Using tikz graphdrawing library within RMarkdown ... Need to use lualatex engine, but can't get it to work - knitr

Question

I have the following code in an rmd file which leverages tikz for diagrams:
---
title: "TestNonTufteLua"
author: "Me"
output:
pdf_document :
latex_engine: lualatex
---
Prove tikz works:
```{r tikTest1, engine = "tikz"}
\usetikzlibrary{shapes}
\begin{tikzpicture}
\node[ellipse, draw=black, align = center] (Data) {Data $y_{n}$};
\end{tikzpicture}
```
Then, when you set `eval = TRUE` in the below code, it will not work.
```{r tikTest2, eval = FALSE, engine = "tikz"}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{layered}
\tikz [gr/.style={gray!50}, font=\bfseries]
\graph [layered layout] {
% A and F are horizontally aligned if you also set weight=0.5 for A -- C.
A -- [minimum layers=2] C -- F,
{ [nodes=gr, edges=gr] A -- B -- { E, D -- F } }
};
```
When changing to eval=TRUE in the second chunk, I get the following
error:
Quitting from lines 24-29 (testNonTufteLua.Rmd) Error: running
'texi2dvi' on '.\tikz36747a021b22.tex' failed
LaTeX errors: rarygraphdrawing.code.tex:22: Package pgf Error: You
need to run LuaTeX to use the graph drawing library.
This error occurs when using the knit button from RStudio or using render("testNonTufteLua.Rmd", output_format = pdf_document(keep_tex = TRUE, latex_engine = "lualatex"). I have also experimented with setting options(tikzDefaultEngine = "luatex") to get tikzDevice to handle it properly, but it still does not work. I just can't seem to get the graphdrawing library to work even though the tikz-shapes library can be loaded and also that the rest of the document seems to be compiled with lualatex. Thanks for any help!!

Answer 1

Update: Meanwhile knitr no longer uses tools::texi2dvi but tinytex::latexmk. One therefore has to use options(tinytex.engine = 'lualatex') in a set-up chunk.
This is rather tricky, since you are not using tikzDevice but the tikz engine, which uses tools::texi2dvi to convert to PDF. You can change this using options(texi2dvi = "lualatex"). However, the default template does not work with LuaLaTeX. I have therefore created a modified template:
\RequirePackage{luatex85}
\documentclass{article}
\usepackage[luatex,active,tightpage]{preview}
\usepackage{amsmath}
\usepackage{tikz}
\usetikzlibrary{matrix}
\begin{document}
\begin{preview}
%% TIKZ_CODE %%
\end{preview}
\end{document}
And specify that file with engine.opts = list(template = "tikz2pdf.tex"). Putting it all together here my working file:
---
title: "TestNonTufteLua"
author: "Me"
output:
pdf_document :
latex_engine: lualatex
---
```{r}
options(texi2dvi = "lualatex")
```
```{r tikTest2, eval = TRUE, engine = "tikz", engine.opts = list(template = "tikz2pdf.tex")}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{layered}
\tikz [gr/.style={gray!50}, font=\bfseries]
\graph [layered layout] {
% A and F are horizontally aligned if you also set weight=0.5 for A -- C.
A -- [minimum layers=2] C -- F,
{ [nodes=gr, edges=gr] A -- B -- { E, D -- F } }
};
```
Result:
References:
how to set engine options
preview and LuaLaTeX
knitr using texi2pdf

Answer 2

A small running variation of the example above is the following using tinytex.
---
title: "lualatex. Using `tinytex.engine`"
output:
html_document:
df_print: paged
pdf_document:
latex_engine: lualatex
---
## Latex engines
By default, PDF documents are rendered using `pdflatex`. You can specify an
alternate engine using the `latex_engine` option. Available engines
are `pdflatex`, `xelatex`, and `lualatex.`
```{r setup}
options(tinytex.engine = "lualatex")
```
```{r tikzLua, eval = TRUE, engine = "tikz", engine.opts = list(template = "tikz2pdf.tex")}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{layered}
\tikz [gr/.style={gray!50}, font=\bfseries]
\graph [layered layout] {
% A and F are horizontally aligned if you also set weight=0.5 for A -- C.
A -- [minimum layers=2] C -- F,
{ [nodes=gr, edges=gr] A -- B -- { E, D -- F } }
};
```
After an update in knitr the example above stopped running.