Recently I received a few bug reports about the PDF generation in R Markdown. Eventually I figured out one of the reasons: spaces in filenames. For example, in rstudio/rmarkdown#1285, xelatex failed to compile the .tex file because there was a space in a folder name (but pdflatex succeeded). From this issue, you can also see how many replies it takes to get a reproducible example.
I had been bothered by spaces for long enough before (not only in LaTeX), so I had developed a habit of not using spaces in any of my filenames. When I need to separate words, I always use dashes (-) instead of other characters such as underscores (_) or dots (.). I have no idea why spaces are bad in file paths in LaTeX. In HTML, spaces in file paths are often encoded to %20. In command line, when a path contains spaces, it has to be quoted (e.g., rm "abc def.txt"). For underscores, they are special characters in LaTeX (e.g., in the math mode, an underscore indicates a subscript). By comparison, dashes are much safer everywhere, and they are not special characters in HTML or LaTeX.
For the same reason, I always recommend knitr and R Markdown users to use dashes in chunk labels instead of spaces or underscores, e.g., this is good:
```{r, hello-world, fig.width=8}
```
These could be bad chunk labels:
```{r, hello world, fig.width=8}
```
```{r, hello_world, fig.width=8}
```
Chunk labels will be used to name figure files (if any plots are generated in the code chunk), so you have to use more portable characters in the labels. Usually I only use letters a-z, A-Z, numbers 0-9, and dashes. If your code chunk won’t generate any plots, it should not matter which characters you used in the label, and knitr itself puts no restrictions on that.
Sigh. Technology.
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