R Markdown: openBinaryFile: does not exist (No such file or directory)

I had a similar problem. I was not using the full file path. I was using ~/path/to/file. I changed it to the full path (i.e. removed the ~/) and it worked.

I just had this issue as well, but for me the reason was that the RStudio project was on a shared drive, and I had opened it through the network location. The problem was resolved when I closed out of the project, and opened it back up through a mapped network drive. (If when you run getwd() your location starts with \\, this is probably what is happening to you.)