Did you re-document? You’ll need that to correctly regenerate the .Rd, I think. (Sorry I’m on vacation so I’m guessing at stuff from my phone)
Hadley On Thursday, January 4, 2024, Daniel Kelley <kel...@dal.ca> wrote: > Thanks. I installed the latest roxygen2 and pkgdown, and tried to make a > simple reprex > git clone https://github.com/dankelley/mooring.git > cd mooring > git checkout S7 > Rscript -e "pkgdown::clean_site()" > Rscript -e "pkgdown::build_site()" > > but it still fails. (Full output is below, for completeness.) I wonder > whether I ought to be doing something extra in the Roxygen code (in file > R/plot.R within this directory.). Please note that I can rename it as > "draw()" or something, but I'm hoping to learn S7 properly, because I'm > really quite keen to leave my S3 and S4 days behind me. (PS to Hadley: I > loved the presentation you gave on what was then R7, and have recommended > it to colleagues not just for the R7 information, but for the concise > explanation of the benefit of OOP and generics.) > > ── Installing package mooring into temporary library > ─────────────────────────── > ── Building pkgdown site for package mooring ────────────────────────────── > ───── > Reading from: /Users/kelley/wednesday/mooring > Writing to: /Users/kelley/wednesday/mooring/docs > ── Initialising site ────────────────────────────── > ───────────────────────────── > Copying > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/bootstrap-toc.css, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/bootstrap-toc.js, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/docsearch.css, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/docsearch.js, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/link.svg, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/pkgdown.css, > and > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/pkgdown.js > to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, > link.svg, > pkgdown.css, and pkgdown.js > ── Building home ────────────────────────────── > ───────────────────────────────── > Writing authors.html > Copying man/figures/Makefile, man/figures/README-example-1.png, > man/figures/README-example-2.png, man/figures/force_diagram.R, and > man/figures/force_diagram.png > to reference/figures/Makefile, reference/figures/README-example-1.png, > reference/figures/README-example-2.png, reference/figures/force_diagram.R, > and > reference/figures/force_diagram.png > Writing 404.html > ── Building function reference ────────────────────────────── > ─────────────────── > Error: > ! in callr subprocess. > Caused by error in `map2(.x, vec_index(.x), .f, ...)`: > ! In index: 1. > --- > Standard error: > ── Building pkgdown site for package mooring ────────────────────────────── > ───── > Reading from: /Users/kelley/wednesday/mooring > Writing to: /Users/kelley/wednesday/mooring/docs > ── Initialising site ────────────────────────────── > ───────────────────────────── > Copying > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/bootstrap-toc.css, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/bootstrap-toc.js, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/docsearch.css, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/docsearch.js, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/link.svg, > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/pkgdown.css, > and > ../../../../Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/ > library/pkgdown/BS3/assets/pkgdown.js > to bootstrap-toc.css, bootstrap-toc.js, docsearch.css, docsearch.js, > link.svg, > pkgdown.css, and pkgdown.js > ── Building home ────────────────────────────── > ───────────────────────────────── > Writing authors.html > Copying man/figures/Makefile, man/figures/README-example-1.png, > man/figures/README-example-2.png, man/figures/force_diagram.R, and > man/figures/force_diagram.png > to reference/figures/Makefile, reference/figures/README-example-1.png, > reference/figures/README-example-2.png, reference/figures/force_diagram.R, > and > reference/figures/force_diagram.png > Writing 404.html > ── Building function reference ────────────────────────────── > ─────────────────── > --- > 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_reference(pkg, lazy = lazy, examples = examples, > run_dont_run = 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. 