Flextable label not created in rmarkdown - r-markdown

Question

I am using flextable to produce tables for a pdf document rendered with rmarkdwown. I want to cross-reference the tables, but they do not produce the label needed for the cross reference to work.
My Minimum Reproducible Example
What follows is the content of the file test.Rmd:
---
title: "document title"
author: "author here"
date: "2022-01-20"
output:
pdf_document:
fig_caption: yes
includes:
in_header: header.tex
number_sections: yes
toc: yes
toc_depth: 4
latex_engine: xelatex
keep_tex: true
---
```{r, include = FALSE}
library(flextable)
library(bookdown)
opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, out.width = "85%", fig.align = "center")
```
```{r, tab.id = "anyTable", tab.cap = "Invented data", tab.lp = "tab:"}
a = data.frame(id = LETTERS[1:3], x = 1:3)
flextable(a) |> theme_vanilla()
```
```{r secondTable}
b = data.frame(id = LETTERS[4:6], x = 4:6)
flextable(b) |> theme_vanilla() |> set_caption(caption = "This is secondTable")
```
# Standard rmarkdown crossreference
Trying anyTable: \ref{tab:anyTable}.
Trying secondTable: \ref{tab:secondTable}.
# Bookdown crossreference
Trying anyTable: \#ref(tab:anyTable).
Trying secondTable: \#ref(tab:secondTable).
Contents of header.tex:
\usepackage{caption}
\renewcommand{\contentsname}{Contenidos}
\captionsetup[table]{name=Tabla}
\captionsetup[figure]{name=Figura}
%\usepackage{float} #use the 'float' package
%\floatplacement{figure}{H}
\usepackage{fancyhdr}
\pagestyle{fancy}
\usepackage{xcolor}
\usepackage{multicol}
\usepackage{pdflscape}
\newcommand{\blandscape}{\begin{landscape}}
\newcommand{\elandscape}{\end{landscape}}
When I do rmarkdown::render("test.Rmd", output_file = "test.pdf") the file is rendered in pdf, but the following warning comes out:
Output created: test.pdf
Warning message:
LaTeX Warning: Reference `tab:anyTable' on page 1 undefined on input line 198.
LaTeX Warning: Reference `tab:secondTable' on page 1 undefined on input line 20
0.
LaTeX Warning: There were undefined references.
If I check the .tex file, I can see that the captions are there, but they do not have the labels. The relevant lines of the intermediate test.tex file:
lines 106 to 109
\begin{longtable}[c]{|p{0.75in}|p{0.75in}}
\caption{Invented data
}\\
lines 153 to 156
\begin{longtable}[c]{|p{0.75in}|p{0.75in}}
\caption{This is secondTable
}\\
I expected that the caption line in the tex file was something like \caption{This is secondTable}\label{tab:secondTable}\\
What I've tried
Changing latex engines (lualatex, pdflatex, xelatex).
Editing the tex file (adding the label after the caption), but it fails to convert to dvi with multiple errors (mostly "undefined control sequence")
What am I doing wrong?
How can I cross-reference the tables produced by flextable?
Alternatively, I am open to other packages you may suggest. As some of the headers in my real data are somewhat complex (multi-span headers and the like), I would like to steer away from kable and kableExtra if at all possible.

Answer 1

You need to use a format from bookdown to get cross references, see https://bookdown.org/yihui/rmarkdown-cookbook/cross-ref.html
---
title: "document title"
author: "author here"
date: "2022-01-20"
output:
bookdown::pdf_document2:
fig_caption: yes
number_sections: yes
toc: yes
toc_depth: 4
latex_engine: xelatex
keep_tex: true
---
```{r, include = FALSE}
library(flextable)
library(knitr)
library(bookdown)
opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, out.width = "85%", fig.align = "center")
```
```{r, tab.id = "anyTable", tab.cap = "Invented data"}
a = data.frame(id = LETTERS[1:3], x = 1:3)
flextable(a) |> theme_vanilla()
```
```{r secondTable}
b = data.frame(id = LETTERS[4:6], x = 4:6)
flextable(b) |> theme_vanilla() |> set_caption(caption = "This is secondTable")
```
# Bookdown crossreference
Trying anyTable: \#ref(tab:anyTable).
Trying secondTable: \#ref(tab:secondTable).