Packages not found in hello-r docker image

While working on #538, I went to test out running the hello-python and hello-R docker images, and had difficulty running the analysis in the the hello-R image. The image built fine, but there were issues with renv -

I built the image and launched a container with:

docker buildx build --platform linux/amd64 --tag hello-r:latest .

docker run --rm -it --platform linux/amd64 --mount type=bind,source=/Users/sjspielman/ALSF/open-scpca/OpenScPCA-analysis,target=/OpenScPCA-analysis hello-r:latest bash

Then in the container:

cd OpenScPCA-analysis/analyses/hello-R

bash run_hello.R

Which led to:

- One or more packages recorded in the lockfile are not installed.
- Use `renv::status()` for more details.
Error in loadNamespace(x) : there is no package called ‘rmarkdown’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

Packages were indeed installed from the renv.lock file as expected, but because of this line in the Dockerfile, there is no renv cache that knows about it. https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/8ec8fa0dde4670bc440fefa58cf8d3e75aa6b984/analyses/hello-R/Dockerfile#L12-L13 As a consequence, when this script tries to load up the renv environment since we still have .Rprofile activating it, we end up with errors that packages aren't installed.

Off the top of my head, here's one not-awful idea and one bad idea, and one idea whose quality I'm unsure of, to address this...

Not-awful: We could add a line to the Dockerfile to remove the module's .Rprofile file so that renv doesn't get activated.
Bad: We could add Rscript -e 'renv::restore()' into run_hello-R.sh. This seems like a not great idea, since we'd have to maintain something like this in every R module.
Unsure: We could just not disable the cache

AlexsLemonade / OpenScPCA-analysis

Packages not found in hello-r docker image #542