The R programming language is almost synonymous with data science for a number of different reasons. The most obvious is the sheer ease with which you can run complex mathematical processes in R. It’s generally quite easy to convert most formulas or concepts into R code. Likewise, you can usually import and work with a huge amount of data in R without needing to put too much work into resource allocation.
But there’s another important part of this process – presentation. R also makes it easy to visualize and export the results of these processes within different formats. And the combination of markdown and LaTeX is one of the more powerful ways of doing so. However, this can often produce a latex failed to compile error. In general, the error will usually mean that there’s some form of improper formatting in your R markdown that’s preventing the LaTeX code from being converted into the finalized document. But there are a few different permutations of this problem that need to be examined.
Markdown, Latex, and R
It’s important to clarify and define a few concepts before looking at possible causes and solutions for the error message. First, what exactly is your code trying to do? On a surface level, you’re simply exporting data from your R code into a printable report. But there’s a lot more going on under the hood. And the process of fixing the error often means backtracking your steps until you reach the source of the underlying issue.
Basically, the workflow begins with your R code. LaTeX is then used to convert the R-formatted markdown. The end result is a file that contains your fully formatted data. But to get to that point you have to work through multiple points of conversion. R works through the markdown rmd file and turns it into an intermediate tex file. This latex document is then converted into a pdf.
In fact, this is similar in many respects to taking the output of a web app’s HTML, turning it into an intermediate format, and then exporting it as a PDF. If you’ve ever gone through that process then you know that incompatibilities can crop up in a number of different places. And the same is true, if to a lesser extent, with R’s very own markdown. Thankfully markdown is a lot more straightforward than hypertext markup language. And, likewise, it’s generally easier to track down the problem with a markdown error. This is further aided by the fact that the procedure to convert R objects to a pdf is generally fairly simple in comparison.
Basic Fixes
Unfortunately, all of the previous discussions can be summed up with one statement – there’s no single reason for the error. It simply means that something’s failing during the conversion process. Ideally, processes involving multiple systems handing off work to each other would fail with a detailed analysis of where the problem came from. But it’s just the nature of multi-system procedures like this to have some ambiguity in their error formatting. So the best way to fix the error is to look through the most common causes.
One of the most common and easily fixed comes down to the underlying LaTeX package and libraries. Missing packages will often cause a markdown error, latex error, etc. You’ll also need a basic LaTeX distribution on your development system. For Windows and Linux this is typically tex live. Mac users will want to install MacTeX or macos httpstugorgmactex. You might also try reinstalling the relevant packages just in case there’s file corruption, missing path settings, etc. Any of those issues might lead your system to think that there’s a missing latex package.
You should also make sure that you have all of the R packages that might impact your pdf generation. Try running the following to ensure you have every package you might need to generate your data and output files.
install.packages(“rmarkdown”)
install.packages(“tinytex”)
install.packages(“knitr”)
install.packages(“ggplot2”)
install.packages(“dplyr”)
If the problem persists after double checking those prereqs then it’s best to move on to the actual R markdown document. You can think of this as, again, somewhat analogous to HTML. What would break a standard HTML page? One of the most common issues is missing elements that should be embedded within a page. And we see the same with markdown. And in this context, it’s especially common with images. Again, very similar to HTML. So make sure to double-check all linked files. For example, look at the following line.
\includegraphics{missingFile.jpg}
The appropriately named missingFile.jpg would break the compilation and pdflatex to pdf output if it wasn’t present. You might assume that you have all of your files in place. But keep in mind that it’s very easy for typos to appear. And that applies to both the name of the file on your drive and in your markup. A typo in the file name is essentially the same thing as a missing file. At least as far as the interpreter understands things. You should also check for any other possible typos. For example, it’s very easy for a typo to slip into math mode. Additionally, Unicode support is dependent on the underlying LaTex engine on your system. This can sometimes cause compatibility problems with specific Unicode character choices.
Additional Considerations
The vast majority of problems will be solved with the prior steps. But if you’re still having trouble there are a few more possible causes to consider. You can begin by looking at the template you’re using. LaTeX uses specific templates, which you can specify in your markdown. You might double-check it to make sure that there are no obvious problems. Likewise, you can try switching around to different templates to see if the problem persists.
You can also look at any additional programs you’re using for LaTeX formatting, such as fmtutil. But even less obvious compatibility issues are also worth looking into. For example, issues can come up from missing files. But the problem can also occur with corrupt files. So you might have a jpg file in the proper place. But if the jpg isn’t properly compressed or has become corrupted then your script might not be able to work with it. As such, loading up embedded files in another editing program to ensure they’re usable might turn up some hints.