Chunk with `eval = FALSE` is evaluated by "Run Above"

[etiennebacher]

Bug description

I have the following foo.Rmd file:

```{r, eval = FALSE}
print("hi")
```

```{r}
1 + 1
```

Using the Quarto extension in Positron, if I press the "Run Above" button in the second chunk, then it evaluates the first code chunk while it shouldn't. Using #| eval: false correctly skips running this chunk but I'm working with a lot of Rmd vignettes and I'd rather not translate all the chunk options to the #| syntax. The chunk with eval = FALSE is correctly ignored in RStudio.

Might be the same root cause as in #942 but the problematic use case is a bit different.

Steps to reproduce

Using the example file above, click the "Run Above" button on top of the second chunk.

Actual behavior

It executes the first chunk.

Expected behavior

The first chunk shouldn't be evaluated.

Your environment

Positron Version: 2026.07.0 build 209
Code - OSS Version: 1.118.0
Commit: c9e80d775fe6c04db293d8f79260c43200746fea
Date: 2026-06-17T22:10:27+02:00
Electron: 39.8.8
Chromium: 142.0.7444.265
Node.js: 22.22.1
V8: 14.2.231.22-electron.0
OS: Linux x64 6.17.0-1025-oem

Quarto extension: 1.134.0

[juliasilge]

That's because syntax like {r, eval = FALSE} is actually knitr syntax, and Quarto doesn't know about anything about it. This works when you render because it has the ability to go through knitr to decide what to do, but the extension is not currently not able to parse those.

What you'll want to do is use the Quarto syntax for special comments, like this:

Here, if you click "Run Above" on the last chunk, it will not run the first chunk and then run the second chunk. We don't currently plan to re-implement full support for knitr-specific syntax in the Quarto extension here, but you can use knitr::convert_chunk_header() to convert to the Quarto-style headers.

[cscheid]

I agree with the diagnostic and outlook, but I kind of have to point out that this is an Rmd file:

I have the following foo.Rmd file:

and it's a bit unfortunate that we ask for Quarto syntax in an RMarkdown document. @etiennebacher, RMarkdown syntax wasn't designed with IDE tooling in mind, and it makes it very hard for us to do the right thing in general. Quarto's syntax is slightly nicer in that way, which is why that works.

I think this, ultimately, is an instance of the following "bug": Quarto's extension (which is what ships with Positron) cannot support the full range of Rmd constructs, and yet it attempts to open Rmd files. The alternative of refusing Rmd files would, of course, be a worse "bug" at the moment.

[etiennebacher]

Thanks both for the explanations. I think I was mostly surprised that those knitr options are understood by quarto render but not by "Run above", I would have expected the extension to internally call the CLI tool and therefore have the same capabilities. It was also unexpected that "Run above" doesn't understand knitr options in Positron but works just fine in RStudio (I get that the Quarto extension and the RStudio integration are different, but from an end user perspective that doesn't really matter).

Since this is not a bug, I don't know whether I should close this or not so I'll let you decide that.

[juliasilge]

Thanks, @etiennebacher! I definitely understand that this would feel surprising from the user side, coming from RStudio which has built-in understanding of both Quarto and R Markdown. FWIW we are pretty confident that it's the right call for us not to re-implement full support for knitr-specific syntax in the Quarto extension here (and then of course that trickles over to Positron).

We appreciate the thoughtful feedback very much, and will keep an eye on how this plays out for users!