Recently (within the last week) some .Rmd files that used to compile some Beamer slides starting failing to knit to pdf using TinyTex in RStudio. I was able to narrow the problem down to trying, and failing, to run the following in a .Rmd file:
---
title: "Habits"
author: John Doe
date: March 22, 2005
output:
#bookdown::html_document2:
#bookdown::pdf_document2:
bookdown::beamer_presentation2:
keep_tex: true
---
```{r setup, include=FALSE}
options(tinytex.verbose = TRUE)
```
# In the morning
\begin{equation}
1=1
(\#eq:binom)
\end{equation}
Look at \@ref(eq:binom).
The error I get changes depending on what I comment out, but for the version above the Render tab looks like this:
|......................................... | 67% [setup]
processing file: beamer-frame-test.Rmd
/Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/pandoc +RTS -K512m -RTS beamer-frame-test.knit.md --to beamer --from markdown+autolink_bare_uris+tex_math_single_backslash --output beamer-frame-test.tex --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --table-of-contents --number-sections --highlight-style tango --pdf-engine pdflatex --embed-resources --standalone --wrap preserve --variable tables=yes --standalone -Mhas-frontmatter=false
output file: beamer-frame-test.knit.md
This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
tlmgr search --file --global '/l3backend-pdftex.def'
Trying to automatically install missing LaTeX packages...
tlmgr install l3backend l3backend-dev
tlmgr: package repository https://za.mirrors.cicku.me/ctan/systems/texlive/tlnet (verified)
tlmgr install: package already present: l3backend
tlmgr install: package already present: l3backend-dev
This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
tlmgr search --file --global '/l3backend-pdftex.def'
! Undefined control sequence.
<recently read> \ltx@label
Error: LaTeX failed to compile beamer-frame-test.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See beamer-frame-test.log for more info.
Execution halted
And the log file looks like this (partially edited for brevity):
This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025) (preloaded format=pdflatex 2025.8.10) 11 AUG 2025 21:02
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**beamer-frame-test.tex
(./beamer-frame-test.tex
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L3 programming layer <2025-07-20>
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Package hyperref Info: Hyper index ON on input line 4203.
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[1
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No file beamer-frame-test.toc.
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)
LaTeX Font Info: Trying to load font information for U+msb on input line 118.
(/Users/mark/Library/TinyTeX/texmf-dist/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
)
LaTeX Font Info: Font shape `T1/lmss/m/it' in size <10.95> not available
(Font) Font shape `T1/lmss/m/sl' tried instead on input line 118.
LaTeX Font Info: Font shape `T1/lmss/m/it' in size <8> not available
(Font) Font shape `T1/lmss/m/sl' tried instead on input line 118.
LaTeX Font Info: Font shape `T1/lmss/m/it' in size <6> not available
(Font) Font shape `T1/lmss/m/sl' tried instead on input line 118.
! Undefined control sequence.
<recently read> \ltx@label
l.118 \end{frame}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
Here is how much of TeX's memory you used:
23358 strings out of 469782
448810 string characters out of 5481627
822283 words of memory out of 5000000
51275 multiletter control sequences out of 15000+600000
662079 words of font info for 67 fonts, out of 8000000 for 9000
14 hyphenation exceptions out of 8191
101i,11n,107p,420b,450s stack positions out of 10000i,1000n,20000p,200000b,200000s
! ==> Fatal error occurred, no output PDF file produced!
And the result of running tinytex::tlmgr_search('/l3backend-pdftex.def') is:
tlmgr search --file --global '/l3backend-pdftex.def'
tlmgr: package repository https://za.mirrors.cicku.me/ctan/systems/texlive/tlnet (verified)
l3backend:
texmf-dist/tex/latex/l3backend/l3backend-pdftex.def
l3backend-dev:
texmf-dist/tex/latex-dev/l3backend/l3backend-pdftex.def
The error suggests some unhappiness with the \label in the equation (or, indeed a \label anywhere in any environment including tables, figure captions, amsmath environments, etc). If I comment the \label out, it does compile but obviously without a working equation reference.
