Printing issue for JSS style

[benkeser]

I'm running into a situation where printing certain objects does not render to .tex properly. I can't sort out what is causing the error and I'm not certain whether this is an issue with rticles or with pandoc. Here's a MWE:

RMD document:

---

author:

• name: A girl has no name
  affiliation: An affiliation
  address: >
  An address
  email: \email{anemail@aninstitution.edu}
  url: http://website.com
  title:
  formatted: '\pkg{apackage}'
  plain: 'apackage'
  short: 'apacakge'
  abstract: >
  blah blah blah
  keywords:
  formatted: [key1]
  plain: [key2]
  documentclass: jss
  classoption: article
  output: rticles::jss_article

---

Introduction

if(!("SuperLearner" %in% row.names(installed.packages()))){
  install.packages("SuperLearner")
}
library(SuperLearner)

This non-exported function prints fine.

SuperLearner:::.SL.require

This one does not.

SuperLearner:::predict.SL.glm

When I build, the relevant part of the .tex file looks like

This one does not.

\textbackslash{}begin\{CodeChunk\}

\begin{CodeInput}
R> SuperLearner:::predict.SL.glm
\end{CodeInput}

\textbackslash{}begin\{CodeOutput\} function (object, newdata, \ldots{})
\{ if (is.matrix(newdata)) \{ newdata = as.data.frame(newdata) \} pred
\textless{}- predict(object = object\$object, newdata = newdata, type =
``response'') pred \} \textless{}environment:
namespace:SuperLearner\textgreater{} \textbackslash{}end\{CodeOutput\}
\textbackslash{}end\{CodeChunk\}

END RMD DOCUMENT

Any guesses as to why the \textbackslash{} is being introduced?

[yihui]

Yes, it is caused by the dollar sign. It is a known issue (see #10 and #49), but no one seems to have time to fix it. Technical background: jgm/pandoc#2493

[JanMarvin]

Could we add a latex raw attribute to hook_chunks like: ```{=latex} if not using kable? Added that in jss_article, but it breaks if a chunk uses cache=TRUE. This should fix the problem above and new a behavior of pandoc 2.0 which treats underscores similar to the dollar sign:

# test.Rmd
\begin{foo}
a_b
\end{foo}`

pandoc test.Rmd -f markdown+raw_tex -t native
[Para [Str "\\begin{foo}",SoftBreak,Str "a_b",SoftBreak,Str "\\end{foo}"]]

previously

pandoc test.Rmd -f markdown+raw_tex -t native
[RawBlock (Format "latex") "\\begin{foo}\na_b\n\\end{foo}"]

[yihui]

@JanMarvin Thanks! The new raw attributes in Pandoc 2.0 sounds like the right way to go.

[jimvine]

Until the Pandoc 2.0 solution comes in, this worked for me as a workaround, where I had one CodeOutput CodeChunk that had unbalanced $ signs. I added, immediately after it, a CodeChunk with just one dollar sign in it:

\begin{CodeChunk}
\begin{CodeOutput}
  # $
\end{CodeOutput}
\end{CodeChunk}

This gets placed after the r code block, in a normal markdown area.

That does leave a spurious $ on the page, but at least with the # if someone tries to paste it into R it won't do anything! It is, of course, pretty hack-ish, but if I could turn the manual code block white I would almost be happy with this!

With this forcing the desired CodeChunk to be correctly converted into valid LaTeX, I have then been able to use the retained .tex version, strip out this manual hack, and re-compile that to PDF to get a 'clean' version. For some reason, opening the .tex version in RStudio and clicking "Compile PDF" did not work for me, so I called texi2pdf from the console:

tools::texi2pdf("myfile.tex")

One other oddity: this threw an error about the bibliography file, saying "BibTeX errors:
I couldn't open database file myfile.bib.bib". The solution to that was to find the bibliography definition at the end of the .tex version and change it from:

\bibliography{myfile.bib}

to:

\bibliography{myfile}

[yihui]

Fixed. Please try devtools::install_github('rstudio/rticles'). Note that it will require Pandoc 2.2.1. You can use the Preview version of RStudio if you do not want to install Pandoc separately: https://www.rstudio.com/products/rstudio/download/preview/

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