Why does using 'actions/checkout' on GitHub Actions mean that renv can no longer use R library?

So I have a {targets} pipeline which runs on GitHub Actions. The required packages are recorded with {renv} and the whole thing runs in a docker container. Because I would prefer to have a long image build time and a short image run time, renv builds the library when the docker container is built so everything is available at runtime. The actual pipeline is not part of the image - it is checked out at runtime.

Here's the problem - if I run any R code in the GitHub workflow before using 'actions/checkout', renv works fine. But if I run anything after 'actions/checkout' renv can't find the library and instead needs to reinstall everything.

Dockerfile

FROM rocker/verse:4.3.0

ENV RENV_VERSION 0.17.3
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

WORKDIR /project
COPY renv.lock renv.lock

ENV RENV_PATHS_LIBRARY renv/library

RUN R -e "renv::restore()"

GitHub Workflow

on:
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master
  schedule:
    - cron: '0 13 * * 0,2,4'

name: targets

jobs:
  targets:
    runs-on: ubuntu-latest
    container:
      image: (above image)
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      LANG: en_US.UTF-8 
    steps:      
      - name: Test if renv works
        shell: Rscript {0}
        run: renv::restore() # Works - up to date with lock file

      - uses: actions/checkout@v3

      - name: Test if renv works after checkout
        shell: Rscript {0}
        run: renv::restore() # Fails - reinstalls library from lockfile

My guess is that the checkout action changes the working directory and so the library that docker made isn't found. But I don't know how to fix that.

Edit: Tested it and it doesn't change the working directory - it's checked out to the same folder.

I think this might have to do with activate.R changing one of the settings. Here is a screenshot of two steps of the action that both just install dplyr (all the dependencies of which should already be installed).

Note how the first time there's none of the bootstrapping or install renv, because activate.R does not exist until the checkout step. Could this be what is causing the problem?

I think I've found the solution, although I'll confess to not being 100% sure about the cause.

When the repository is checked out, it copies over the renv/ folder and the .Rprofile which sources renv/activate.R. Something in that process (possibly the settings.json) seems to override the environment variable that is set in the docker image that tells renv where to find the library.

My solution is to just not check these files out. That is:

      - uses: actions/checkout@v3
        with:
          sparse-checkout: |
            .
            /*
            !renv/
            !.Rprofile

The pipeline then runs as expected.