Rendering issue

[davidjanmassgov]

I am reading in a file from file path using a R environ file.
projections <- read_csv(file.path(Sys.getenv("DATABASE"), "datasets", "lt_proj", "2023_2033", "LTProjections2023_2033.csv"))

This runs well in Positron, but when I want to render/knit the qmd file, I get this error that it can't locate the file because it doesn't recognize the initial file path called in the R Environ file.

occ_explorer/step1c_process_projections.qmd" --no-browser --no-watch-inputs

processing file: step1c_process_projections.qmd
1/14                     
2/14 [Setup]             
3/14                     
4/14 [Read and process]  
Error:
! '/datasets/lt_proj/2023_2033/LTProjections2023_2033.csv' does not exist.
Backtrace:
 1. ... %>% ...
 7. vroom (local) `<fn>`("/datasets/lt_proj/2023_2033/LTProjections2023_2033.csv")
 8. vroom:::check_path(path)

Quitting from lines 48-121 [Read and process] (step1c_process_projections.qmd)
Execution halted

I've tried this exact same thing in R studio and I'm able to run and knit without issue.

Has anyone experienced this issue?

Thanks

[jennybc]

It looks like the DATABASE env var is undefined in the render that you show. What gesture did you use to invoke that? What method are you using to define this environment variable?

[davidjanmassgov]

Hi Jenny, In my .Renviron file, I keep some file paths that I use Sys.genev() to read in some files. One of the file paths is DATABASE = “C:/Users/David.Jan/…/database”. Calling Sys.getenv("DATABASE") in Positron works well. It prints the file path that I’m trying to read the file from. One thing that I just noticed is that trying to pull up the .Renviron in my Positron environment using `usethis::edit_r_environ()` creates an error. ***@***.*** That could possibly be the issue, when I try to render. The usethis command works well in R studio. Hopefully I’m answering your questions! From: Jennifer (Jenny) Bryan ***@***.***> Sent: Friday, July 18, 2025 5:29 PM To: posit-dev/positron ***@***.***> Cc: Jan, David (DUA) ***@***.***>; Author ***@***.***> Subject: Re: [posit-dev/positron] Rendering issue (Discussion #8586) 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. It looks like the DATABASE env var is undefined in the render that you show. What gesture did you use to invoke that? What method are you using to define this environment variable? — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/posit-dev/positron/discussions/8586*discussioncomment-13812162__;Iw!!CPANwP4y!SojoOD_EYgMoLtbsQjwCI7U7WkEAy3V3jly55nUh6xiidyBLJXzIGGMJSjkwJ5q09XiQr1ZNHKk_uX3_hoX-NaeKxw$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/BAMN4WIXSNQ5CHTT7A3XNJD3JFRJXAVCNFSM6AAAAACB3PPHESVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTGOBRGIYTMMQ__;!!CPANwP4y!SojoOD_EYgMoLtbsQjwCI7U7WkEAy3V3jly55nUh6xiidyBLJXzIGGMJSjkwJ5q09XiQr1ZNHKk_uX3_hoVnqZ8xWg$>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[juliasilge]

We might need some more info on the details of your setup. If I put an env var in an .Renviron file and then try to access that via Sys.getenv() when rendering, I see that working correctly:

Could you share some more details of your situation, or maybe try to make a dead simple example .qmd that demonstrates the problem you are experiencing?

[davidjanmassgov]

Here's my quarto check:

Quarto 1.4.541
[>] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.4.541
Path: C:\Users\David.Jan\AppData\Local\Programs\Quarto\bin
CodePage: 1252

[>] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)

[>] Checking LaTeX....................OK
Using: TinyTex
Path: C:\Users\David.Jan\AppData\Roaming\TinyTeX\bin\windows
Version: 2025

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
Version: 3.12.5
Path: C:/Users/David.Jan/AppData/Local/Programs/Python/Python312/python.exe
Jupyter: (None)

  Jupyter is not available in this Python installation.
  Install with python -m pip install jupyter

[>] Checking R installation...........OK
Version: 4.3.2
Path: C:/PROGRA1/R/R-431.2
LibPaths:
- C:/Users/David.Jan/AppData/Local/R/win-library/4.3
- C:/Program Files/R/R-4.3.2/library
knitr: 1.47
rmarkdown: 2.27

