I use the Hugo Coder template along with Rstudio’s Blogdown package to generate and deploy this website to github pages. I use this setup to generate blog posts (via Rmarkdown) that render \(\LaTeX\) math and output from R code.

Sometimes, I’d like to run Python code inside Rmarkdown too, and this is supported, via the reticulate package. That said, the following steps need to be followed to make sure everything runs smoothly (all of these steps worked on a macOS Ventura operating system)

  1. In your Rmarkdown file, always have this code chunk to setup Python use for later:
# setup for using python code later in the page
# import the reticulate package
library(reticulate)
# specify the version of python to use
use_python("/Users/<username>/.pyenv/shims/python")

  1. Note: In the chunk above, replace <username> with your username. In addition, I use pyenv to manage python versions on my system, as explained here. If you don’t have pyenv already, be sure to set it up using the instructions in the previous link.

  2. You might hit an error when you run a python code chunk in Rmarkdown:

    Error: '/Users/<username>/.pyenv/shims/python' was not built with a shared library.
    reticulate can only bind to copies of Python built with '--enable-shared'.
    Execution halted
    Error : Failed to render content/post/<name_of_post>/index.en.Rmd

  1. This just means I must build a version of python with the --enable-shared flag. I do this using pyenv.

  2. First, choose a version of python that you want to use. You can do this by going to the terminal and typing

    pyenv install --list
  1. This should show you a long output, some of them will be python versions, as shown below:
    ...
    3.10.1
    3.10.2
    3.10.3
    3.10.4
    3.10.5
    3.10.6
    3.10.7
    3.10.8
    3.10.9
    3.10.10
    3.11.0
    ...
  1. Choose an appropriate version and use the command below to install said version, like so (in the example below, I choose to install 3.11.0):
    env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.11.0
  1. In the previous step, note the --enable-shared option has now been added
  2. We now want to set this Python version to be the global Python version. Type the following command (replace 3.11.0 in the command below with the version you installed):
    pyenv global 3.11.0
  1. You can also check if the global version set is the correct version using the following command:
    pyenv versions

  1. If you’re using python packages (i.e. numpy, pandas, etc.) in your code chunks, make sure to install them first (i.e. by using pip3 install numpy, pip3 install pandas, etc. in the terminal)

  2. With all of this set up, you should no longer see the error above when you knit Rmarkdown documents with Python code chunks in them.