Problem with rendering to PDF on Windows in Positron: which Quarto does the R package choose to use?

[juliasilge]

Hello! We have folks who have are having trouble using quarto::quarto_render() with format: pdf in Positron on Windows only, as reported in posit-dev/positron#9081. Rendering from the command line works properly, including from the Positron terminal itself. The error we see (reproducible) is:

NotFound: The system cannot find the file specified. (os error 2): lstat 'C:\Users\JonVanausdeln\AppData\Local\Programs\Positron\resources\app\quarto\share\formats\pdf\pandoc\before-bib.tex'

Do you have ideas of what might be going on? Is this something that would be better fixed in the R package? Or something on the Positron side?

[badge-18]

I'm seeing the same error. Have R Studio and R installed on a Windows 11 machine. Quarto report runs fine in R Studio. Installed Positron on Windows for all users. Open and run same Quarto report. Get this error:

ERROR: NotFound: The system cannot find the file specified. (os error 2): lstat 'c:\Program Files\Positron\resources\app\quarto\share\formats\pdf\pandoc\before-bib.tex'

That directory does exist on this system and has 21 files in it, mostly .TEX files but NOT the specific one referenced in the error message. There is a before-body.tex file. Could this be what it's actually looking for?

[badge-18]

@juliasilge The issue appears to be that there are different files in the R Studio supplied Quarto and the Positron supplied one.

The R Studio supplied Quarto at (C:\Program Files\RStudio\resources\app\bin\quarto\share\formats\pdf\pandoc) has three additional files that are needed to render the Quarto document:

before-bib.tex
after-body.tex
before-title.tex

I manually copied these files from the R Studio Quarto to the Positron Quarto and my Quarto document rendered correctly from Positron.

[juliasilge]

I put two and two together, and realized this is the same as posit-dev/positron#5553.

If rendering from the command line works, I think (???) that means that the R package is preferring Positron's bundled Quarto (which doesn't include tinytex currently) to a non-bundled version that does. Maybe we should check which Quarto the R package is deciding to use, and harmonize that with what happens from the command line.

[badge-18]

I believe the Quarto installed with R Studio does come with tinytex in recent versions. It may be beneficial to add tinytex to the Quarto installed by Positron.

[CorradoLanera]

@badge-18 , @juliasilge
As mentioned here, you do not need to "copy" those three files; "create" them: they are all empty files! I suppose the issue (as, for example, git does for empty folders) is that they were skipped during the installation process. Creating those three empty files resolves the problem.

positron_quarto_missing_pdf_files.mp4

[cderv]

It seems that there are several issues here.

About missing before-bib.tex

NotFound: The system cannot find the file specified. (os error 2): lstat 'C:\Users\JonVanausdeln\AppData\Local\Programs\Positron\resources\app\quarto\share\formats\pdf\pandoc\before-bib.tex'

I am surprised that this file is not available quarto\share\formats\pdf\pandoc\before-bib.tex

It should be available as part of the Quarto installation. It is in RStudio provided one

❯ ls C:\Users\chris\scoop\apps\rstudio-daily\current\resources\app\bin\quarto\share\formats\pdf\pandoc\ | grep 'before-title.tex'
-----          05/09/2025    19:38              0 before-title.tex

and as part of Quarto one

❯ ls C:\Users\chris\scoop\apps\quarto\current\share\formats\pdf\pandoc\ | grep 'before-title.tex'
-----          29/09/2025    23:14              0 before-title.tex

but missing in Positron

❯ ls C:\Users\chris\scoop\apps\positron-daily\current\resources\app\quarto\share\formats\pdf\pandoc\ | grep 'before-title.tex'

So what @CorradoLanera shared seems definitely to be the problem

I suppose the issue (as, for example, git does for empty folders) is that they were skipped during the installation process. Creating those three empty files resolves the problem.

Those file should not be deleted when Quarto is bundled inside Positron installation. They are expected to be there but empty.

About quarto::quarto_render() selection of quarto version

The fact that the error happens inside Positron when calling quarto::quarto_render() means that indeed the R package is choosing this version of Quarto.

So about that, quarto::quarto_binary_sitrep(TRUE, TRUE) can help you investigate which version the package will used. (I need to teach about Positron maybe). Otherwise, quarto::quarto_path() will return the path used.

By default it will be using the one set on QUARTO_PATH env var, or using the one on PATH when unset. (By a simple call to Sys.which()

quarto-r/R/quarto.R

Lines 13 to 25 in d50ba11

	quarto_path <- function(normalize = TRUE) {
	path_env <- get_quarto_path_env()
	quarto_path <- if (is.na(path_env)) {
	path <- unname(Sys.which("quarto"))
	if (nzchar(path)) path else return(NULL)
	} else {
	path_env
	}
	if (!normalize) {
	return(quarto_path)
	}
	xfun::normalize_path(quarto_path)
	}

So inside Positron the bundled version will be used if no other is set on PATH I believe.

So I don't think the problem encountered is related to Quarto R package. Though I can add some knowledge about Positron like I did with RStudio. The RStudio IDE add a RSTUDIO_QUARTO that could be set, which could have made the version used by the package completely different

quarto-r/R/quarto.R

Lines 296 to 313 in d50ba11

	# RStudio IDE > Render button will use RSTUDIO_QUARTO env var with higher priority than latest version on path $PATH
	rstudio_env <- Sys.getenv("RSTUDIO_QUARTO", unset = NA)
	if (!is.na(rstudio_env)) {
	rstudio_env <- xfun::normalize_path(rstudio_env)
	if (!identical(rstudio_env, quarto_found)) {
	same_config <- FALSE
	if (verbose) {
	cli::cli_alert_danger(c(
	"RStudio IDE render button seems configured to use {.path {rstudio_env}}."
	))
	if (debug) {
	cli::cli_alert_warning(c(
	" It is configured through {.envvar RSTUDIO_QUARTO} environment variable."
	))
	}
	}
	}
	}

[juliasilge]

In posit-dev/positron#9820, I've got a fix for how Positron bundles Quarto. Thanks so much for the help, @cderv! 🙌

We do still need to bundle a PDF engine in Positron. With the fix in posit-dev/positron#9820, folks will see an error saying:

No TeX installation was detected.

And a prompt to do quarto install tinytex instead of the inscrutable missing before-bib.tex.