build_site() fails to build knitr::markdown vignette with css

Question

build_site() fails to build knitr::markdown vignette with css

jangorecki opened this issue 7 months ago · comments

This basic minimal example package
https://github.com/jangorecki/mdpkg
that passed cleanly build and check in R
is failing during pkgdown build_site()

it is using knitr::knitr vignette engine.
fyi @yihui

usethis::use_pkgdown()

✔ Setting active project to '/mdpkg'
✔ Adding '^_pkgdown\\.yml$', '^docs$', '^pkgdown$' to '.Rbuildignore'
✔ Adding 'docs' to '.gitignore'
✔ Writing '_pkgdown.yml'
• Modify '_pkgdown.yml'
sh: 1: vi: not found
Warning message:
error in running command

cat _pkgdown.yml

url: ~
template:
  bootstrap: 5

pkgdown::build_site()

-- Installing package into temporary library -----------------------------------
== Building pkgdown site =======================================================
Reading from: '/mdpkg'
Writing to:   '/mdpkg/docs'
-- Initialising site -----------------------------------------------------------
Copying '../usr/local/lib/R/site-library/pkgdown/BS5/assets/link.svg' to 'link.svg'
Copying '../usr/local/lib/R/site-library/pkgdown/BS5/assets/pkgdown.js' to 'pkgdown.js'
-- Building home ---------------------------------------------------------------
Writing 'authors.html'
Writing '404.html'
-- Building function reference -------------------------------------------------
Writing 'reference/index.html'
Reading 'man/hello.Rd'
Writing 'reference/hello.html'
-- Building articles -----------------------------------------------------------
Writing 'articles/index.html'
Reading 'vignettes/vign.Rmd'
-- RMarkdown error -------------------------------------------------------------
--------------------------------------------------------------------------------
Error: 
! in callr subprocess.
Caused by error in `map(.x, .f, ..., .progress = .progress)`:
! In index: 1.
ℹ See `$stdout` for standard output.
Type .Last.error to see the more details.

.Last.error

<callr_error/rlib_error_3_0/rlib_error/error>
Error: 
! in callr subprocess.
Caused by error in `map(.x, .f, ..., .progress = .progress)`:
! In index: 1.
ℹ See `$stdout` for standard output.
---
Backtrace:
1. pkgdown::build_site()
2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run_dont_run = run_dont_run, …
3. callr::r(function(..., cli_colors, pkgdown_internet) { …
4. callr:::get_result(output = out, options)
5. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. pkgdown::build_site(...)
 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_dont_run = run_dont_run, …
 3. pkgdown::build_articles(pkg, lazy = lazy, override = override, preview = FALSE)
 4. purrr::walk(pkg$vignettes$name, build_article, pkg = pkg, quiet = quiet, …
 5. purrr::map(.x, .f, ..., .progress = .progress)
 6. purrr:::map_("list", .x, .f, ..., .progress = .progress)
 7. purrr:::with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, …
 8. base::withCallingHandlers(expr, error = function(cnd) { …
 9. purrr:::call_with_cleanup(map_impl, environment(), .type, .progress, …
10. local .f(.x[[i]], ...)
11. pkgdown:::render_rmarkdown(pkg, input = input, output = output_file, output_format = format, …
12. base::tryCatch(callr::r_safe(function(...) rmarkdown::render(...), …
13. base::tryCatchList(expr, classes, parentenv, handlers)
14. base::tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. value[[3L]](cond)
16. rlang::abort("Failed to render RMarkdown", parent = cnd)
17. | rlang:::signal_abort(cnd, .file)
18. | base::signalCondition(cnd)
19. (function (cnd) …
20. cli::cli_abort(message, location = i, name = name, parent = cnd, …
21. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, …
22. | rlang:::signal_abort(cnd, .file)
23. | base::signalCondition(cnd)
24. global (function (e) …

