Windows CI Errors on Package Re-build

[coatless]

Windows CI fails during vignette creation step of R CMD check, while macOS and Ubuntu CI builds pass. Pre-building the package locally resolves the issue across all platforms. Further, adding local::. under setup-r-dependencies resolves the issue on the Windows CI; but, I don't think that's an optimal solution.

Build reference:

https://github.com/stanford-stats290/netid-package/actions/runs/11763068834/job/32766629444

Windows CI Check log

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'D:\a\netid-package\netid-package/DESCRIPTION' ... OK
* preparing 'netid':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building 'hello.qmd' using html
processing file: hello.qmd
1/13                  
2/13 [setup]          
Error in `library()`:
! there is no package called 'netid'
Backtrace:
  1. global .main()
  2. execute(...)
  3. rmarkdown::render(...)
  4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  5. knitr:::process_file(text, output)
     ...
 16. base::withRestarts(...)
 17. base (local) withRestartList(expr, restarts)
 18. base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 19. base (local) docall(restart$handler, restartArgs)
 21. evaluate (local) fun(base::quote(`<pckgNtFE>`))
Quitting from lines 11-12 [setup] (hello.qmd)
Execution halted
Error: Error: processing vignette 'hello.qmd' failed with diagnostics:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto.exe' failed
--- failed re-building 'hello.qmd'
SUMMARY: processing the following file failed:
  'hello.qmd'
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.

[cderv]

I re-ran the check on this repo and it passes https://github.com/quarto-dev/quarto-r/actions/runs/11798002514

We do use local::. though

quarto-r/.github/workflows/R-CMD-check.yaml

Lines 68 to 72 in 0fcb998

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	# install the package itself as we register vignette engine
	extra-packages: any::rcmdcheck, local::.
	needs: check

And this is because of an "issue" in R I would say where an engine is registered to be used in R CMD Check only if the package is installed.
I can't find the references to this but this is something that is impacting all packages that register and uses the vignette engine directly

However, the issue you get in CI does not seem to be related to the quarto vignette engine not being registered...

So I think what happens is that the package netid is used in the vignette, so it should be loaded by R when called inside Quarto. This means R process needs to find it in lib path and it seems R CMD check in installing the package in a way that this is not passed to the quarto sub process.

I wonder if I can detect the information, and pass it to the vignette engine when this is run in R CMD check context... 🤔

[cderv]

It seems R CMD build will use a lib dir in a temporary folder and install package there
https://github.com/wch/r-source/blob/f50aab97c98615643db276bb034701816ab43143/src/library/tools/R/build.R#L254-L261

It seems I would need to use R_BUILD_TEMPLIB as the information is recorded there...
https://github.com/wch/r-source/blob/f50aab97c98615643db276bb034701816ab43143/src/library/tools/R/build.R#L232

But it seems to be undocumented environment variable, so maybe this should not be used directly. 🤔

[cderv]

Though it is setting R_LIBS so I don't know why the package would not be found 🤔
https://github.com/wch/r-source/blob/f50aab97c98615643db276bb034701816ab43143/src/library/tools/R/build.R#L293-L300

I'll check that first.

[cortinah]

This is happening for me in Github Actions which 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'

[coatless]

@cortinah and anyone else; the interim fix would be to modify the R-CMD-check.yml workflow's setup step to include local:., e.g.

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          # Force install the package itself
          extra-packages: any::rcmdcheck, local::.
          needs: check

[cortinah]

@cortinah and anyone else; the interim fix would be to modify the R-CMD-check.yml workflow's setup step to include local:., e.g.

  - uses: r-lib/actions/setup-r-dependencies@v2
    with:
      # Force install the package itself
      extra-packages: any::rcmdcheck, local::.
      needs: check

Thank you very much -- that fixed the Github Actions error on Windows.

[astamm]

I jump into this conversation because we were having the same issue and fixed the Windows CI with this thread. The pkgdown GHA though remains an issue (permaverse/flipr#25).

I just wanted to point out that in some R package repo, there are Quarto vignettes and the pkgdown GHA runs smoothly, as in https://github.com/jolars/qualpalr.

I could not spot what makes it actually work but maybe it can help you guys narrow it down.

Hope that helps.

[cderv]

So I tried something with #228 and it seems it does not help
Still same issue on windows: https://github.com/cderv/pkgdown.quarto.issue/actions/runs/13901722420/job/38894903302

This would confirm the problem is much more complex, and setting R_LIBS is not enough - something else happens on windows (as R_LIBS is set already in R CMD build #217 (comment))

I still need to investigate what is the problem. Setting local::. in the CI is the current workaround

[astamm]

Thanks @cderv for looking into this! You suggests that also setting local::. in the pkgdown Github action works or is that only for R CMD check?

[cderv]

@astamm I couldn't reproduce on pkgdown the problem. I tested with https://github.com/cderv/pkgdown.quarto.issue and it passes.

The .qmd vignette is built.

This is the same for pkgdown issue, where not reproduction was able to be found

• Quarto vignettes use the installed version of the package, but Rmd vignettes use the current dev version r-lib/pkgdown#2830

However, they did try something there and fix doing the following

• Set lib path for quarto render r-lib/pkgdown#2864

Though I am unsure it fixes something;

Does your flipr package still have the problem for pkgdown ?

[astamm]

Yes, still seeing:

Error in `quarto::quarto_render()`:
✖ Error running quarto cli.
ℹ Rerun with `quiet = FALSE` to see the full error message.
Caused by error:
! System command 'quarto' failed

Details here: https://github.com/permaverse/flipr/actions/runs/13627243517/job/38898623580.

[cderv]

Ok. Cryptic error as quiet = FALSE is set by pkgdown internally.

I can reproduce and yes using local::. should solve it. The problem is because pkgdown default to install in a temporary library the package, which is not seen by quarto R process afterward.

I'll fork you and try with your package. Thanks for sharing

BTW, #228 should solve the issue so if you use it for your CI run, it should work. (unless you have other issues in vignette)