Thanks for writing this up, Mo! Can you share a bit more detail about what happens here:
Is there an error message or log message that would give a bit more detail about why / how it is failing? For instance, does the Rmd reference the data using a relative path? If so it may be necessary to "change / set the working directory" before rendering the Rmd.
Also, do you have the tree command installed? I think tree ./ would help give us a picture of what the folder structure looks like here.
For example, with this folder structure:
./
├── app.R
├── data
│ └── myfile.rds
└── report
└── myreport.Rmd
2 directories, 3 files
If myreport.Rmd uses ../data/myfile.rds to refer to the data file, then I will want to make sure that rmarkdown::render("report/myreport.Rmd") is running in the report folder. This seems to be the default behavior of knitr, but it is probably worth adding a log message inside myreport.Rmd that outputs getwd(), or specify the knit_root_dir argument to rmarkdown::render() when you render the file.
Does that help? I'm curious to see what error message you are getting when rendering your report!