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux trixie/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: Etc/UTC
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5     cli_3.6.1       knitr_1.45      rlang_1.1.2    
 [5] xfun_0.41       processx_3.8.2  purrr_1.0.2     glue_1.6.2     
 [9] rprojroot_2.0.4 htmltools_0.5.7 ps_1.7.5        fansi_1.0.5    
[13] rmarkdown_2.25  evaluate_0.23   tibble_3.2.1    fastmap_1.1.1  
[17] yaml_2.3.7      lifecycle_1.0.4 memoise_2.0.1   compiler_4.3.2 
[21] fs_1.6.3        pkgconfig_2.0.3 digest_0.6.33   R6_2.5.1       
[25] utf8_1.2.4      pillar_1.9.0    callr_3.7.3     magrittr_2.0.3 
[29] tools_4.3.2     withr_2.5.2     pkgdown_2.0.7   cachem_1.0.8   
[33] desc_1.4.2

Etienne Bacher · Answer 1 · Mon Dec 04 2023 22:58:02 GMT+0800 (China Standard Time)

Sorry if I missed something obvious but shouldn't this be markdown::html_format instead?

https://github.com/jangorecki/mdpkg/blob/edaa8d0906a3fe98cad6512fe57932433479216d/vignettes/vign.Rmd#L4

I no longer see this error with markdown::html_format

Jan Gorecki · Answer 2 · Mon Dec 04 2023 23:48:15 GMT+0800 (China Standard Time)

changing to html_format did not help:

root@e2b15d9dae7f:/mdpkg# cat vignettes/vign.Rmd 
---
title: "Title of a vignette"
output:
  markdown::html_format
vignette: >
  %\VignetteIndexEntry{Example vignette}
  %\VignetteEngine{knitr::knitr}
  \usepackage[utf8]{inputenc}
---

## Hello

library(mdpkg)
hello()

## Bye

Bye!
root@e2b15d9dae7f:/mdpkg# Rscript -e 'pkgdown::build_site()'
-- Installing package into temporary library -----------------------------------
== Building pkgdown site =======================================================
Reading from: '/mdpkg'
Writing to:   '/mdpkg/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing '404.html'
-- Building function reference -------------------------------------------------
Reading 'man/hello.Rd'
-- Building articles -----------------------------------------------------------
Reading 'vignettes/vign.Rmd'
-- RMarkdown error -------------------------------------------------------------
--------------------------------------------------------------------------------
Error: 
! in callr subprocess.
Caused by error in `map(.x, .f, ..., .progress = .progress)`:
! In index: 1.
---
Standard output:
== Building pkgdown site =======================================================
Reading from: '/mdpkg'
Writing to:   '/mdpkg/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing '404.html'
-- Building function reference -------------------------------------------------
Reading 'man/hello.Rd'
-- Building articles -----------------------------------------------------------
Reading 'vignettes/vign.Rmd'
-- RMarkdown error -------------------------------------------------------------
--------------------------------------------------------------------------------
---
Backtrace:
1. pkgdown::build_site()
2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run_dont_run = run_don…
3. callr::r(function(..., cli_colors, pkgdown_internet) { …
4. callr:::get_result(output = out, options)
5. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
 1. pkgdown::build_site(...)
 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_dont_run = run_dont_r…
 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, ..., .progress = .progress)
 6. purrr:::map_("list", .x, .f, ..., .progress = .progress)
 7. purrr:::with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, …
 8. base::withCallingHandlers(expr, error = function(cnd) { …
 9. purrr:::call_with_cleanup(map_impl, environment(), .type, .progress, …
10. local .f(.x[[i]], ...)
11. pkgdown:::render_rmarkdown(pkg, input = input, output = output_file, output_format =…
12. base::tryCatch(callr::r_safe(function(...) rmarkdown::render(...), …
13. base::tryCatchList(expr, classes, parentenv, handlers)
14. base::tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. value[[3L]](cond)
16. rlang::abort("Failed to render RMarkdown", parent = cnd)
17. | rlang:::signal_abort(cnd, .file)
18. | base::signalCondition(cnd)
19. (function (cnd) …
20. cli::cli_abort(message, location = i, name = name, parent = cnd, …
21. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, …
22. | rlang:::signal_abort(cnd, .file)
23. | base::signalCondition(cnd)
24. global (function (e) …
Execution halted

I don't have good ideas how to debug it further on my side. Did you used a docker image? I can try to use the same.

