Incorrectly rendering of a code snippet

[terrytangyuan]

The following code snippet

library(dlm)
form <- function(theta){ dlmModPoly(order = 1, dV = exp(theta[1]), dW = exp(theta[2])) }
model <- form(dlmMLE(Nile, parm = c(1, 1), form)$par)
filtered <- dlmFilter(Nile, model)

was rendered incorrectly using R Journal template. The following text is displayed in the generated PDF file.

\begin{Schunk} \begin{Sinput} library(dlm) form <- function(theta){ dlmModPoly(order = 1, dV= exp(theta[1]), dW = exp(theta[2])) } model <- form(dlmMLE(Nile, parm = c(1, 1), form)$par) filtered<- dlmFilter(Nile, model) \end{Sinput} \end{Schunk}

Any ideas on what I might have done incorrectly here?

[yihui]

Duplicate of #6 #10 #49 #132 etc. You didn't do anything wrong. It is our bug, which we haven't had a chance to fix yet.

[jaredhuling]

Any idea of how to go about to fixing this? The underscore problem is making it impossible to use rticles for jss. I'm willing to work on this but I'm really not sure where to start

[jaredhuling]

If there is a way to grep through the resulting .tex file created after pandoc, one hack would be to insert a \begin{verbatim} \end{verbatim} around calls to CodeChunk, CodeOutput in jss_article.R and then clear out the verbatims after pandoc is done.
ie
hook_chunk <- function(x, options) {
if (output_asis(x, options)) return(x)
paste0('\begin{verbatim}\n\begin{CodeChunk}\n', x, '\end{CodeChunk}\n\end{verbatim}')
}
This way pandoc will properly handle the inside contents. But here I guess there is a risk of stripping out actual calls written by the user to verbatim, so maybe some unique identifier after the \begin{verbatim} could be used, like \begin{verbatim}%removethis\n

[yihui]

@jaredhuling That is exactly the hack on my mind. I just haven't had time to do it. You could use a post_processor in the output format to post-process the .tex file, e.g., https://github.com/rstudio/bookdown/blob/cd2fb76f818528e/R/latex.R#L45-L79 (certainly not the best example but shows the idea).

[jaredhuling]

Does anything special need to be done to enable the prost_processor to be run? I've gotten the wrapper part to work, but the post_processor doesn't seem to be called when I put it into jss_article()

[yihui]

@jaredhuling You need to add it to base$post_process: https://github.com/rstudio/rticles/blob/master/R/jss_article.R

[jaredhuling]

I think what's happening is the intermediate .tex file doesn't compile and it bombs out before it gets to the post processing step.
edit:scratch that

[yihui]

Also look at https://github.com/rstudio/bookdown/blob/cd2fb76f818528e/R/latex.R#L43

[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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