extra_dependencies and includes:in_header not working for PDF output.

[jonathan-g]

Steps to reproduce:

1. Create a basic bookdown project using RStudio new project and choosing "Book project using bookdown"
2. Test that bookdown::render_book("index.Rmd", bookdown::pdf_book()) builds correctly.
3. Edit _output.yml to add extra_dependencies: "subfig" to the pdf_book output:

bookdown::pdf_book:
  includes:
    in_header: preamble.tex
  latex_engine: xelatex
  citation_package: natbib
  keep_tex: yes
  extra_dependencies: "subfig"

4. Edit 04-application.Rmd to add the example code from https://bookdown.org/yihui/rmarkdown-cookbook/latex-subfigure.html:

## Example one

```{r subfig-test, fig.cap='Figure 1', fig.subcap=c('(a)', '(b)', '(c)'), fig.ncol=2, fig.align="center", out.width="50%"}
plot(1:10)
plot(cars, pch = 19)
boxplot(Sepal.Width ~ Species, data = iris)
```

## Example two

5. Build using bookdown::render_book("index.Rmd", bookdown::pdf_book()).

Expected result:

I expect a PDF document like the one in the example at https://bookdown.org/yihui/rmarkdown-cookbook/latex-subfigure.html

Actual result:

XeLaTeX reports an error:

! Undefined control sequence
l.249 {\centering \subfloat
                           [(a)\label{fig:subfig-test-1}]{\includegraphics[w...

Error: LaTeX failed to compile Foo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Foo.log for more info.

After this error I tried again, adding the line

\usepackage{subfig}

to preamble.tex, but I still got the same error.

Inspecting the generated Foo.tex file, there is neither an include{preamble.tex} nor a \usepackage{subfig}.

This error is similar to #888

> xfun::session_info("bookdown")
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363), RStudio 1.3.1056

Locale:
  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
  LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
  LC_TIME=English_United States.1252    

Package version:
  base64enc_0.1.3      bookdown_0.20.3      digest_0.6.25       
  evaluate_0.14        glue_1.4.1           graphics_4.0.2      
  grDevices_4.0.2      highr_0.8            htmltools_0.5.0     
  jsonlite_1.7.0       knitr_1.29           magrittr_1.5        
  markdown_1.1         methods_4.0.2        mime_0.9            
  rlang_0.4.7          rmarkdown_2.3.2.9003 stats_4.0.2         
  stringi_1.4.6        stringr_1.4.0        tinytex_0.25        
  tools_4.0.2          utils_4.0.2          xfun_0.16           
  yaml_2.2.1          

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[jonathan-g]

The problem here is passing a constructed bookdown::pdf_book() object to render_book. If I pass a string instead:

bookdown::render_book("index.Rmd", "bookdown::pdf_bpok")

the book renders correctly.

I am closing this issue.

[cderv]

Seems like an issue 🤔 it should work the them with both type of input.

[yihui]

I know why the previous way fails, but don't have time to explain in detail. I strongly recommend that you pass a character string instead of a function to the output format. In short, if you pass a function, you must provide all options in the function call. If you pass a string, it uses options provided in _output.yml.

https://bookdown.org/yihui/bookdown/usage.html

[cderv]

Oh ok ! Noted. Don’t need more explanation 😅
Short and clear. I understand now.

[jonathan-g]

It might be useful to add @yihui's comment above to the documentation for bookdown::render_book and rmarkdown::render:

If you pass an output format object to output_format, you must set all the options when you construct the object.
If you pass a string, the output format will use the options provided in _output.yml.

[cderv]

I completely agree as I was also thinking about that. This would be a great addition. You can submit a PR or I’ll do that Monday.

[jonathan-g]

PR #931 submitted.

[jonathan-g]

I have closed PR #931 and submitted two new PRs: #958 and rstudio/rmarkdown#1907 to address the documentation primarily in rmarkdown, with a note in the bookdown::render_book() docs to look at the rmarkdown::render() docs for details on how the output_format argument is handled.

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