This seems to be the same issue/bug as unresolved previously.
Opened up an Rmarkdown file this morning, which ran normally yesterday. Tried to "run all chunks above" the 5th-ish chunk and got a partial green bar and red stop button in the interface below the source. The first (setup) chunk had run correctly, but the second chunk never started to run. (The setup chunk has additional data-loading code in it besides the default document setup code.)
Attempting to run the code in the second chunk either by selecting "run chunk" or using "run selected code" keyboard shortcut has same result: the setup chunk runs and then the interface hangs before starting the third chunk.
The code from chunk 2 runs when pasted into the console and the document knits normally.
New information since last report: adding a blank code chunk between the first and second chunks "fixes" the problem, in that the newly-third chunk will run via both options, but it does rerun the first chunk. And if executable code is placed in that second dummy chunk (went with r a <- 1+1), it does not execute.
Running the fourth code chunk reruns the first again, and then skips to the fourth.
Opened a fresh Rmd file and it's doing the same thing, but not hanging on the second chunk.
Relabeling the first chunk "cheese" instead of "setup", saving and starting a new session resolved the issue... but only in this document. A new markdown document with the default code replicated the bug.
Version information: R version 4.5.2 (2025-10-31 ucrt)
RStudio 2026.01.0+392 "Apple Blossom" Release (49fbea7a09a468fc4d1993ca376fd5b971cb58e3, 2026-01-04) for windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2026.01.0+392 Chrome/140.0.7339.249 Electron/38.7.2 Safari/537.36, Quarto 1.8.25