config()
Error: Python shared library not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
I suspect this has something to do with libpython: [NOT FOUND] seen above, but I have made sure libpython is installed in the venv-Rstudio virtual environment:
(venv-Rstudio) my_username@MBP15 Rstudio % pip list
Package Version
---------------------- ---------
...
Keras 2.4.3
Keras-Preprocessing 1.1.2
libpython 0.2
Markdown 3.2.2
multidict 4.7.6
numpy 1.18.5
...
Any ideas what I might be missing and how to fix this? I'm running macOS 10.15.7 Catalina, RStudio 1.3 with R version 4.0.2.
After posting my question, this question appeared in the Related list, and this answer by @nucholab solved my problem. In short, re-installing Python with pyenv using the following command enables shareable libraries:
env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.8.5
After that and re-creating my virtual environment (and for the record, installing numpy), loading Python in RStudio works as expected:
> py_config()
python: /Users/my_username/.pyenv/versions/3.8.5/envs/venv-Rstudio/bin/python
libpython: /Users/my_username/.pyenv/versions/3.8.5/lib/libpython3.8.dylib
pythonhome: /Users/my_username/.pyenv/versions/3.8.5:/Users/andreas/.pyenv/versions/3.8.5
version: 3.8.5 (default, Oct 2 2020, 13:54:11) [Clang 12.0.0 (clang-1200.0.32.2)]
numpy: /Users/my_username/.pyenv/versions/3.8.5/envs/venv-Rstudio/lib/python3.8/site-packages/numpy
numpy_version: 1.19.2
tensorflow: [NOT FOUND]
NOTE: Python version was forced by RETICULATE_PYTHON