Using in-body syntax for knitr chunk options creates problems for pkgdown in presence of child documents

[IndrajeetPatil]

While converting from the in-header chunk option syntax to new the in-body syntax, I have noticed that this new syntax trips up {pkgdown}'s vignette rendering when child documents are present.

For a minimal reprex, see this PR:
IndrajeetPatil/minimalReprex#3

When I try to build the website locally, I see the following backtrace:

Backtrace:
1. pkgdown::build_site()
2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run_dont_run = run_dont_run, …
3. callr::r(function(..., cli_colors, pkgdown_internet) { …
4. callr:::get_result(output = out, options)
5. callr:::throw(callr_remote_error(remerr))
6. callr:::callr_remote_error(remerr)
7. callr:::throw(err, parent = remerr[[3]])
---
Subprocess backtrace:
 1. pkgdown::build_site(...)
 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_dont_run = run_dont_run, …
 3. pkgdown::build_articles(pkg, lazy = lazy, override = override, preview = FALSE)
 4. purrr::walk(pkg$vignettes$name, build_article, pkg = pkg, quiet = quiet, …
 5. purrr::map(.x, .f, ...)
 6. local .f(.x[[i]], ...)
 7. pkgdown:::render_rmarkdown(pkg, input = input, output = output_file, output_format = format, …
 8. base::tryCatch(callr::r_safe(function(...) rmarkdown::render(...), …
 9. base::tryCatchList(expr, classes, parentenv, handlers)
10. base::tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. value[[3L]](cond)
12. rlang::abort("Failed to render RMarkdown", parent = cnd)
13. | rlang:::signal_abort(cnd, .file)
14. | base::signalCondition(cnd)
15. global (function (e) …

[maelle]

👋 @IndrajeetPatil! Thanks for the reprex and bug report.

Setting a browser() deeply enough in the functions I get the actual error message!

Quitting from lines 12-13 (/tmp/RtmpeywYCq/../man/rmd-fragments/boilerplate.Rmd) 
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/tmp/RtmpeywYCq/../man/rmd-fragments/boilerplate.Rmd': No such file or directory

🤔

[IndrajeetPatil]

Thanks for digging into this!

This is strange. Why does this happen only with in-body syntax?

cannot open file '/tmp/RtmpeywYCq/../man/rmd-fragments/boilerplate.Rmd': No such file or directory

The child document is there and {pkgdown} works fine on the main branch where in-header chunk option is used to specify child document.

[maelle]

btw shouldn't the syntax for the in-body option be

#| child: "../man/rmd-fragments/boilerplate.Rmd"

Sadly it does not make the problem go away.

[maelle]

ah no your syntax is the correct one anyway

[IndrajeetPatil]

Btw, I used the new {knitr} function to convert the old syntax to the new syntax.

[maelle]

oh good to know about, thank you!

[maelle]

I wonder if somehow the problem could be linked to https://github.com/yihui/knitr/blob/553b6929f0b737f02fffc20cd10a10d0268b1487/NEWS.md?plain=1#L234

I'm stuck so will leave this aside for now.

[maelle]

Posting the whole trace

Quitting from lines 12-13 (/tmp/RtmpXwp60l/../man/rmd-fragments/boilerplate.Rmd) 
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/tmp/RtmpXwp60l/../man/rmd-fragments/boilerplate.Rmd': No such file or directory
Backtrace:
  1. knitr::knit(..., tangle = TRUE)
  2. knitr:::process_file(text, output)
  5. knitr:::process_tangle.block(group)
  6. base::lapply(sc_split(params$child), knit_child)
  7. knitr (local) FUN(X[[i]], ...)
  8. knitr::knit(..., tangle = opts_knit$get("tangle"), envir = envir)
  9. xfun::read_utf8(input)
 10. base::readLines(con, encoding = "UTF-8", warn = FALSE)
 11. base::file(con, "r")

[maelle]

I see the same error with rmarkdown::render("vignettes/test2.Rmd", intermediates_dir = tempdir())

[IndrajeetPatil]

Thanks for digging deeper!

Do you think this is {rmarkdown} issue then?

[maelle]

I think so, I'm about to open an issue, I'm 99% I found the problem 😸

[maelle]

rstudio/rmarkdown#2393

[IndrajeetPatil]

Thanks! Closing this issue in favour of that issue then :)

[maelle]

And we'll re-open if I'm wrong there 😅