Quarto PDF render fails in Positron: before-bib.tex missing

[davidjanmassgov]

Hi, I’m trying to render multiple .qmd files to PDF from R using quarto::quarto_render() inside Positron, but I keep hitting an error.

Here’s the workflow I’m running:

doc_base <- "documentation"
ts <- format(Sys.time(), "%Y-%m-%d_%H-%M")
run_dir <- file.path(doc_base, ts)
dir.create(run_dir, recursive = TRUE)

docs <- c(
  "step1a_setup_lightcast_data.qmd",
  "step1b_other_data.qmd",
  "step1c_process_projections.qmd",
  "step1d_process_oews.qmd",
  "step1e_create_baseframe.qmd",
  "step1f_process_ipeds.qmd",
  "step2a_calculate_demand_star.qmd",
  "step2b_industry_concentration_calcs.qmd",
  "step2c_location_quotient.qmd",
  "step2d_supply_gap.qmd",
  "step2e_suppress.qmd",
  "step2f_clean_up.qmd"
)

for (input_file in docs) {
  quarto::quarto_render(input = input_file)
}

When rendering, I 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'

What I’ve tried:

• Verified that quarto runs from command line (where quarto points to Positron’s embedded Quarto).
• Installed a standalone Quarto, and set "quarto.path" in Positron settings.
• PDFs get rendered manually and successfully without using quarto_render
• This Quarto render script works on R studio
• Still getting the same before-bib.tex missing error.

[juliasilge]

I was not able to reproduce this problem, but FWIW I am not on Windows.

Could you ask about what you are observing at https://github.com/quarto-dev/quarto-r/issues? I think we are doing the right thing in Positron in terms of where we've bundled Quarto and its resources. You might want to check if you observe the problem for a very simple quarto::quarto_render() for PDF with a single file.

[davidjanmassgov]

I forgot to mention that this error only comes up on Positron. It works in R studio. Should I still post it on the quarto boards? From: Julia Silge ***@***.***> Sent: Monday, August 18, 2025 2:51 PM To: posit-dev/positron ***@***.***> Cc: Jan, David (DUA) ***@***.***>; Author ***@***.***> Subject: Re: [posit-dev/positron] Quarto PDF render fails in Positron: before-bib.tex missing (Discussion #9081) CAUTION: This email originated from a sender outside of the Commonwealth of Massachusetts mail system. Do not click on links or open attachments unless you recognize the sender and know the content is safe. I was not able to reproduce this problem, but FWIW I am not on Windows. Could you ask about what you are observing at https://github.com/quarto-dev/quarto-r/issues<https://urldefense.com/v3/__https:/github.com/quarto-dev/quarto-r/issues__;!!CPANwP4y!VCqomPvU7GFppCK4wJxjkh5xwbHG-k31Wa0cmHYEBzxMgAJItzomG7Fh1DELJDl5z0tDDu2S8neIy1NCtIKeyuwWMg$>? I think we are doing the right thing in Positron in terms of where we've bundled Quarto and its resources. You might want to check if you observe the problem for a very simple quarto::quarto_render() for PDF with a single file. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/posit-dev/positron/discussions/9081*discussioncomment-14144939__;Iw!!CPANwP4y!VCqomPvU7GFppCK4wJxjkh5xwbHG-k31Wa0cmHYEBzxMgAJItzomG7Fh1DELJDl5z0tDDu2S8neIy1NCtIIwvyZjxg$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/BAMN4WJ3MFVTY64GJWY4JED3OIOBJAVCNFSM6AAAAACEFZN62WVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJUGQ4TGOI__;!!CPANwP4y!VCqomPvU7GFppCK4wJxjkh5xwbHG-k31Wa0cmHYEBzxMgAJItzomG7Fh1DELJDl5z0tDDu2S8neIy1NCtILfTtDRvA$>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[jonvanausdeln]

I am also seeing that same error.

Simple .qmd file:

---
title: "Diamond sizes"
date: 2022-09-12
format: pdf
---

```{r}
#| label: setup
#| include: false

library(tidyverse)

smaller <- diamonds |> 
  filter(carat <= 2.5)

> quarto::quarto_render('workspaces\\quarto_basic\\quarto_basic.qmd')
cat from .Rprofile

processing file: quarto_basic.qmd
1/4                        
2/4 [setup]                
3/4                        
4/4 [plot-smaller-diamonds]
output file: quarto_basic.knit.md

ERROR: 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'

Stack trace:
    at Object.lstatSync (ext:deno_fs/30_fs.js:415:3)
    at copyTo (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:42285:26)
    at stageContext (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:42519:21)
    at stageTemplate (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:42527:26)
    at runPandoc (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:78157:42)
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async renderPandoc (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:79473:26)
    at async Object.onRender (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:87109:36)
    at async renderFileInternal (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:87086:17)
    at async renderFiles (file:///C:/Users/JonVanausdeln/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:86910:17)

[juliasilge]

I opened quarto-dev/quarto-r#283 to get some info from the folks who make the R package.

[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]

Ah, of course, this is the same as #5553! Apologies on my end for not seeing the connection.

The fact that it is working from the command line means you do have a version of Quarto installed that does have tinytex installed, while the version that is bundled with Positron does not. The R package must be preferring the bundled one.

[badge-18]

I'm having the same issue.

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?

Also posted on @juliasilge 's Quarto issue.