Debugging the LaTeX output on its own

This is a relatively advanced topic. The following was written by Chris Grandin. Sean Anderson's approach is simply to move the .tex file (e.g., resdoc.tex) from _book to the main folder (wherever index.Rmd is) and troubleshoot the .tex file there using tinytex::pdflatex() or similar or working directly on the command line.

Sometimes a document will knit perfectly but there will be an error in the LaTeX part. It can be very helpful fix the LaTeX error manually, then implement that fix into your R code. The easiest way to do this is to run the following from the root directory of your project (where your .Rproj file is located):

  root_dir <- getwd()
  tmp_dir <- create_tempdir_for_latex(type = "resdoc", where = "r")
  # or tmp_dir <- create_tempdir_for_latex(type = "sr", where = "r")
  # or tmp_dir <- create_tempdir_for_latex(type = "techreport", where = "r")
  setwd(tmp_dir)
  tinytex::latexmk("resdoc.tex")
  # or tinytex::latexmk("sr.tex")
  # or tinytex::latexmk("techreport.tex")

This code creates a temporary directory somewhere on your file system. In Windows this will be in C:\Users\your_user_name\AppData\Local\Temp unless you provide a directory to the tmp_dir argument in the create_tempdir_for_latex() function.

The where = "r" part in the create_tempdir_for_latex(type = "resdoc", where = "r") call tells the function to look for the resdoc.tex file in the root directory of your project. If the compilation of the document fails for any reason, this file is left in the root directory. If it succeeds, it is found in the _book subdirectory. In that case you would use create_tempdir_for_latex(type = "resdoc", where = "b"). Usually you want to debug when compilation fails, so you would usually use where = "r" (the default).

When you run the tinytex::latexmk("resdoc.tex") command from within that temporary directory, LaTeX will be run on the resdoc.tex file and the PDF or Word file will be generated. You can debug LaTeX errors here by modifying the .tex file directly and re-running the tinytex::latexmk("resdoc.tex") function to see if it compiles. Once it does it is up to you to figure out what R code in your project needs to be modified to fix this issue. Note this directory is garbage-collected by R meaning it will be destroyed once the R session is closed. Don't write any code in the .tex file that you intend to keep.

When you are done, return to your project's root directory:

  setwd(root_dir)