Reticulate python not recognizing local python : Error: Python shared library not found, Python bindings not loaded

Question

I have downloaded the python tar and extracted locally in linux ubuntu /app folder, When I configure this python using the R reticulate I get the error message " Error: Python shared library not found, Python bindings not loaded. Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment."

Here is the code I am running on R


> Python_Script_version<<-paste0("/app/bin/Python-3.9.1")
> Sys.setenv(RETICULATE_PYTHON= Python_Script_version)
> reticulate ::use_python(Python_Script_version, required = TRUE)

> Sys.which("python")
                               python 
"/app/bin/Python-3.9.1/python" 

> library(reticulate)
> py_config()
Error in py_config() : could not find function "py_config"
> reticulate::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.

Thank you for your time and response.

I was able to fix this after installing python again with python dev dependencies, however now I get the below error : <Rcpp::exception in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'pandas' File "/usr/local/lib/R/site-library/reticulate/python/rpytools/loader.py", line 19, in _import_hook module = _import * Note the pandas library in installed in the python but reticulate is looking into some other library, I tried to print the RETICULATE PYTHON path but it is showing the correct python path to /usr/bin/python3 — Pawan Rama Mali
– Pawan Rama Mali, Commented Feb 3, 2021 at 7:29

Takuro Ikeda · Accepted Answer · 2021-08-18 09:27:24Z

1

This worked for me!

> apt-get update && apt-get upgrade -y  
> apt-get install -y r-base python3 python3-dev python3-pip python3-venv  
> R  
> install.packages("reticulate")  
> library(reticulate)  
> reticulate::py_discover_config()  
python:         /usr/bin/python3  
libpython:      /usr/lib/python3.6/config-3.6m-x86_64-linux-gnu/libpython3.6.so  
pythonhome:     /usr:/usr  
version:        3.6.8 (default, Oct  7 2019, 12:59:55)  [GCC 8.3.0]  
numpy:           [NOT FOUND]  
> py_install("pandas") # install another python package as a test  
> pandas <- import("pandas")

from this issue.
https://github.com/rstudio/reticulate/issues/637

answered Aug 18, 2021 at 9:27

Takuro Ikeda

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Comments

Mriti Agarwal · Accepted Answer · 2021-02-02 09:14:24Z

0

You need to extract the python files in the same directory as your python and r scripts

answered Feb 2, 2021 at 9:14

Mriti Agarwal

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1 Comment

Pawan Rama Mali Over a year ago

Have extracted the python files in the same directory as python and r scripts, but still same error.

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