sessioninfo ver 1.2.3: conflicts with get_quatro_version

[efletcherPIFSC]

This issue also affects users without renv

R project packages under renv conflict with sessionInfo version 1.2.3. Primarily where sessionInfo is attempting to get the quarto version.
This affects devtools::check and devtools::session_info.

Checking a R package under renv, via devtools::check(), will output this error.

  ERROR: Unknown command "TMPDIR=C:/Users/[username]/AppData/Local/Temp/RtmpQVxG6G/filefc86550135f". Did you mean command "create"?
   Warning message:
   In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
     running command '"quarto" TMPDIR=C:/Users/[username]/AppData/Local/Temp/RtmpQVxG6G/filefc86550135f -V' had status 1

Projects attached with renv, sessioninfo::session_info (specifically sessioninfo::platform_info) will return "ERROR: Unknown Command" message for the quarto version.

Deactivating renv for the project, will alleviate the issue.

If R package project is dependent on renv, reverting sessionInfo to version 1.2.2 alleviates this renv conflict.

Reproduce

• Create a new R package (RStudio: New Project > New Directory > R package > Create R Package and use renv with this project)
  • renv::install("devtools")
  • Add license
  • devtools::check()
    • Expect that R CMD check succeeded w/ ERROR: unknown command and Warning Message
  • sessioninfo::session_info()
    • Session Info message with "ERROR: unknown command ..." for quarto value; and Warning message

Session

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default



attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.4.1    gitcreds_0.1.2    tools_4.4.1       rstudioapi_0.16.0 yaml_2.3.8        renv_1.1.1       

[sfcheung]

A similar and probably related problem occurred even if renv is not used.

I installed a new copy of R 4.4.2 in Windows 11. Updated all packages. Installed only sessioninfo, and ran session_info():

> install.packages("sessioninfo")
also installing the dependency ‘cli’

trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.4/cli_3.6.4.zip'
Content type 'application/zip' length 1393464 bytes (1.3 MB)
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.4/sessioninfo_1.2.3.zip'
Content type 'application/zip' length 198314 bytes (193 KB)
downloaded 193 KB

package ‘cli’ successfully unpacked and MD5 sums checked
package ‘sessioninfo’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\xxxxx\AppData\Local\Temp\RtmpOIN358\downloaded_packages
> library(sessioninfo)
> session_info()
ERROR: Unknown command "TMPDIR=C:/Users/xxxxx/AppData/Local/Temp/RtmpOIN358/file129834e341db". Did you mean command "update"?
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 (2024-10-31 ucrt)
 os       Windows 11 x64 (build 26100)
 system   x86_64, mingw32
 ui       Rgui
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       Asia/Hong_Kong
 date     2025-02-28
 pandoc   3.1.12.1 @ C:\\Users\\xxxxx\\AppData\\Local\\Pandoc\\pandoc.exe
 quarto   NA @ C:\\Users\\xxxxx\\AppData\\Local\\Programs\\Quarto\\bin\\quarto.exe

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 cli           3.6.4   2025-02-13 [1] CRAN (R 4.4.2)
 sessioninfo * 1.2.3   2025-02-05 [1] CRAN (R 4.4.2)

 [1] C:/Statistics/R/R-4.4.2-Test/library
 * ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────
Warning message:
In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=C:/Users/xxxxx/AppData/Local/Temp/RtmpOIN358/file129834e341db -V' had status 1

This problem disappeared if I removed sessioninfo 1.2.3, existed and started R, and installed sessioninfo 1.2.2:

> install.packages("C:/Temp/sessioninfo_1.2.2.tar.gz", repo = NULL, type = "source")
* installing *source* package 'sessioninfo' ...
** package 'sessioninfo' successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sessioninfo)
> library(sessioninfo)
> session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 (2024-10-31 ucrt)
 os       Windows 11 x64 (build 26100)
 system   x86_64, mingw32
 ui       Rgui
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       Asia/Hong_Kong
 date     2025-02-28
 pandoc   3.1.12.1 @ C:\\Users\\xxxxx\\AppData\\Local\\Pandoc\\pandoc.exe

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 cli           3.6.4   2025-02-13 [1] CRAN (R 4.4.2)
 sessioninfo * 1.2.2   2021-12-06 [1] CRAN (R 4.4.2)

 [1] C:/Statistics/R/R-4.4.2-Test/library

────────────────────────────────────────────────────────────────────────────── 

Session Info (Before removing 1.2.3 and installing 1.2.2)

> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Asia/Hong_Kong
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sessioninfo_1.2.3

loaded via a namespace (and not attached):
[1] compiler_4.4.2 cli_3.6.4      tools_4.4.2   

[tjmahr]

The problem, I think, is this line:

      ver <- system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", tmp))[1]

The docs on ?system2 say:

On Windows, env is only supported for commands such as R and make which accept environment variables on their command line.

[NicChr]

I'm also seeing a similar error when running devtools::check() on my R package.