[>] Checking Knitr engine render......OK

And more detailed error of the rendering issue:

$ export QUARTO_PRINT_STACK=true
quarto render step1c_process_projections.qmd

processing file: step1c_process_projections.qmd
1/14
2/14 [Setup]
3/14
4/14 [Read and process]
Error:
! '/datasets/lt_proj/2023_2033/LTProjections2023_2033.csv' does not exist.
Backtrace:

1. ... %>% ...
2. vroom (local) <fn>("/datasets/lt_proj/2023_2033/LTProjections2023_2033.csv")
3. vroom:::check_path(path)

Quitting from lines 48-117 [Read and process] (step1c_process_projections.qmd)
Execution halted
ERROR: Error
at renderFiles (file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:77059:29)
at eventLoopTick (ext:core/01_core.js:183:11)
at async renderProject (file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:77374:25)
at async Command.fn (file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:81939:32)
at async Command.execute (file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:8102:13)
at async quarto (file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:114953:5)
at async file:///C:/Users/David.Jan/AppData/Local/Programs/Quarto/bin/quarto.js:114971:9

I can try to create a reproducible example later if you need!

[jennybc]

Are we talking about a user-level .Renviron or an .Renviron embedded in a project?

One thing that I just noticed is that trying to pull up the .Renviron in my Positron environment using usethis::edit_r_environ() creates an error.

Can you show us the actual error?

[davidjanmassgov]

user-level .Renviron! I do not have .Renviron set up by project.

Here's the error message:

It says consult the log. Let me know if there's something specific you need from that as well.

[jennybc]

I suspect you are seeing this, in terms of (not) opening .Renviron:

#8374

[davidjanmassgov]

That seems like the same error message

[juliasilge]

• What version of Positron are you using?
• What happens if you run Sys.getenv("MY_IMPORTANT_ENV_VAR") in your R console?

For a more simple example to try, if I have a user-level .Renviron that contains this:

MY_IMPORTANT_ENV_VAR='potato'

And then a Quarto file that does this:

---
title: "My simple Quarto file"
format: html
---

## Make a plot

You can embed plots in a Quarto file, for example:

```{r}
#| echo: false
plot(pressure)
```

What a great plot!

## What happens with env vars?

```{r}
Sys.getenv("MY_IMPORTANT_ENV_VAR")
```

I see this when I preview or render the file, for example via the "Preview" button the toolbar:

Can you try out this simple setup to see if you have your env vars accessible when you render?

[davidjanmassgov]

Hi Julia,

Here's my Positron info:
Positron Version: 2025.07.0 (system setup) build 204
Code - OSS Version: 1.100.3
Commit: 03ae7a5
Date: 2025-06-30T16:48:59.334Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Windows_NT x64 10.0.26100

I put MY_IMPORTANT_ENV_VAR='potato' in my user .Renviron file and the sys.get.env(MY_IMPORTANT_ENV_VAR) works well in Rstudio, but not in Positron.

[jennybc]

It really catches my eye that the path to user's home directory is:

• on OneDrive
• contains spaces

[jennybc]

It would be interesting to compare the output of these in working / not working contexts:

Sys.getenv("R_ENVIRON_USER")
Sys.getenv("HOME")
Sys.getenv("R_USER")
normalizePath("~")
file.exists("~/.Renviron")

[juliasilge]

On Windows with Positron, I see that normalizePath("~") results in "C:\\Users\\Julia\\Documents"!!!

Does RStudio do something special to look in the more typical home directory, i.e. not Documents?

[jennybc]

The notion of home directory on Windows, for R users, is a quagmire, because R made an arguably regrettable decision to default to the Documents directory. The documentation of fs::path_home() and fs::path_home_r() gives a pretty good summary of the situation:

https://fs.r-lib.org/reference/path_expand.html

TL;DR there's a lot more ambiguity around the home directory on Windows than on other OSes. But usually self-consistency will still make things work out. usethis, for example, is careful to use R's notion of where it thinks the user's .Renviron should live:

https://github.com/r-lib/usethis/blob/d4a878e4931570220e77fddb71ee4d5152c155ed/R/edit.R#L202