Further to this I tried to compile a straight LaTeX approximation of this (I have stripped out a lot of the frontmatter to try to make this as MWE as possible, but perhaps too much?):
\documentclass[
ignorenonframetext,
t]{beamer}
\usepackage{amsmath}
\usepackage{hyperref}
\begin{document}
\begin{frame}
\begin{equation}
1 = 1
\label{eq:binom}
\end{equation}
Look at \eqref{eq:binom}.
\end{frame}
\end{document}
For me, trying to compile this in RStudio (using TinyTex) fails unless I comment out ignorenonframetext or the \label{...} command, and it also fails if I try to use the pdflatex command bundled with RStudio on the command line. The fatal error is an undefined control sequence, implicating labels again:
Dictionary: translator-theorem-dictionary, Language: English
) (./beamer-frame-test.nav)
LaTeX Font Info: Trying to load font information for U+msa on input line 14.
(/home/rstudio/.TinyTeX/texmf-dist/tex/latex/amsfonts/umsa.fd
File: umsa.fd 2013/01/14 v3.01 AMS symbols A
)
LaTeX Font Info: Trying to load font information for U+msb on input line 14.
(/home/rstudio/.TinyTeX/texmf-dist/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
)
! Undefined control sequence.
<recently read> \ltx@label
l.14 \end{frame}
I (think) this is a red herring though. Indeed, if I comment out the \label then it compiles but it also compiles if instead I comment out ignorenonframetext, and then has working label references.
I have tried this on both a Windows 11 machine and MacOS machine and in a Docker rocker container - same problem.
Am I missing some basic syntax error?
Is it possible that all my TinyTex installations are corrupted somehow? I have reinstalled TinyTex (both using tinytex::reinstall_tinytex() and also by deleting the TinyTex folder and installing from scratch.
I have reinstalled R and updated all my packages. I get the same error if I try to make Beamer slides using Yihui's .Rmd example on cross-referencing.
My xfun::session_info() on the MacOS machine is:
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6, RStudio 2025.5.0.496
Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
Package version:
base64enc_0.1.3 bslib_0.9.0 cachem_1.1.0 cli_3.6.5
compiler_4.5.1 digest_0.6.37 evaluate_1.0.4 fastmap_1.2.0
fontawesome_0.5.3 fs_1.6.6 glue_1.8.0 graphics_4.5.1
grDevices_4.5.1 highr_0.11 htmltools_0.5.8.1 jquerylib_0.1.4
jsonlite_2.0.0 knitr_1.50 lifecycle_1.0.4 memoise_2.0.1
methods_4.5.1 mime_0.13 R6_2.6.1 rappdirs_0.3.3
rlang_1.1.6 rmarkdown_2.29 rstudioapi_0.17.1 sass_0.4.10
stats_4.5.1 tinytex_0.57 tools_4.5.1 utils_4.5.1
xfun_0.52 yaml_2.3.10
Whilst commenting out ignorenonframetext "solves" my problem, that piece of code appears in the vanilla pandoc Beamer template, which is used by RStudio. If this were a troublesome line surely thousands of people would have encountered this problem? Equally, I'm sure \label appears in (hundreds) of thousands of R markdown documents used to generate beamer slides. If I change the document class to article everything works perfectly so it seems to be an issue with Beamer specifically. Also, the same LaTeX code above compiles with no issue on Overleaf, so it is "compilable" but just not by the TinyTex installation on my (two) machines and Docker container.
I have run out of things to try, so would appreciate any suggestions! If someone can confirm that either the .Rmd above or the .tex above compiles in RStudio using TinyTex that would at least narrow the problem down to me (my machines), which is my issue, not everyone else's.
This has been fixed in the beamer development version: https://github.com/josephwright/beamer/commit/0590aca2f8a175904994dc0693ae42aed1feca11
Until a new beamer version is released, Latex users can temporarily add the file https://raw.githubusercontent.com/josephwright/beamer/0590aca2f8a175904994dc0693ae42aed1feca11/base/beamerbaseoverlay.sty to the same folder as their .tex file.