Understanding the Problem: Passing shell-escape Option to LaTeX in R Package Vignettes

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LaTeX is a powerful tool used extensively in academic publishing and technical writing. The minted package, in particular, provides excellent syntax highlighting capabilities for code snippets within documents written in LaTeX. However, this package requires that the LaTeX compiler be invoked with the -shell-escape flag to execute shell commands safely.

In this blog post, we will explore how to configure R to pass the shell-escape option to LaTeX when building vignettes of an R package.

Background: Vignettes and Sweave

Vignettes are an essential part of many R packages. They provide a concise introduction to the package’s functionality, its features, and typically include examples or tutorials on how to use the package effectively.

R packages often rely on Sweave (a combination of Sweater and LaTeX) for creating vignette documents. These documents are written using Org-mode syntax in an .Rnw file and then compiled into a PDF document that includes executable code.

Understanding the shell-escape Option

The -shell-escape flag tells the LaTeX compiler to allow it to execute shell commands during compilation. This is necessary for packages like minted, which relies on executing shell commands from within the LaTeX environment to perform syntax highlighting.

Unfortunately, this flag cannot be specified directly when compiling a .Rnw file using R’s R CMD build. Instead, we need to configure how R invokes the LaTeX compiler to include this option.

Configuring LaTeX Compilation Options

The solution lies in configuring R to include the -shell-escape flag during LaTeX compilation. There are several ways to achieve this:

1. Environment Variable Approach

One way is by setting an environment variable TEXINPUTS to include additional directories with LaTeX-related files, such as the tex directory that comes with TeX Live distributions.

For instance, you can set it like so:

export TEXINPUTS=.:/usr/local/texlive/2019/tex/latex mktex --shell-escape

The first line sets the environment variable TEXINPUTS, which tells the LaTeX compiler where to look for LaTeX-related files. The second line invokes mktex from within this new environment.

Please note that these commands are specific to Linux and may need modifications if you’re using a different operating system.

2. Using --shell-escape with R’s R CMD build

Another approach is by setting the --shell-escape option when invoking R’s R CMD build. This can be done in your .Renv file which is usually located in the root directory of your package.

Here’s how you would specify it:

BuildOptions <- c("--shell-escape")

You would then include this line within your .Renv file:

.Renv:
# R environment variables
BuildOptions <- c("--shell-escape")

Please note that --shell-escape is not a standard option for R CMD build. It’s just an example of how one might achieve similar functionality.

3. Using TeX Live’s Batch Mode

Another approach involves using TeX Live’s batch mode to compile your LaTeX document with the -shell-escape flag.

For this, you’ll need to download a script that can be placed in a shell alias and set up R as follows:

You will then need to run:

Rscript --vanilla -e "cat('
) > /home/user/compile.sh"

Then, set it up in your .Renv file like so:

.Renv:
# R environment variables
PATH <- paste0(PATH, ":./bin")
system("chmod u+x compile.sh")
BuildOptions <- c("--shell-escape")

Also note that setting the --vanilla option is necessary to avoid executing any packages during the compilation.

4. Configuring TeX Distribution

In case you’re compiling on Linux or macOS (with XCode), the distribution comes with a default LaTeX compiler that does include --shell-escape. The only thing required here would be setting up your environment variables so that tex and latex point to these compilers.

For instance, in your .Renv file, you can set them like this:

.Renv:
# R environment variables
system("export TEXINPUTS=.:/usr/local/texlive/2019/tex/latex mktex --shell-escape")

Note that mktex is not available on macOS and would need to be replaced with a suitable alternative.

Additional Considerations

While setting up the environment to include the -shell-escape flag may seem complicated, there are some general steps you can take to simplify your workflow:

• Check if you’re using an existing LaTeX distribution: Many Linux distributions come with a TeX Live installation that supports --shell-escape. macOS, however, does not.
• Use online LaTeX compilers or local servers: If the above options don’t suit your needs, consider using an online LaTeX compiler to compile your files. These services are typically available for free and do not require any additional configuration.

By following these steps, you should be able to pass the shell-escape option to LaTeX when building vignettes of R packages.

Conclusion

LaTeX is a powerful tool used extensively in academic publishing and technical writing. The minted package provides excellent syntax highlighting capabilities for code snippets within documents written in LaTeX. However, this package requires that the LaTeX compiler be invoked with the -shell-escape flag to execute shell commands safely.

In this blog post, we explored how to configure R to pass the shell-escape option to LaTeX when building vignettes of an R package. The approach varied depending on the operating system and TeX distribution being used.

We covered four primary methods for including the -shell-escape flag during LaTeX compilation:

• Environment Variable Approach
• Using --shell-escape with R’s R CMD build
• Using TeX Live’s Batch Mode
• Configuring TeX Distribution

Each method presents its own set of challenges and solutions. While setting up the environment to include this flag may seem complicated, there are some general steps you can take to simplify your workflow.

By following these methods and tips, you should be able to successfully compile LaTeX documents with minted syntax highlighting within R packages.

Recommendation for Further Reading

For those who want to learn more about LaTeX and its applications in academia, I would recommend the “LaTeX Companion” by Frank Mittelbach and Michel Goossens. This book provides a comprehensive introduction to LaTeX and covers everything from basic usage to advanced features and customization.

Similarly, if you’re interested in learning more about R packages, their development, and best practices for creating user-friendly and well-documented R packages, I would recommend the “R for Data Science” by Hadley Wickham.

Last modified on 2024-12-02