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etiennebacher / altdoc

Alternative to pkgdown to document R packages
https://altdoc.etiennebacher.com
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Processing vignettes fails when there are child documents to include, maybe? #279

Closed bryanhanson closed 3 months ago

bryanhanson commented 3 months ago

Decided to try out altdoc. I'm working on the package here; main branch is fine for testing. I set up the environment using docsify.

I tried to render and got an error:

R > render_docs()
✔ Converting vignette 11/11: works_consulted.md [5ms][939ms]s]ms]s]

✖ 3The conversion failed for the following vignettes:
  • 'Vig_01_Start_Here.Rmd'
  • 'Vig_02_Conceptual_Intro_PCA.Rmd'
  • 'Vig_03_Step_By_Step_PCA.Rmd'
  • 'Vig_04_Scores_Loadings.Rmd'
  • 'Vig_05_Visualizing_PCA_3D.Rmd'
  • 'Vig_06_Math_Behind_PCA.Rmd'
  • 'Vig_07_Functions_PCA.Rmd'
  • 'Vig_08_Notes.Rmd'

Error in `render_docs()`:
! There were some failures when rendering vignettes and man pages.
Run `rlang::last_trace()` to see where the error occurred.

Runinng last_trace was not informative. These vignettes have three supporting files: works_consulted.md and top_matter.md and refer_to_works_consulted.md These supporting files are included in the numbered vignettes via a knit_child approach. None of them should be presented as vignettes by themselves.

Not sure what the exact problem is here, so I thought you should know about it. Perhaps there needs to be an "ignore" or "skip" argument somewhere so these supporting files are not processed, but will be found for inclusion purposes. Or maybe the problem is something entirely different...

I don't see any open or closed issue along these lines; hopefully I didn't miss one that applies. Thanks.

vincentarelbundock commented 3 months ago

Can you run it again with verbose=TRUE to see if you get a more informative error message?

bryanhanson commented 3 months ago

Sure... More loquacious than verbose! Tons of complaints. I do have a development version of quarto installed if that's relevant.

R > render_docs(verbose = TRUE)
Error in rmarkdown:::abs_path(input) : atpackage [1.6s]
  The file 'docs/man/PCAtoXhat.qmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
pandoc ction reference 3/4: PCsearcht [1.6s]
  to: >-
    markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links
  output-file: PCsearch.md
  standalone: true
  default-image-extension: png

Output created: PCsearch.md

Error in rmarkdown:::abs_path(input) : oXhat8s]
  The file 'docs/man/XtoPCAtoXhat.qmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : e.Rmdted.md [5ms]
  The file 'docs/vignettes/Vig_01_Start_Here.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
ERROR: Validation of YAML front matter failed.Rmd
ERROR: (line 21, columns 17--20) Field "link-citations" has value yes, which must instead be `true` or `false`

✖ The value yes is a string.
ℹ The error happened in location link-citations.
ℹ Quarto uses YAML 1.2, which interprets booleans strictly.
ℹ Try using true instead.

ERROR: Render failed due to invalid YAML.

Stack trace:
    at renderFileInternal (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:581:19)
    at async renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:325:9)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : tep_PCA.Rmd.Rmd [518ms]
  The file 'docs/vignettes/Vig_03_Step_By_Step_PCA.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : adings.Rmdd [945ms]
  The file 'docs/vignettes/Vig_04_Scores_Loadings.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : ng_PCA_3D.Rmd26ms]
  The file 'docs/vignettes/Vig_05_Visualizing_PCA_3D.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
ERROR: Validation of YAML front matter failed.d [939ms]
ERROR: (line 22, columns 17--20) Field "link-citations" has value yes, which must instead be `true` or `false`

✖ The value yes is a string.
ℹ The error happened in location link-citations.
ℹ Quarto uses YAML 1.2, which interprets booleans strictly.
ℹ Try using true instead.

ERROR: Render failed due to invalid YAML.

Stack trace:
    at renderFileInternal (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:581:19)
    at async renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:325:9)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : _PCA.Rmdmd [515ms]
  The file 'docs/vignettes/Vig_07_Functions_PCA.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Error in rmarkdown:::abs_path(input) : dPCA.Rmd [943ms]
  The file 'docs/vignettes/Vig_08_Notes.Rmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
ERROR: Error
    at renderFiles (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async Command.actionHandler (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/command/render/cmd.ts:248:26)
    at async Command.execute (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:156:3)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:170:5
    at async mainRunner (file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/core/main.ts:35:5)
    at async file:///Users/bryanh/Documents/Professional/Research/R_Pkgs/quarto-cli/src/quarto.ts:160:3
Error in quarto::quarto_render(input = path.expand(tar_file), output_format = "md",  : 
  ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
✔ Converting vignette 11/11: works_consulted.md [5ms]

✖ 3The conversion failed for the following vignettes:
  • 'Vig_01_Start_Here.Rmd'
  • 'Vig_02_Conceptual_Intro_PCA.Rmd'
  • 'Vig_03_Step_By_Step_PCA.Rmd'
  • 'Vig_04_Scores_Loadings.Rmd'
  • 'Vig_05_Visualizing_PCA_3D.Rmd'
  • 'Vig_06_Math_Behind_PCA.Rmd'
  • 'Vig_07_Functions_PCA.Rmd'
  • 'Vig_08_Notes.Rmd'

