Extra dependencies aren't always added

[dmurdoch]

This SO post describes the issue and a workaround. The problem is that the usepackage_latex() calls in zzz.R:

kableExtra/R/zzz.R

Lines 5 to 18 in 292f607

	usepackage_latex("booktabs")
	usepackage_latex("longtable")
	usepackage_latex("array")
	usepackage_latex("multirow")
	usepackage_latex("wrapfig")
	usepackage_latex("float")
	usepackage_latex("colortbl")
	usepackage_latex("pdflscape")
	usepackage_latex("tabu")
	usepackage_latex("threeparttable")
	usepackage_latex("threeparttablex")
	usepackage_latex("ulem", "normalem")
	usepackage_latex("makecell")
	usepackage_latex("xcolor")

won't be executed if kableExtra is already loaded when rmarkdown::render() is called.

This would be the typical state if you are calling rmarkdown::render() explicitly, rather than having RStudio set up a separate session to call it via the Knit button.

To Reproduce

Try to run this document test.Rmd:

---
title: "Test document"
output: pdf_document
---

```{r setup}
library(dplyr)
```

```{r}
iris %>%
    knitr::kable(format="latex") %>%
    kableExtra::kable_styling() %>%
    kableExtra::column_spec(2, width = "10em")
```

using rmarkdown::render("test.Rmd") in an R session. It might succeed the first time, but the second and following calls will fail with a LaTeX error, because the LaTeX array package is not used:

! Undefined control sequence.
<argument> r|>{\raggedleft \arraybackslash 
                                           }p{10em}|r|r|l
l.139 ...\raggedleft\arraybackslash}p{10em}|r|r|l}

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

A fix for this would be to run the usepackage_latex() calls every time a kableExtra function is called; a more efficient fix would be to set a flag when they are run, and check that flag every time. The flag needs to be cleared at the start of a knitr run.

[paulrougieux]

Here is a session rendering the above notebook twice, it fails on the second attempt. Running unloadNamespace("kableExtra") before the third attempt makes it successful again.

Full console output of `rmarkdown::render("notebook.Rmd")` 3 times

> rmarkdown::render("notebook.Rmd")


processing file: notebook.Rmd
  |..............                                                        |  20%
  ordinary text without R code

  |............................                                          |  40%
label: setup
  |..........................................                            |  60%
  ordinary text without R code

  |........................................................              |  80%
label: unnamed-chunk-1
  |......................................................................| 100%
  ordinary text without R code


output file: notebook.knit.md

/usr/bin/pandoc +RTS -K512m -RTS notebook.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output notebook.tex --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --highlight-style tango --pdf-engine pdflatex --variable graphics --variable 'geometry:margin=1in' --include-in-header /tmp/Rtmp1Khcp1/rmarkdown-str126b56c64270c.html

Output created: notebook.pdf
> rmarkdown::render("notebook.Rmd")


processing file: notebook.Rmd
  |..............                                                        |  20%
  ordinary text without R code

  |............................                                          |  40%
label: setup
  |..........................................                            |  60%
  ordinary text without R code

  |........................................................              |  80%
label: unnamed-chunk-1
  |......................................................................| 100%
  ordinary text without R code


output file: notebook.knit.md

/usr/bin/pandoc +RTS -K512m -RTS notebook.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output notebook.tex --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --highlight-style tango --pdf-engine pdflatex --variable graphics --variable 'geometry:margin=1in'
! Undefined control sequence.
<argument> r|>{\raggedleft \arraybackslash
                                           }p{10em}|r|r|l
l.128 ...\raggedleft\arraybackslash}p{10em}|r|r|l}

Error: LaTeX failed to compile notebook.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See notebook.log for more info.
> unloadNamespace("kableExtra")
> rmarkdown::render("notebook.Rmd")


processing file: notebook.Rmd
  |..............                                                        |  20%
  ordinary text without R code

  |............................                                          |  40%
label: setup
  |..........................................                            |  60%
  ordinary text without R code

  |........................................................              |  80%
label: unnamed-chunk-1
  |......................................................................| 100%
  ordinary text without R code


output file: notebook.knit.md

/usr/bin/pandoc +RTS -K512m -RTS notebook.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output notebook.tex --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/paul/R/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --highlight-style tango --pdf-engine pdflatex --variable graphics --variable 'geometry:margin=1in' --include-in-header /tmp/Rtmp1Khcp1/rmarkdown-str126b54aee94e7.html

Output created: notebook.pdf

Note:

• adding library(kableExtra) to the notebook doesn't fix the issue.
• as explained in my SO question, the real use case is a a loop within which I render the same notebook several times for different product groups. Similar to the use case described in bookdown where a report is rendered "for each state of a country".

[dmurdoch]

Adding unloadNamespace("kableExtra") to the setup code chunk before the first use of anything from the package fixes it for me.

[paulrougieux]

The fix works for me, but I guess there is a better way to solve this in kableExtra without having to add unloadNamespace("kableExtra") to the setup chunk.

[dmurdoch]

I took a look, and couldn't spot a simple one. kableExtra needs to call the usepackage_latex functions once per document, but I don't think knitr provides a hook that is run at the right time. The "document" hook runs a little bit too late: the markdown that goes to Pandoc has already been produced. I guess you could write a document hook that edited the YAML header to add the dependencies that kableExtra needs, but if the header already contains extra dependencies, that could be really messy.

[dmurdoch]

Some kableExtra functions add "kableExtra" to the class of the object being printed, and then the knit_print.kableExtra method will be called. Probably the conceptually easiest way to implement this would be to add that class name (or a different one) to all functions that might create extra package dependencies, then add them in the knit_print method. (Or maybe all functions that take kable() results and modify them.)

That's a lot of changes to make, but they're all small changes. I might try it and put in a PR.