   ERROR: Unknown command "TMPDIR=MYPATH". Did you mean command "create"?
   Warning message:
   In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
     running command '"quarto" TMPDIR=MYPATH -V' had status 1

[kevinushey]

See also: rstudio/rstudio#15805

[gaborcsardi]

For the record, this is not an error, even if it says that it is, but it is a warning.

[jslatane]

Forgive me if this is a totally ignorant question, but why is the get_quarto_version() function bothering to try and clean up quarto's mess? When I run quarto -V on the command line, I can see that temp files get created, but what does this really matter? I can't see where it is the responsibility of this library to clean those up.

[cderv]

For the record, this is not an error, even if it says that it is, but it is a warning.

@gaborcsardi the command that is used from this call

sessioninfo/R/platform-info.R

Line 105 in 5d07442

ver <- system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", tmp))[

will be, at least on windows, not correct for Quarto CLI. As the warning shows

Warning message:
In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpWQrWrx/filec350656e46de -V' had status 1

it will be

"quarto" TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpWQrWrx/filec350656e46de -V

And this is an error for Quarto, as the second argument after quarto is supposed to be a valid Quarto command or argument.

ERROR: Unknown command "TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpWQrWrx/filec350656e46de". Did you mean command "create"?

This is usual Quarto error - it can be recreated in terminal

❯ quarto TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpWQrWrx/filec350656e46de --version
ERROR: Unknown command "TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpWQrWrx/filec350656e46de". Did you mean command "create"?

❯ quarto dummy
ERROR: Unknown command "dummy". Did you mean command "use"?

system2 help page mentions that env is to be used on Windows with CLI tools that accept environment variable as argument

On Windows, env is only supported for commands such as R and make which accept environment variables on their command line.

from https://stat.ethz.ch/R-manual/R-devel/library/base/html/system2.html

So I don't think this should be done on windows.

Why is there a need to change TMPDIR? Maybe from a past version where we did not clean up the leftovers correctly?

Minimal reprex

• Windows

> sessioninfo:::get_quarto_version()
ERROR: Unknown command "TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpgJDt0n/file7a7c1adb3f9f". Did you mean command "create"?
[1] "NA @ C:\\Users\\chris\\scoop\\shims\\quarto.exe"
Message d'avis :
Dans system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  l'exécution de la commande '"quarto" TMPDIR=C:/Users/chris/AppData/Local/Temp/RtmpgJDt0n/file7a7c1adb3f9f -V' renvoie un statut 1

• Linux (no issue)

> sessioninfo:::get_quarto_version()
[1] "99.9.9 @ /home/cderv/.local/bin/quarto"

When I run quarto -V on the command line, I can see that temp files get created

@jslatane is this happening with the latest Quarto? Please share with us a quarto-dev/quarto-cli so that we can improve. I don't see a temporary file left over when calling quarto -V in an empty directory.

[jslatane]

@cderv I was incomplete with my previous comment - I meant that I could see new files getting created in my AppData/Local/Temp folder, not in the directory where I called quarto -V from. Hopefully this shows clearly what I am seeing:

C:\Empty> (Get-ChildItem | Measure-Object).Count
0
C:\Empty> (Get-ChildItem | Measure-Object -Property Length -Sum).Sum / 1MB
0
C:\Empty> $temp_dir = 'C:\Users\latanej\AppData\Local\Temp'
C:\Empty> (Get-ChildItem $temp_dir | Measure-Object).Count
318
C:\Empty> (Get-ChildItem $temp_dir | Measure-Object -Property Length -Sum).Sum / 1MB
17.6886730194092
C:\Empty> quarto -V
1.4.554

C:\Empty> (Get-ChildItem | Measure-Object).Count
0
C:\Empty> (Get-ChildItem | Measure-Object -Property Length -Sum).Sum / 1MB
0
# A new file is created:
C:\Empty> (Get-ChildItem $temp_dir | Measure-Object).Count
319
# But it is apparently empty:
C:\Empty> (Get-ChildItem $temp_dir | Measure-Object -Property Length -Sum).Sum / 1MB
17.6886730194092

I also realize I did not phrase well above when I said "quarto's mess" - if quarto needs to make a file in the AppData/Local/Temp directory, I have absolutely no problem with that because I assume it will get emptied out later somehow.

So to be clear, I don't think quarto is doing anything wrong here as far as I can tell, which led to my confusion on why this sessioninfo code is trying to do any handling or clean-up of temp files in this situation.

FWIW I also went through some similar steps that you showed in your comment above and I don't think the quarto TMPDIR=... -V command is valid in Linux either, but there's some difference between R's versions of system2 that exposes the error on Windows and not on Linux (at least on my machine/WSL instance). It seems like this sessioninfo::get_quarto_version() function could call system2 without any env argument and be fine. Though to be fair, I did not do any testing to see if/where temp files get created in Ubuntu when you call quarto -V.

[TobiasFellinger]

Just to note: this also happens without using renv when quarto is not installed at all.