NKInstinct
commented
3 years ago Sorted out all notes on both devtools::check and BiocCheck, and was successful in splitting out the app into several different helper functions (one of which even has unit tests now!). BiocCheckGitClone still gives the error about .Rproj and I cannot figure out how to remove it but I'm still working on it.
There are a few notes but not warnings or errors with BiocCheck - some of the notes are not things I understand, and one in particular (that my function is too long) is something I do fully understand but can't fix right now - trying to split shiny apps out into smaller modules is much more complex than splitting functions out into smaller functions and so I tried a bunch but couldn't get it to work.
Unfortunately, BiocCheckGitClone gives an error about files that shouldn't be tracked but then won't tell me which file it is. I did have a .Rproj in there by mistake but I took it out and removed it from the git cache and it doesn't show up anymore when I run git ls-tree --full-tree -r --name-only HEAD, so I'm pretty sure it's gone. Hoping that on submission, someone can help sort out exactly what is wrong here.