Hello! This is a strange error which I cannot get to the bottom of.
I've been building a data access package, using roxygen2 for documentation. For everything thus-far things have gone swimmingly, but today I decided to take on the task of using pkgdown to create the documentation site for the package.
Unfortunately I cannot get pkgdown to build the site from the Rd files for love nor money.
When I get to the "Building function reference" step, it immediately fails out on the first file with the following error:
── Building function reference ──────────────────────────────────────────
Reading man/check_db_status.Rd
Error:
! in callr subprocess.
Caused by error in `build_reference()`:
! Failed to parse Rd in check_db_status.Rd
ℹ See `$stdout` and `$stderr` for standard output and error.
Type .Last.error to see the more details.
The file it is complaining about looks like this:
#' @title Generate a base request string for the AREAdata database
#' @description This string is used as the basis for all calls to AREAdata.
#' It does not contain any tokens or session ids, and thus can be regenerated at any time.
#'
#' @author Francis Windram
#' @return Returns a string containing the root address of the AREAdata dataset.
#'
#' @examples
#' \dontrun{
#' basereq <- ad_basereq()
#' }
#'
#'
#' @export
#'
ad_basereq <- function() {
return("https://github.com/pearselab/areadata/raw/main/")
}
It builds fine using document() and the documentation shows up perfectly rendered afterwards with ?ad_basereq()
The full stack trace upon calling .Last.error is as follows:
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! in callr subprocess.
Caused by error in `build_reference()`:
! Failed to parse Rd in ad_basereq.Rd
ℹ See `$stdout` and `$stderr` for standard output and error.
---
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, hyperlinks, 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_reference(pkg, lazy = lazy, examples = examples, run_dont_run = run_dont_run, …
4. pkgdown:::unwrap_purrr_error(purrr::map(topics, build_reference_topic, …
5. base::withCallingHandlers(code, purrr_error_indexed = function(err) { …
6. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, …
7. purrr:::map_("list", .x, .f, ..., .progress = .progress)
8. purrr:::with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, …
9. base::withCallingHandlers(expr, error = function(cnd) { …
10. purrr:::call_with_cleanup(map_impl, environment(), .type, .progress, …
11. local .f(.x[[i]], ...)
12. base::withCallingHandlers(data_reference_topic(topic, pkg, examples_env = examples_env, …
13. pkgdown:::data_reference_topic(topic, pkg, examples_env = examples_env, …
14. pkgdown:::run_examples(tags$tag_examples[[1]], env = if (is.null(examples_env)) NULL else new.env(parent = examples_env), …
15. pkgdown:::highlight_examples(code, topic, env = env)
16. downlit::evaluate_and_highlight(code, fig_save = fig_save_topic, …
17. evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
18. evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, …
19. output_handler$source(source)
20. base::.handleSimpleError(function (err) …
21. local h(simpleError(msg, call))
22. cli::cli_abort("Failed to parse Rd in {.file {topic$file_in}}", …
23. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, …
24. | rlang:::signal_abort(cnd, .file)
25. | base::signalCondition(cnd)
26. (function (cnd) …
27. cli::cli_abort(message, location = i, name = name, parent = cnd, …
28. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, …
29. | rlang:::signal_abort(cnd, .file)
30. | base::signalCondition(cnd)
31. (function (err) …
32. rlang::cnd_signal(err$parent)
33. rlang:::signal_abort(cnd)
34. base::signalCondition(cnd)
35. global (function (e) …
For completeness, the generated ad_basereq.Rd file contains this code:
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ad_basereq.R
\name{ad_basereq}
\alias{ad_basereq}
\title{Generate a base request string for the AREAdata database}
\usage{
ad_basereq()
}
\value{
Returns a string containing the root address of the AREAdata dataset.
}
\description{
This string is used as the basis for all calls to AREAdata.
It does not contain any tokens or session ids, and thus can be regenerated at any time.
}
\examples{
\dontrun{
basereq <- ad_basereq()
}
}
\author{
Francis Windram
}
Finally the packages and versions are:
| Package | Version |
|---|---|
| devtools | 2.4.5 |
| usethis | 2.2.3 |
| roxygen2 | 7.3.2 |
| pkgdown | 2.1.0 |
| downlit | 0.4.4 |
| purrr | 1.0.2 |
I listed the last two as functions from those pop out in the stack trace.
It looks like the error is coming out of downlit::evaluate_and_highlight()but I really can't see any particular reason why that might be.
The only other thing I can think of is that build_site() will only run if I unload the dev package prior, using detach("package:ohvbd", unload=TRUE), but I don't particularly see why that would cause this issue.
Anyone seen anything like this? Is there something super obvious that I am missing?
Thank you!