Identify additional system dependencies for the README

The specific version of R and the loaded packages is the most crucial information that should go into the README (or that is stored in the renv lockfile). Ideally, you list other system dependencies, such as the version of Quarto¹ that you used to render your paper.

An overview over the system dependencies of R packages can be created using the function pak::pkg_sysreqs(). In combination with renv, we can obtain the system dependencies of all R packages the current project directly depends on:

Console

# Find all R package dependencies
deps <- renv::dependencies()$Package |>
  unique() |>
  pak::pkg_deps(dependencies = NA) |>
  getElement("package")

# Identify their system dependencies
pak::pkg_sysreqs(deps)

The output may look like the following:

── Install scripts ────────────────── Fedora 40 ── 
dnf install -y make pandoc git

── Packages and their system dependencies ────────
fs        – make
knitr     – pandoc
remotes   – git
rmarkdown – pandoc
sass      – make

We can see that the programs make, pandoc, and git were identified as system dependencies. Often, one can obtain their version by running them with the --version argument:

Terminal

make --version
pandoc --version
git --version

However, this does not work for all system dependencies. Specifically, it does not work for libraries – software that is not supposed to be run on its own. Identifying their version is beyond the scope of this tutorial.

We also know that we need Quarto to create the PDF, so let’s find out its version as well:

Terminal

quarto --version

If you installed apaquarto or any other Quarto extension, one can query their versions as follows:²

Terminal

quarto list extensions

Finally, we know that we installed a \(\TeX\) distribution to create the PDF, so let’s find out its version by running:

Terminal

quarto check

The output is quite long and it might look slightly different for you, but the relevant sections are the following:

[✓] Checking tools....................OK
      TinyTeX: v2024.09
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/r155953/.TinyTeX/bin/x86_64-linux
      Version: 2024

Add these dependencies to the section Computational Requirements / Dependencies of your README file.

Of course, all the system dependencies identified until now may have dependencies on their own. Use your own judgement to decide when not to dig deeper.

Footnotes

As of August 2024, a proposal for renv to record the version of Quarto has not been implemented, see rstudio/renv#1143.↩︎
Luckily, the extensions are included in the project folder, so technically their version is already recorded in the project’s files.↩︎