I've required my students to turn in knitted pdf's from their R Markdown code. This course is more of an applied stats class, rather than stat computing, which

I've required my students to turn in knitted pdf's from their R Markdown code. This course is more of an applied stats class, rather than stat computing, which I guess might make more sense. But it does ensure reproducibility (mostly, once we do away with working directories!). My difficulty is more that for most of these students, this is their first time using R or a real programming language. I had hoped that R Markdown would make the process simpler and more sensible. But the tendency of a student is to try different things, and not have a strong understanding of the logic behind those processes. So they create R Markdown files, and then gripe about how the code works in their IDE, but doesn't knit, and so knitr must be broken!