Error in `render_docs()`:
! There were some failures when rendering vignettes and man pages.
Run `rlang::last_trace()` to see where the error occurred.
R > rlang::last_trace()
<error/rlang_error>
Error in `render_docs()`:
! There were some failures when rendering vignettes and man pages.
---
Backtrace:
    ▆
 1. └─altdoc::render_docs(verbose = TRUE)
Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.
R > rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error in `render_docs()`:
! There were some failures when rendering vignettes and man pages.
---
Backtrace:
    ▆
 1. └─altdoc::render_docs(verbose = TRUE)
 2.   └─cli::cli_abort("There were some failures when rendering vignettes and man pages.")
 3.     └─rlang::abort(...)
R >
etiennebacher commented 3 months ago

Did you try with the github version of altdoc? https://github.com/etiennebacher/altdoc/pull/272 should have improved this unhelpful message "There were some failures..." even when verbose = FALSE

vincentarelbundock commented 3 months ago

I tried it with dev and it also broke. I'll look into this eventually but am booked at work right now.

bryanhanson commented 3 months ago

Thanks y'all. I'm not in a hurry, and it looks like a slog to decipher.

vincentarelbundock commented 3 months ago

Not solved yet, but this seems Docsify-specific. I was able to build the website with quarto_website with minimal (mostly documented) changes: https://github.com/bryanhanson/LearnPCA/pull/15

Will try again with docsify when I find time.

bryanhanson commented 3 months ago

Thanks. So I merged your commit over on LearnPCA, tried render_docs(). Then pulled it down locally for play.

First, I needed to remove a copy of docsify.md (I think that was it, complaint was "multiple formats"). Then re-ran render_docs() and it gave the following:

R > render_docs()

── Basic files ─────────────────────────────────────────────────────────────────────────────
✔ 'NEWS' imported.
✔ 'CODE_OF_CONDUCT' imported.
✔ Converting function reference 4/4: XtoPCAtoXhat [492ms]ms]

── Vignettes ───────────────────────────────────────────────────────────────────────────────

── Update HTML ─────────────────────────────────────────────────────────────────────────────
Error in finalize(settings, path, verbose, freeze) : 
  object 'src' not found
R > traceback()
9: which(is.na(x))
8: assert_no_missing(path)
7: fs::dir_ls(src)
6: which(is.na(x))
5: assert_no_missing(path)
4: fs::file_move(fs::dir_ls(src), tar)
3: finalize(settings, path, verbose, freeze)
2: .import_settings(path = path, tool = tool, verbose = verbose, 
       freeze = freeze)
1: render_docs()

Does this point to something simple, an error on my end? Again, no hurry.

vincentarelbundock commented 3 months ago

oops, I think this is probably because I was using the development version of altdoc from GitHub:

remotes::install_github('etiennebacher/altdoc')

Then restart R completely and try again

bryanhanson commented 3 months ago

Yes, that fixes things. Thank you. Will look over the result carefully later today.

bryanhanson commented 3 months ago

Alright, looked over the local files produced by preview_docs(), this is the quarto website version from your PR. Overall, it looks pretty nice! There's some stuff there that results from the vignette files not being formatted for quarto properly, like figure cross-references. No big deal, easily fixed if one wants to make the shift and go with this format. Bonus: found a few typos since I was looking with fresh eyes.

This should probably be in a new issue but will let you all decide how to proceed The one thing that seems that it might come from the particulars of altdoc processing is that the footnotes to the authors' names are repeated 3x. There are 2 authors, and 6 footnotes as a result. These footnotes are created in the yaml entries at the top of the document, and this occurs in every document (not a surprise, the same yaml is present in each). However, maybe this too is an artifact of not formatting things in a quarto-specific manner.

vincentarelbundock commented 3 months ago

Circling back to this. It looks like you may have uncovered a Quarto bug.

Would you mind creating a document with a .qmd extension and the following content:

---
title:  "A Conceptual Introduction to PCA"
author:
  - David T. Harvey^[Professor of Chemistry & Biochemistry, DePauw University, Greencastle IN USA., harvey@depauw.edu]
  - Bryan A. Hanson^[Professor Emeritus of Chemistry & Biochemistry, DePauw University, Greencastle IN USA., hanson@depauw.edu]
---

blah blah blah

Then, use Quarto to compile it to HTML. On my computer I get duplicated footnotes.

bryanhanson commented 3 months ago

Yes, I can confirm that happens. Here's what I see. I processed this using the dev version of Quarto downloaded and installed a few minutes ago. Do you want me to report over there? I'm going to go search their issues.

Screenshot 2024-05-16 at 7 52 31 AM
vincentarelbundock commented 3 months ago

Ah good. That's a relief. Yes, I think it'd be a good idea to report a minimal example there if they don't have an existing issue.

bryanhanson commented 3 months ago

Did not see any issues on this topic for quarto-cli. Someone observed the same thing here. I will report later today.

I think my original issue is fixed, but I'll let you decide on closing. Thanks for your help!

vincentarelbundock commented 3 months ago

Sounds great, thanks!

And thanks for opening the issue in the first place. Your website was a fun one to play with because it uses a bunch of features I had not tried.