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:::where_if(.x, .p, ...) > 15. purrr:::map_(.x, .p, ..., .type = "logical", .purrr_error_call = > .purrr_error_call) > 16. purrr:::vctrs_vec_compat(.x, .purrr_user_env) > 17. purrr::imap(., data_reference_index_rows, pkg = pkg) > 18. purrr::map2(.x, vec_index(.x), .f, ...) > 19. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) > 20. purrr:::with_indexed_errors(i = i, names = names, error_call = > .purrr_error_call, … > 21. base::withCallingHandlers(expr, error = function(cnd) { … > 22. purrr:::call_with_cleanup(map2_impl, environment(), .type, .progress, > … > 23. local .f(.x[[i]], .y[[i]], ...) > 24. pkgdown:::section_topics(section$contents, pkg$topics, pkg$src_path) > 25. base::rbind(topics, ext_topics(ext_strings)) > 26. base::rbind(deparse.level, ...) > 27. pkgdown:::ext_topics(ext_strings) > 28. purrr::map2(pkg, fun, get_rd_from_help) > 29. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) > 30. purrr:::with_indexed_errors(i = i, names = names, error_call = > .purrr_error_call, … > 31. base::withCallingHandlers(expr, error = function(cnd) { … > 32. purrr:::call_with_cleanup(map2_impl, environment(), .type, .progress, > … > 33. local .f(.x[[i]], .y[[i]], ...) > 34. rlang::check_installed(package, "as it's used in the reference > index.") > 35. base::stop(cnd) > 36. (function (cnd) … > 37. cli::cli_abort(message, location = i, name = name, parent = cnd, … > 38. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, … > 39. | rlang:::signal_abort(cnd, .file) > 40. | base::signalCondition(cnd) > 41. (function (cnd) … > 42. cli::cli_abort(message, location = i, name = name, parent = cnd, … > 43. | rlang::abort(message, ..., call = call, use_cli_format = TRUE, … > 44. | rlang:::signal_abort(cnd, .file) > 45. | base::signalCondition(cnd) > 46. global (function (e) … > Execution halted > > > > On Jan 3, 2024, at 1:06 PM, Hadley Wickham <h.wick...@gmail.com> wrote: > > CAUTION: The Sender of this email is not from within Dalhousie. > This bug is fixed in the dev version (I don’t remember off the top of my > head in which of pkgdown and roxygen2 you need but it might be both). I’m > planning CRAN updates for both in the near future. > > Hadley > > On Thursday, January 4, 2024, Daniel Kelley <kel...@dal.ca> wrote: > >> # Question >> >> Is there an online example online of specializing `plot()` for S7 >> objects, such that `pkgdown::build_site()` will produce webpages? I ask >> because I find lots of users (of other packages) tend to consult websites >> made with pkgdown, rather than using the online help within R. I think the >> problem I am having (discussed in the following sections) has to do with my >> specialization of plot(). I say that because when I was using S3 objects >> in an earlier version of my package, `pkgdown::build_site()` worked as >> intended. >> >> # Background >> >> In my 'mooring' package (https://github.com/dankelley/mooring/tree/S7), >> I am writing code like (https://github.com/dankelley/ >> mooring/blob/f70b53ca12e88968f65710c205b50a64f750a99d/R/plot.R#L69) >> >> ```R >> #' @aliases plot.mooring >> #' ETC >> `plot.mooring::mooring` <- plot(ETC) ETC >> ``` >> >> to handle objects made with (https://github.com/dankelley/ >> mooring/blob/f70b53ca12e88968f65710c205b50a64f750a99d/R/oo.R#L2) >> >> ```R >> mooringS7 <- S7::new_class("mooring", >> package = "mooring", >> ETC >> ``` >> >> Built up in Rstudio, with Roxygen2 being used to create documentation, >> things seem to work, e.g. >> >> ```R >> m <- mooring(anchor(), wire(length = 80), float(), waterDepth = 100) >> plot(m) >> ``` >> >> produces a plot as intended, and >> >> ```R >> ?plot.mooring >> ``` >> >> produces documentation as intended. >> >> *However* I encounter a problem comes when I try building a website with >> >> ```R >> pkgdown::build_site() >> ``` >> >> This yields results as in the next section. (I apologize for the length. >> I'm including the whole thing because I thought that would be less >> bothersome than writing another email to the list.) >> >> I am not sure how to find the problem, and so I hope that someone on this >> list can point out an example of how to set up `plot()` to work with S7 >> objects, in such a way that documentation can be created with Roxygen2 and >> websites can be made with `pkgdown::build_site()`. >> >> # What pkgdown::build_site() gives >> >> ``` >> > library(pkgdown) >> > build_site() >> Warning: Failed to parse usage: >> >> S3method(`plot`, ``mooring::mooring``)( >> x, >> which = "shape", >> showInterfaces = TRUE, >> showDepths = FALSE, >> showLabels = TRUE, >> showDetails = FALSE, >> fancy = FALSE, >> title = "", >> mar = c(1.5, 3.5, 3.5, 1), >> mgp = c(2, 0.7, 0), >> xlim = NULL, >> xaxs = "r", >> yaxs = "r", >> type = "l", >> debug = 0, >> ... >> ) >> >> -- Installing package into temporary library ---------------- >> == Building pkgdown site ============================== >> ========================= >> Reading from: '/Users/kelley/git/mooring' >> Writing to: '/Users/kelley/git/mooring/docs' >> -- Initialising site ------------------------------ >> ----------------------------- >> -- Building home ------------------------------ >> --------------------------------- >> Writing '404.html' >> -- Building function reference ------------------------------ >> ------------------- >> Error: >> ! in callr subprocess. >> Caused by error in `map2(.x, vec_index(.x), .f, ...)`: >> ! 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 `map2(.x, vec_index(.x), .f, ...)`: >> ! In index: 1. >> ℹ See `$stdout` for standard output. >> --- >> Backtrace: >> 1. pkgdown::build_site() >> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run… >> 3. callr::r(function(..., cli_colors, pkgdown_internet) { … >> 4. callr:::get_result(output = out, options) >> 5. callr:::throw(callr_remote_error(remerr, output), parent = fix_… >> --- >> Subprocess backtrace: >> 1. pkgdown::build_site(...) >> 2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do… >> 3. pkgdown::build_reference(pkg, lazy = lazy, examples = examples, … >> 4. pkgdown::build_reference_index(pkg) >> 5. pkgdown::render_page(pkg, "reference-index", data = data_referen… >> 6. pkgdown:::render_page_html(pkg, name = name, data = data, depth =… >> 7. utils::modifyList(data_template(pkg, depth = depth), da… >> 8. base::stopifnot(is.list(x), is.list(val)) >> 9. pkgdown:::data_reference_index(pkg) >> 10. meta %>% purrr::imap(data_reference_index_rows, pkg = p… >> 11. base::unlist(., recursive = FALSE) >> 12. purrr::compact(.) >> 13. purrr::discard(.x, function(x) is_empty(.f(x))) >> 14. purrr:::where_if(.x, .p, ...) >> 15. purrr:::map_(.x, .p, ..., .type = "logical", .purrr_error_call … >> 16. purrr:::vctrs_vec_compat(.x, .purrr_user_env) >> 17. purrr::imap(., data_reference_index_rows, pkg = pkg) >> 18. purrr::map2(.x, vec_index(.x), .f, ...) >> 19. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) >> 20. purrr:::with_indexed_errors(i = i, names = names, error_call = … >> 21. base::withCallingHandlers(expr, error = function(cnd) { … >> 22. purrr:::call_with_cleanup(map2_impl, environment(), .type, .pro… >> 23. local .f(.x[[i]], .y[[i]], ...) >> 24. pkgdown:::section_topics(section$contents, pkg$topics, pkg$src_pa… >> 25. base::rbind(topics, ext_topics(ext_strings)) >> 26. base::rbind(deparse.level, ...) >> 27. pkgdown:::ext_topics(ext_strings) >> 28. purrr::map2(pkg, fun, get_rd_from_help) >> 29. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress) >> 30. purrr:::with_indexed_errors(i = i, names = names, error_call = … >> 31. base::withCallingHandlers(expr, error = function(cnd) { … >> 32. purrr:::call_with_cleanup(map2_impl, environment(), .type, .pro… >> 33. local .f(.x[[i]], .y[[i]], ...) >> 34. rlang::check_installed(package, "as it's used in the reference… >> 35. base::stop(cnd) >> 36. (function (cnd) … >> 37. cli::cli_abort(message, location = i, name = name, pare… >> 38. | rlang::abort(message, ..., call = call, use_cli_format … >> 39. | rlang:::signal_abort(cnd, .file) >> 40. | base::signalCondition(cnd) >> 41. (function (cnd) … >> 42. cli::cli_abort(message, location = i, name = name, pare… >> 43. | rlang::abort(message, ..., call = call, use_cli_format … >> 44. | rlang:::signal_abort(cnd, .file) >> 45. | base::signalCondition(cnd) >> 46. global (function (e) … >> ``` >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > > > -- > http://hadley.nz > > > -- http://hadley.nz [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
