This is a first for me. I have a large Rmarkdown file 1184 lines ... hah and that solved this!
I still have a large Rmarkdown file that was baffling me because it seemed I could run each separate code block OK but any of the calls to run multiple blocks: run all, run all above, run all below, resulted in nothing happening but knitting the file worked fine. Going to the end of file showed that it was missing the closing "```" on the last block. Fixing that fixed it! I'm posting this here as someone else may hit this. Two thoughts: (a) I'm surprised it would knit OK (and the last block, a one line save() did run OK), (b) I think it might be good if Rstudio could add a check for unclosed code blocks to avoid someone else wasting time on this.
(Yes, I know it must have been my error to have lost that block closing line but Rstudio is very tolerant and wise alerting me to many other stupid things I do!)
Very best all, Chris