pkgdown 2.0.0 erroring for class names containing colons.

[stefanoborini]

It seems that pkgdown incorrectly parses an S3 method for a class called "maraca::maraca", and assumes plot.maraca::maraca is coming from a package plot.maraca.

Rscript -e "pkgdown::build_site()"
Using environment r4 (R version: 4.0.4, platform: x86_64-apple-darwin17.0)
Warning: Failed to parse usage:

S3method(`plot`, ``maraca::maraca``)(
  x,
  continuous_grid_spacing_x = 10,
  trans = "identity",
  density_plot_type = "default",
  vline_type = "median",
  ...
)

-- Installing package into temporary library -----------------------------------
Using environment r4 (R version: 4.0.4, platform: x86_64-apple-darwin17.0)
== Building pkgdown site =======================================================
Reading from: '/Users/Work/Repos/AstraZeneca/maraca'
Writing to:   '/Users/Work/Repos/AstraZeneca/maraca/site'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing 'authors.html'
Reading 'AUTHORS.md'
Writing 'AUTHORS.html'
Reading 'CONTRIBUTING.md'
Reading 'LICENSE.md'
Writing '404.html'
-- Building function reference -------------------------------------------------
Error in .f(.x[[1L]], .y[[1L]], ...) : 
  The package ``plot.maraca` is required as it's used in the reference
index.
Error: 
! error in callr subprocess
Caused by error in `.f(.x[[1L]], .y[[1L]], ...)`:
! The package ``plot.maraca` is required as it's used in the reference index.
---
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_reference(pkg, lazy = lazy, examples = examples, run_dont_run = run_dont_run, …
 4. pkgdown::build_reference_index(pkg)
 5. pkgdown::render_page(pkg, "reference-index", data = data_reference_index(pkg), …
 6. pkgdown:::render_page_html(pkg, name = name, data = data, depth = depth)
 7. utils::modifyList(data_template(pkg, depth = depth), data)
 8. base::stopifnot(is.list(x), is.list(val))
 9. pkgdown:::data_reference_index(pkg)
10. magrittr::meta %>% purrr::imap(data_reference_index_rows, pkg = pkg) %>% …
11. base::unlist(., recursive = FALSE)
12. purrr::compact(.)
13. purrr::discard(.x, function(x) is_empty(.f(x)))
14. purrr:::probe(.x, .p, ...)
15. purrr::map_lgl(.x, .p, ...)
16. purrr::imap(., data_reference_index_rows, pkg = pkg)
17. purrr::map2(.x, vec_index(.x), .f, ...)
18. local .f(.x[[1L]], .y[[1L]], ...)
19. pkgdown:::section_topics(section$contents, pkg$topics, pkg$src_path)
20. base::rbind(topics, ext_topics(ext_strings))
21. base::rbind(deparse.level, ...)
22. pkgdown:::ext_topics(ext_strings)
23. purrr::map2(pkg, fun, get_rd_from_help)
24. local .f(.x[[1L]], .y[[1L]], ...)
25. rlang::check_installed(package, "as it's used in the reference index.")
26. base::stop(cnd)
27. global (function (e) …
Execution halted
make: *** [site] Error 1

[stefanoborini]

possible fix, but not sure: if one specifies @method plot maraca::maraca it should work.

[stefanoborini]

Verified not to work with the above fix. The problem was not present in pkgdown 1.6.1, but it is present in 2.0.0

[jsilve24]

I am running into the same error but its not because of class names... I think it has to do with @examples.

[jsilve24]

Here is (what I think should be) a reproducible example.

git clone https://github.com/jsilve24/fido.git
git checkout develop
R

then in R

pkgdown::clean_site()
pkgdown::build_site()

I have been stuck on this for the past 2 hours. I keep getting this error.

> pkgdown::clean_site()
> pkgdown::build_site()
-- Installing package into temporary library -----------------------------------
== Building pkgdown site =======================================================
Reading from: '/home/jds6696/Dropbox/Research/src/fido'
Writing to:   '/home/jds6696/Dropbox/Research/src/fido/docs'
-- Initialising site -----------------------------------------------------------
Copying '../../../../R/x86_64-pc-linux-gnu-library/4.2/pkgdown/BS5/assets/link.svg' to 'link.svg'
Copying '../../../../R/x86_64-pc-linux-gnu-library/4.2/pkgdown/BS5/assets/pkgdown.js' to 'pkgdown.js'
-
Warning message:
In utils::install.packages(pkg$src_path, repos = NULL, type = "source",  :
  installation of package ‘/home/jds6696/Dropbox/Research/src/fido’ had non-zero exit status
> pkgdown::build_site()
-- Installing package into temporary library -----------------------------------
== Building pkgdown site =======================================================
Reading from: '/home/jds6696/Dropbox/Research/src/fido'
Writing to:   '/home/jds6696/Dropbox/Research/src/fido/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing 'authors.html'
Writing '404.html'
-- Building function reference -------------------------------------------------
Writing 'reference/index.html'
Reading 'man/Y.Rd'
Writing 'reference/Y.html'
Reading 'man/access_dims.Rd'
Writing 'reference/access_dims.html'
Reading 'man/alr.Rd'
Writing 'reference/alr.html'
Reading 'man/alrInv.Rd'
Writing 'reference/alrInv.html'
Reading 'man/alrInv_array.Rd'
Writing 'reference/alrInv_array.html'
Reading 'man/alr_array.Rd'
Writing 'reference/alr_array.html'
Reading 'man/as.list.orthusfit.Rd'
Writing 'reference/as.list.orthusfit.html'
Reading 'man/as.list.pibblefit.Rd'
Writing 'reference/as.list.pibblefit.html'
Reading 'man/as.orthusfit.Rd'
Writing 'reference/as.orthusfit.html'
Reading 'man/as.pibblefit.Rd'
Writing 'reference/as.pibblefit.html'
Reading 'man/basset_fit.Rd'
Writing 'reference/basset_fit.html'
Reading 'man/check_dims.Rd'
Error: 
! in callr subprocess.
Caused by error in `purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, …`:
! In index: 12.
ℹ See `$stdout` for standard output.
Type .Last.error to see the more details.

The error goes away when I remove the @examples section of every one of my functions. Adding \dontrun{} doesnot make a difference. I think the bug is comming up from one of the dependencies downlit but I am not sure.

[dkarletsos]

@maelle - please, are you able to share what is the likely ETA for the resolution of this?

[dmurdoch]

@dkarletsos : I'm not @maelle, but I think the fact that this issue has been sitting untouched for more than a year would suggest that it's not going to happen soon, unless you do it. So if you don't want to track down the issue and submit a PR, I'd suggest renaming your class to something that doesn't contain colons. (It appears that fido has chosen that workaround.)

[hadley]

Given that there's no reprex, and it seems folks have figured our workarounds, I'm going to close this issue. If anyone really cares about it, please feel free to file a new issue accompanied by a minimal package that illustrates the problem.