Quarto vignettes use the installed version of the package, but Rmd vignettes use the current dev version

[venpopov]

I just found out you can have Quarto vignettes and to try them out, I created a new package. I added a quarto vignette, but when I tried to build the site with build_site(), I got the following error:

── Installing package mytestpkg into temporary library ───────────────────────────────────────────
Error: 
! in callr subprocess.
Caused by error in `quarto::quarto_render(path, metadata_file = metadata_path, execute_dir = output_dir, …`:
! ✖ Error running quarto cli.
ℹ Rerun with `quiet = FALSE` to see the full error message.
Caused by error:
! System command 'quarto' failed
ℹ See `$stderr` for standard error.
Type .Last.error to see the more details.

Rendering regular .Rmd vignettes was fine. I was finally able to track down the issue: the code library(mytestpkg) in the vignette failed for the Quarto vignette, because in contrast to the Rmd vignette, it did not use see the temporary library.

Ok, so I install() the package locally and then it renders successfully. The problem is that if you make any updates, and you rebuild the website, the Quarto vignette will be built with the locally installed version, while the Rmd vignettes will be built with the current version that build_site() installs to a temporary library.

The deployment via github pages workflow doesn't have this problem and everything works fine, but locally Rmd and Qmd vignettes are built differently.

[hadley]

Hmmm, probably need to set R_LIBS to the temporary directory that we install the package into so that quarto uses it.

[Robinlovelace]

This may be related or the same: quarto-dev/quarto-actions#120

[Robinlovelace]

Update: @cderv confirmed that the above issue is the same as this. It is a bug that hinders use of .qmd files for vignettes and, unlike @venpopov's statement above, we found it can lead to error messages in Actions. I would say this is fairly high priority, anything I can do to help with diagnostics/fix testing let me know 🙏

[cderv]

Hmmm, probably need to set R_LIBS to the temporary directory that we install the package into so that quarto uses it.

I agree with this. @jayhesselberth I can help with that. I'll try to do a PR to fix this.

[jayhesselberth]

@cderv If is something that will come up frequently maybe this could also be adressed in the quarto R package with a lib_dir param for quarto_render()?

[cderv]

I am not sure it will be often, but surely in some context like pkgdown when

• A package is installed in a temp directory added to current session .libPath()
• quarto_render() is run with expectation of the library being available, which won't be the case if R_LIBS was not modified and passed to the new process.

pkgdown being the one to install in a temp directory, it would make sense for it to be sure this libs is known to the new process.

Thouhg, I wonder if this can create some issue with vignette engine too, so I'll check.

[b-rodrigues]

Just was confronted to the same issue, glad to see it's being worked on 👍

[cortinah]

Perhaps related, R CMD build in Github Actions fails for my hockeystick package where I just added a Quarto vignette. this only happens on Windows, ubuntu and macos are fine.
Hope this is useful. thanks

Run r-lib/actions/check-r-package@v2
Run ## --------------------------------------------------------------------
── R CMD build ─────────────────────────────────────────────────────────────────

• checking for file 'D:\a\hockeystick\hockeystick/DESCRIPTION' ... OK
• preparing 'hockeystick':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ... ERROR
  Error: --- re-building 'usinghockeystick.qmd' using html
  processing file: usinghockeystick.qmd
  1/25
  2/25 [carbon]
  Error in library():
  ! there is no package called 'hockeystick'

[jayhesselberth]

@cortinah your issue is likely unrelated, pkgdown includes some test quarto vignettes and builds on all platforms.

[cortinah]

@cortinah your issue is likely unrelated, pkgdown includes some test quarto vignettes and builds on all platforms.

ok, thanks!

[davidkane9]

Any updates on this? Any suggestions for how to deal with it in the meantime? I just switched my vignettes from Rmd to qmd. I think that the above issue is giving me a similar failure.