Bug report: Windows failure in system2() call to quarto -V due to environment handling

[sshunsuke]

Description

On Windows, Quarto availability/version checks fail during R CMD check and testthat runs due to an incorrect system2() invocation in the quarto R package.

The failure occurs even though:

• quarto.exe exists on disk
• Sys.which("quarto") returns the correct path
• system2(Sys.which("quarto"), "--version") works interactively

The error indicates that an environment variable (TMPDIR=...) is being passed as a command-line argument, causing the Quarto CLI to interpret it as a subcommand.

The root cause was identified by tracing failing system2() calls during R CMD check on Windows, with assistance from Microsoft Copilot.

---

Error message

Observed during R CMD check / testthat on Windows:

ERROR: Unknown command "TMPDIR=C:/Users/UserName/AppData/Local/Temp/Rtmpm6j3m7/file42241e1d6052".
Did you mean command "install"?

Warning in system2("quarto", "-V", stdout = TRUE,
    env = paste0("TMPDIR=", ...)) :
  running command '"quarto" TMPDIR=C:/Users/UserName/AppData/Local/Temp/Rtmpm6j3m7/file42241e1d6052 -V' had status ...

Note the constructed command:

"quarto" TMPDIR=... -V

which is invalid for the Quarto CLI.

---

Minimal reproducible evidence

On the same Windows machine:

q <- Sys.which("quarto")
q
# "C:/Users/UserName/AppData/Local/Programs/Quarto/bin/quarto.exe"

system2(q, "--version")
# works

system2(
  "quarto",
  "-V",
  stdout = TRUE,
  env = paste0("TMPDIR=", tempdir())
)
# fails on Windows

This suggests that the environment variable is not being passed correctly to system2() on Windows.

---

Root cause (Windows-specific)

On Windows, system2() does not invoke a shell. Environment variables must be passed as a named character vector, for example:

env = c(TMPDIR = tmpdir)

Passing env = paste0("TMPDIR=", tmpdir) can result in the variable being treated as a positional argument, yielding:

quarto TMPDIR=... -V

which Quarto correctly rejects.

---

Expected behavior

On Windows, Quarto availability/version checks should:

• Not fail when quarto.exe is present
• Pass environment variables via env = c(NAME = value)
• Avoid constructing commands where environment variables appear as CLI arguments

---

Platform

• OS: Windows 11
• R version: 4.5.2
• quarto R package version: 1.5.1
• Quarto CLI version: 1.8.27

---

Additional context

This issue appears similar to previously reported Windows failures involving Quarto during vignette rendering, but in this case it occurs during test execution (testthat), not during vignette building.

---

Suggested fix (conceptual)

Replace patterns like:

system2("quarto", "-V", env = paste0("TMPDIR=", tmpdir))

with:

system2("quarto", "-V", env = c(TMPDIR = tmpdir))

This should make the version check robust on Windows.

[cderv]

Thanks for the report.

Did you find any pattern like system2("quarto", "-V", env = paste0("TMPDIR=", tmpdir)) in this codebase ?

I can't find some, so I don't know if you reported or search in the right place.

I believe this is related to issue in sessioninfo

• sessioninfo ver 1.2.3: conflicts with get_quatro_version r-lib/sessioninfo#112 (fixed in avoid using system2(..., env =) on Windows r-lib/sessioninfo#122)

Observed during R CMD check / testthat on Windows:

IIUC you are encountering this only in using other tools that calls quarto. Currently this is fixed only in dev version of sessioninfo. So you could use it or wait for its CRAN release.

I'll close this as I do believe this is directly related. If I am wrong, please reopen.

[sshunsuke]

Thank you for your information. I overlooked that issue. I wait for the CRAN release.