rjournal_article fails with plain pandoc code segment over Shaded undefined

[eddelbuettel]

The rjournal template used to support plain pandoc blocks. It no longer does.

The following is a mvce log:

edd@rob:/tmp/rmarkdownbug$ Rscript -e 'rmarkdown::draft("mypaper.Rmd", template="rjournal_article", package="rticles", edit=TRUE)'
edd@rob:/tmp/rmarkdownbug$ cd mypaper/
edd@rob:/tmp/rmarkdownbug/mypaper$ ls
mypaper.Rmd  preamble.tex  RJournal.sty  RJreferences.bib  Rlogo.png
edd@rob:/tmp/rmarkdownbug/mypaper$ Rscript -e 'rmarkdown::render("mypaper.Rmd")'
Error: pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
edd@rob:/tmp/rmarkdownbug/mypaper$ Rscript -e 'rmarkdown::render("mypaper.Rmd")'


processing file: mypaper.Rmd
  |......................                                           |  33%
  ordinary text without R code

  |...........................................                      |  67%
label: unnamed-chunk-1
  |.................................................................| 100%
  ordinary text without R code


output file: mypaper.knit.md

/home/edd/bin/pandoc +RTS -K512m -RTS mypaper.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output mypaper.tex --template /usr/local/lib/R/site-library/r\
ticles/rmarkdown/templates/rjournal_article/resources/template.tex --highlight-style tango --pdf-engine pdflatex --include-in-header preamble.tex
/home/edd/bin/pandoc +RTS -K512m -RTS /tmp/RtmppOeUFb/file5c4b7f41fc3d.md --to markdown --output /tmp/rmarkdownbug/mypaper/RJwrapper.tex --template=/usr/local/lib/R/site-library/rticles/rmarkdown/templates/r\
journal_article/resources/RJwrapper.tex
! LaTeX Error: Environment Shaded undefined.

Error: Failed to compile RJwrapper.tex. See RJwrapper.log for more info.
Execution halted
edd@rob:/tmp/rmarkdownbug/mypaper$

Note that I used edit=TRUE to insert a simple

```sh
a=FOO ls
```

as a mock for a general pandoc code segment.

I tried the solution from #182 in both template.tex and RJwrapper.tex but to no avail.

(pandoc from ~/bin as you enforce pandoc 2.2 or later which my distro does not yet have.)

[eddelbuettel]

Took another look on the way in. What appears to be happening is that the

$for(header-includes)$
$header-includes$
$endfor$

in template.tex ends up in the main paper.{Rmd,tex} body -- and that leads to a LaTeX error (of the "can only be used in preamble" when I add the missing defines from pandoc there.

So I think there is a still a bug here.

[eddelbuettel]

Hm, I just tried with 0.4.1 and it fails there too. Using

```{sh, eval=FALSE}
a=FOO ls
```

works so I have a workaround. Would be nice to have plain pandoc working here too though.

[ivbsoftware]

I am having the same issue. I've tried to update preamble.tex adding:

$if(highlighting-macros)$
$highlighting-macros$
$endif$

Those lines end up as a plain text below the abstract in the body of the PDF text. It looks that preamble.tex is not properly placed during the construction of the document.

[yihui]

Should be fixed now. Thanks for the report!

[github-actions]

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