# bug? help: underscore in temporary directory foils latex compiler, torpedos Rmarkdown

Pandoc is used to generate a PDF from an R markdown document that has a chunk that generates a plot using ggplot2 and a custom function, progress.plot. The chunk looks like this


progress.plot(student)


The PDF is generated using a LaTeX engine. I think it uses PDFlatex via pandoc. This is causing a problem that appears to be close to the pandoc metal.

It seems like pandoc uses a temporary folder to store the diagram I generate with ggplot2. The name of that folder has as underscore. This means the path to the graphic file, a string that's used in the .tex source file, has an underscore. And the latex compiler doesn't like that.

! Missing $inserted. <inserted text>$
l.142 ...de2020-05-06_files/figure-latex/charts-1}


The "_files" in the latex log snippet, above, is the name of a folder created by pandoc (or Rmarkdown). I am getting a "Missing \$ inserted" error before the latex compiler craps out. No PDF is generated and the directory with the figure is deleted.

Is there a pandoc/Rmarkdown configuration change to take the underscore out of the temporary directory's name? Or is there any other workaround that will allow me to generate figures to include in my R markdown document?

Thanks for whatever advice people can share.

(I have posted this question in StackExchange at https://stackoverflow.com/questions/61648974/rmarkdown-pandoc-pdflatex-and-underscores-in-a-temporary-directory-name-a-pr)

I my case knitting a Rmd file with a graph always produces an intermediary folder with the graph.
The folder name is the name of the Rmd file followed by _files . Note the underscore.
When I knit (use knit btton in RStudio) atest.Rmd with the following contents

---
graphics: yes
output:
pdf_document:
keep_tex: true
keep_md: true
---
{r sinus-plot, echo=FALSE,fig.cap="a caption"}
plot(sin(seq(-pi, pi, length.out = 100)))



this will result in the files atest.md, atest.tex and the file atest.pdf with the graph and without a visible error.

The folder ./atest_files/figure-latex (. is the folder with atest.Rmd . ) contains the file sinus-plot-1.pdf .

The relevant contents of atest.md :

![a caption](atest_files/figure-latex/sinus-plot-1.pdf)


The relevant contents of atest.tex :

\begin{figure}
\centering
\includegraphics{atest_files/figure-latex/sinus-plot-1.pdf}
\caption{a caption}
\end{figure}


So in my case I have (see) no problems with an underscore.

My sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.0  htmltools_0.4.0 tools_4.0.0     yaml_2.2.1      Rcpp_1.0.4.6    rmarkdown_2.1   knitr_1.28      xfun_0.13
[9] digest_0.6.25   rlang_0.4.5     evaluate_0.14


Thanks for sharing this! My confusion deepens.

Questions:

1. What happens if you knit my code? Same type of messages?

2. What happens if you replace progress.plot(student) by plot(1:3,3:1) ? Same type of messages?

Knit-ing your code works fine. Replacing my function throws a different type of error. Thanks for opening a new approach for debugging. I appreciate it.

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