Title says it all. See below for a minimal (non-)working example.
---
title: "Untitled"
author: "Anonymous"
date: "09/01/2020"
output: bookdown::word_document2
---
# First Section {#sec1}
Etc.
# Second Section
See section \@ref(sec1).
When I knit the above, I get the following warning:
Output created: mre.docx
Warning message:
The label(s) sec1 not found
The reference in the output is replaced with two question marks (??). When I replace the output option in the YAML header with pdf_document2, there is no error. My template.docx has section numbering enabled for all heading styles and the sections are numbered correctly (just not the references).
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.2 Matrix_1.2-18 bookdown_0.16 htmltools_0.4.0 tools_3.6.2 yaml_2.2.0 reticulate_1.13 Rcpp_1.0.3 rmarkdown_1.17 grid_3.6.2 knitr_1.26 jsonlite_1.6
[13] digest_0.6.22 xfun_0.11 rlang_0.4.1 lattice_0.20-38 evaluate_0.14
> pandoc --version
pandoc 2.8
Compiled with pandoc-types 1.20, texmath 0.12, skylighting 0.8.3
I have been struggling with the same issue and I found a workaround
This is a known issue that the Rstudio group is working on.
https://github.com/rstudio/bookdown/issues/787
I was able to work around this problem by using the version of pandoc that is installed with Rstudio (currently 2.7.2). In windows I did this by removing pandoc from the PATH and then restarting my Rstudio session.