Issues with syntax highlighting and chunk execution in RStudio (macOS Tahoe 26.0)

RStudio IDE
1

Description:

I am experiencing two separate problems in RStudio when working with Quarto projects:

  1. Syntax Highlighting Issue: When editing .qmd files, syntax highlighting disappears in code chunks after modifying the code. The highlighting is restored only after saving the file.
  2. Chunk Execution Issue: In some .qmd files, the run chunk green arrow disappears. Even when the arrow is visible, clicking it does not execute the chunk. This happens inconsistently across chunks.

Steps to Reproduce:

  • Open a Quarto project in RStudio.
  • Open a .qmd file.
  • Modify code inside a chunk.
  • Observe syntax highlighting disappearing.
  • Try running the chunk via the green arrow or Cmd+Shift+Enter. Some chunks do not execute.

Expected Behavior:

  • Syntax highlighting should persist while editing code.
  • Chunks should execute consistently when triggered.

Actual Behavior:

  • Syntax highlighting disappears after editing, reappears only after saving.
  • Some chunks lose the run arrow, and some fail to execute even if the arrow is present.

System Information:

  • RStudio Version: 2025.09.0+387
  • R Version: 4.5.1 (2025-06-13) “Great Square Root”
  • Quarto Version: 1.8.24 (macOS)
  • OS: macOS (Tahoe 26.0)

Additional Notes:

This issue persists even after reinstalling RStudio. It affects both existing projects and newly created ones.

1 Like
2

I am wondering how you initially installed RStudio with your Tahoe 26.0 macOS cause I tried to install RStudio Version 2025.09.0+387 in my macbook that has the same OS with you rs several time but only R Version 4.5.1 works.
I miss R studio so bad....

3

I have this issue too on Ubuntu.

4

I am using RStudio with R version 4.5.1, I didn't try another version.

5

I've opened an issue (haven't tried to reproduce the bug yet): Issues with syntax highlighting and chunk execution in RStudio · Issue #16498 · rstudio/rstudio · GitHub

6

This may be the same as Quarto Code Chunk Options Breaking Chunk · Issue #16463 · rstudio/rstudio · GitHub, which is fixed in the 2025.09.1 patch being released today.

If you want to try it you can install 2025.09.1+401 from Cucumberleaf Sunflower. Please report back if this fixes the issue(s) for you, and sorry for the inconvenience.

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