[vharuck]

Which parts don't work outside of R Studio for you? Is it something recent? I usually create my single-page and bookdown documents as one step in a separate R script, and haven't found any problems beyond the rmarkdown package's poor documentation (I really wish the R Studio developers would write in-package documentation with as much care as with their online documentation).

[mespe]

If I recall correctly, I had issues primarily with more complicated documents, and mostly due to some RStudio "project" and file path configuration issues - I would have to look to see what the specific issues were. Simple, one-file .Rmd docs are typically fine either way.