Etienne Bacher · Answer 3 · Mon Dec 04 2023 23:52:50 GMT+0800 (China Standard Time)

Did you used a docker image? I can try to use the same.

No, nothing in particular. Just built the package locally and used html_format. Works fine for me. Does knitting the vignette only work?

Jan Gorecki · Answer 4 · Tue Dec 05 2023 00:18:00 GMT+0800 (China Standard Time)

OK, this time I forgot to install markdown package (oh, dependencies...), using devel=TRUE shows more details. After installing markdown package it successfully built vignette.

It seems I simplified my problem too much, and because of wrong function used before, not html_format it could have not been reproduced well.

I updated repo to not be over simplified, please try again to reproduce.

I does look that error comes from renderer not being able to find added css style, defined in yaml header.

pkgdown::build_site(devel=TRUE)
== Building pkgdown site =======================================================
Reading from: '/mdpkg'
Writing to:   '/mdpkg/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing '404.html'
-- Building function reference -------------------------------------------------
Reading 'man/hello.Rd'
-- Building articles -----------------------------------------------------------
Reading 'vignettes/vign.Rmd'
-- RMarkdown error -------------------------------------------------------------
Warning message:
In file(con, "r") :
  cannot open file 'css/toc.css': No such file or directory
--------------------------------------------------------------------------------
Error in `map()`:
ℹ In index: 1.
Caused by error in `render_rmarkdown()`:
! Failed to render RMarkdown
Caused by error:
! in callr subprocess.
Caused by error:
! cannot open the connection
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
Caused by error in `render_rmarkdown()`:
! Failed to render RMarkdown
Caused by error:
! in callr subprocess.
Caused by error:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─pkgdown::build_site(devel = TRUE)
  2.   └─pkgdown:::build_site_local(...)
  3.     └─pkgdown::build_articles(...)
  4.       └─purrr::walk(...)
  5.         └─purrr::map(.x, .f, ..., .progress = .progress)
  6.           └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  7.             ├─purrr:::with_indexed_errors(...)
  8.             │ └─base::withCallingHandlers(...)
  9.             ├─purrr:::call_with_cleanup(...)
 10.             └─pkgdown (local) .f(.x[[i]], ...)
 11.               └─pkgdown:::render_rmarkdown(...)

Gut feeling is that it should work because R CMD build . finds and uses added css well.

Etienne Bacher · Answer 5 · Tue Dec 05 2023 00:30:37 GMT+0800 (China Standard Time)

I can reproduce, this looks like a duplicate of #1229

The solution there is to provide a custom CSS and use as_is:

...
vignette: >
  %\VignetteIndexEntry{Example vignette}
  %\VignetteEngine{knitr::knitr}
  \usepackage[utf8]{inputenc}
pkgdown:
  as_is: true
---

However, this works with rmarkdown::html_vignette() but not with markdown::html_format(). Not an expert of pkgdown so I can't help more on that

Jan Gorecki · Answer 6 · Tue Dec 05 2023 01:14:51 GMT+0800 (China Standard Time)

@etiennebacher Thanks for finding that out. Indeed.
I think we should aim for consistency to R CMD build way of building vignettes, anyway. Otherwise each single use case like that will have to debug and eventually find out those issues here (unless won't give it up along the way).

Ultimately if it won't going to be addressed, there should be at least an option to specify that behavior in override argument of build_site() rather than expect users to modify their vignettes to work around limitations in pkgdown.

Anyway, doesn't work for markdown::html_format...

Maëlle Salmon · Answer 7 · Tue Dec 05 2023 21:00:53 GMT+0800 (China Standard Time)

For more context on the as_is option mentioned by @etiennebacher: https://pkgdown.r-lib.org/reference/build_articles.html#output-formats

Hadley Wickham · Answer 8 · Fri Apr 12 2024 05:52:58 GMT+0800 (China Standard Time)

@jangorecki unfortunately because pkgdown has to use a different page template than vignettes (in order to add its own navigation structure), I don't think there's any particularly clean way to do what you want.