Appendix cross-references are broken only in html-based outputs

[jooyoungseo]

The latest bookdown version fails to support cross-references for Appendix section in html-based outputs; there is no issue found in any output based on bookdown::pdf_document2. This might have to do with the recent development on Appendix numbering customization.

Please refer to the following reproducible code and results.

Reproducible Code

test.Rmd:

---
output: bookdown::html_document2
---

Appendix \@ref(appA)

# (APPENDIX) Appendix {-}

# Test {#appA}

Rendering Results

Appendix ??

(APPENDIX) Appendix

Test

Standard output and standard error

`C:/test/reprex/reprex_std_out_err.txt`

Session info

sessioninfo::session_info()
#;-) - Session info ---------------------------------------------------------------
#;-)  setting  value                       
#;-)  version  R version 3.6.1 (2019-07-05)
#;-)  os       Windows 10 x64              
#;-)  system   x86_64, mingw32             
#;-)  ui       RTerm                       
#;-)  language (EN)                        
#;-)  collate  English_United States.1252  
#;-)  ctype    English_United States.1252  
#;-)  tz       America/New_York            
#;-)  date     2019-12-25                  
#;-) 
#;-) - Packages -------------------------------------------------------------------
#;-)  package     * version    date       lib source                            
#;-)  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.1)                    
#;-)  backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.1)                    
#;-)  cli           2.0.0      2019-12-09 [1] CRAN (R 3.6.1)                    
#;-)  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.1)                    
#;-)  digest        0.6.23     2019-11-23 [1] CRAN (R 3.6.1)                    
#;-)  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.1)                    
#;-)  fansi         0.4.0      2018-10-05 [1] CRAN (R 3.6.1)                    
#;-)  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.1)                    
#;-)  glue          1.3.1.9000 2019-12-19 [1] Github (tidyverse/glue@b9ffe6c)   
#;-)  htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.1)                    
#;-)  knitr         1.26.1     2019-12-05 [1] Github (yihui/knitr@33d69c3)      
#;-)  magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.1)                    
#;-)  pillar        1.4.3      2019-12-20 [1] CRAN (R 3.6.2)                    
#;-)  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.1)                    
#;-)  purrr         0.3.3      2019-10-18 [1] CRAN (R 3.6.1)                    
#;-)  Rcpp          1.0.3      2019-11-08 [1] CRAN (R 3.6.1)                    
#;-)  reprex        0.3.0.9001 2019-11-13 [1] Github (tidyverse/reprex@27aa69a) 
#;-)  rlang         0.4.2.9000 2019-12-12 [1] Github (r-lib/rlang@ec7c1ed)      
#;-)  rmarkdown     2.0.5      2019-12-20 [1] Github (rstudio/rmarkdown@7f51e23)
#;-)  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.1)                    
#;-)  stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                    
#;-)  stringr       1.4.0.9000 2019-11-11 [1] Github (hadley/stringr@80aaaac)   
#;-)  styler        1.2.0.9000 2019-11-13 [1] Github (r-lib/styler@a8acde5)     
#;-)  tibble        2.1.3      2019-06-06 [1] CRAN (R 3.6.1)                    
#;-)  withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.1)                    
#;-)  xfun          0.11.3     2019-11-22 [1] Github (yihui/xfun@4fcd6ff)       
#;-)  yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                    
#;-) 
#;-) [1] C:/Program Files/R/R-3.6.1/library

Session info

sessioninfo::session_info()
#;-) - Session info ---------------------------------------------------------------
#;-)  setting  value                       
#;-)  version  R version 3.6.1 (2019-07-05)
#;-)  os       Windows 10 x64              
#;-)  system   x86_64, mingw32             
#;-)  ui       RTerm                       
#;-)  language (EN)                        
#;-)  collate  English_United States.1252  
#;-)  ctype    English_United States.1252  
#;-)  tz       America/New_York            
#;-)  date     2019-12-25                  
#;-) 
#;-) - Packages -------------------------------------------------------------------
#;-)  package     * version    date       lib source                            
#;-)  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.1)                    
#;-)  backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.1)                    
#;-)  cli           2.0.0      2019-12-09 [1] CRAN (R 3.6.1)                    
#;-)  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.1)                    
#;-)  digest        0.6.23     2019-11-23 [1] CRAN (R 3.6.1)                    
#;-)  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.1)                    
#;-)  fansi         0.4.0      2018-10-05 [1] CRAN (R 3.6.1)                    
#;-)  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.1)                    
#;-)  glue          1.3.1.9000 2019-12-19 [1] Github (tidyverse/glue@b9ffe6c)   
#;-)  htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.1)                    
#;-)  knitr         1.26.1     2019-12-05 [1] Github (yihui/knitr@33d69c3)      
#;-)  magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.1)                    
#;-)  pillar        1.4.3      2019-12-20 [1] CRAN (R 3.6.2)                    
#;-)  pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.1)                    
#;-)  purrr         0.3.3      2019-10-18 [1] CRAN (R 3.6.1)                    
#;-)  Rcpp          1.0.3      2019-11-08 [1] CRAN (R 3.6.1)                    
#;-)  reprex        0.3.0.9001 2019-11-13 [1] Github (tidyverse/reprex@27aa69a) 
#;-)  rlang         0.4.2.9000 2019-12-12 [1] Github (r-lib/rlang@ec7c1ed)      
#;-)  rmarkdown     2.0.5      2019-12-20 [1] Github (rstudio/rmarkdown@7f51e23)
#;-)  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.1)                    
#;-)  stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                    
#;-)  stringr       1.4.0.9000 2019-11-11 [1] Github (hadley/stringr@80aaaac)   
#;-)  styler        1.2.0.9000 2019-11-13 [1] Github (r-lib/styler@a8acde5)     
#;-)  tibble        2.1.3      2019-06-06 [1] CRAN (R 3.6.1)                    
#;-)  withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.1)                    
#;-)  xfun          0.11.3     2019-11-22 [1] Github (yihui/xfun@4fcd6ff)       
#;-)  yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                    
#;-) 
#;-) [1] C:/Program Files/R/R-3.6.1/library

[cderv]

Hi,

could you precise your bookdown version (not included in your session info) and also your pandoc version ?

This is important to try reproduce the issue and fix it. Thank you !

[jooyoungseo]

I am sorry, @cderv.

Tested bookdown version is ’0.16.5’
with pandoc version 2.9.

Please kindly let me know if there would be anything I have missed for debugging.

[ColinChisholm]

Writing to confirm this error
In the default example install of bookdown (i.e. Rstudio: New Project >> New Directory >> Book Project Using bookdown)

cross-referencing of sections in html output are displayed as '??' -- the hyperlink works but is displayed as '??'

excerpt from the 01-intro.rmd

# Introduction  {#intro} 

You can label chapter and section titles using `{#label}` after them, 
e.g., we can reference Chapter \@ref(intro). If you do not manually label them,
there will be automatic labels anyway, e.g., Chapter \@ref(methods).

The following warning is produced:

Warning messages:
1: The label(s) intro, methods not found 
2: The label(s) intro, methods not found 

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
 [1] compiler_3.6.1  bookdown_0.16   htmltools_0.4.0 tools_3.6.1    
 [5] yaml_2.2.0      Rcpp_1.0.3      rmarkdown_2.0.5 knitr_1.26     
 [9] xfun_0.11       digest_0.6.23   rlang_0.4.2     evaluate_0.14 

> rmarkdown::pandoc_version()
[1] ‘2.9.1.1’

[yihui]

Should be fixed now. You can install and test the development version via

remotes::install_github('rstudio/bookdown')

Thanks for the report!

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