error running knitr kable with .pdf output after updating Rstudio

Question

I've updated r (4.3.0) and Rstudio (RStudio 2023.03.1 Build 446) and when I tried to run knitr with .pdf output (knitr to pdf) on an rmarkdown (.rmd) document I get an unexpected error when rendering. However, when I run the code directly in the console it generates the table normally:

processing file: apuestas.rmd
  |......................                              |  43% [rmlatitu]       
Quitting from lines 1130-1412 [rmlatitu] (apuestas.rmd)
Error in `footnote()`:
! no se pudo encontrar la función "footnote"
Backtrace:
 1. ... %>% ...
                                                                                                            
Ejecución interrumpida

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Spanish_Spain.utf8  LC_CTYPE=Spanish_Spain.utf8   
[3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.utf8    

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
 [1] kableExtra_1.3.4 knitr_1.43       rmarkdown_2.21   scales_1.2.1    
 [5] gglorenz_0.0.2   ggrepel_0.9.3    fuzzyjoin_0.1.6  lubridate_1.9.2 
 [9] forcats_1.0.0    stringr_1.5.0    dplyr_1.1.2      purrr_1.0.1     
[13] readr_2.1.4      tidyr_1.3.0      tibble_3.2.1     tidyverse_2.0.0 
[17] ggspatial_1.1.8  gridExtra_2.3    ggExtra_0.10.0   ggplot2_3.4.2   
[21] rmapshaper_0.5.0 sf_1.0-13       

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0   viridisLite_0.4.2  farver_2.1.1      
 [4] fastmap_1.1.1      promises_1.2.0.1   digest_0.6.31     
 [7] timechange_0.2.0   mime_0.12          lifecycle_1.0.3   
[10] ellipsis_0.3.2     magrittr_2.0.3     compiler_4.3.0    
[13] sass_0.4.6         rlang_1.1.1        tools_4.3.0       
[16] utf8_1.2.3         yaml_2.3.7         labeling_0.4.2    
[19] sp_1.6-0           classInt_0.4-9     curl_5.0.0        
[22] xml2_1.3.4         KernSmooth_2.23-21 miniUI_0.1.1.1    
[25] withr_2.5.0        grid_4.3.0         fansi_1.0.4       
[28] xtable_1.8-4       e1071_1.7-13       colorspace_2.1-0  
[31] cli_3.6.1          generics_0.1.3     stringdist_0.9.10 
[34] rstudioapi_0.14    httr_1.4.6         tzdb_0.4.0        
[37] cachem_1.0.8       DBI_1.1.3          proxy_0.4-27      
[40] parallel_4.3.0     rvest_1.0.3        s2_1.1.4          
[43] vctrs_0.6.2        V8_4.3.0           webshot_0.5.4     
[46] jsonlite_1.8.4     geojsonsf_2.0.3    hms_1.1.3         
[49] systemfonts_1.0.4  ineq_0.2-13        jquerylib_0.1.4   
[52] units_0.8-2        glue_1.6.2         stringi_1.7.12    
[55] gtable_0.3.3       later_1.3.1        munsell_0.5.0     
[58] pillar_1.9.0       htmltools_0.5.5    R6_2.5.1          
[61] wk_0.7.3           evaluate_0.21      shiny_1.7.4       
[64] lattice_0.21-8     highr_0.10         bslib_0.4.2       
[67] httpuv_1.6.11      class_7.3-22       Rcpp_1.0.10       
[70] svglite_2.1.1      xfun_0.39          pkgconfig_2.0.3

CODE (the complete code as summarized as possible):


---
# title: "title"
# author: "name"
# date: '2023-04-22'
output:
  pdf_document:
    keep_md: true
    keep_tex: true
    number_sections: true
    fig_caption: yes
    fig_width: 10
    fig_height: 9
  html_document: default
  word_document: default
header-includes:
geometry:
- top=2cm
- bottom=1.5cm
- right=1.0cm
- left=1.0cm
graphics: yes
documentclass: article
papersize: a4
lang: es
always_allow_html: yes
editor_options:
  chunk_output_type: console
---

ipak <- function(pkg){
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg))
        install.packages(new.pkg, dependencies = TRUE)
    sapply(pkg, require, character.only = TRUE)
}

packages <- c("rmarkdown","knitr","kableExtra")
ipak(packages)

packages <- c("sf","rmapshaper","ggplot2","ggExtra","gridExtra","ggspatial","tidyverse","fuzzyjoin","ggrepel","gglorenz","scales")
ipak(packages)




título <- "título"
formato.tabla <- c("hover", "condensed", "responsive")

tatilocalesapuestas <- dget(file="tablalocales.R")

tatilocalesapuestas %>%
 kable(caption=`título`, 
  row.names=F, digits = 2, 
  format.args = list(big.mark = ".", decimal.mark = ","),
  centering = FALSE, 
  booktabs = F,
  vline="",
  linesep = "") %>%
  
 kable_styling(bootstrap_options = formato.tabla,
  html_font="\"Trebuchet MS\", verdana, sans-serif",
  latex_options = c("striped","scale_down","HOLD_position"),
  full_width = F, fixed_thead = F) %>%
  
 row_spec(
  0, bold=T, monospace=F, color="white", background="#7B7B7B") %>%
 
 row_spec(
  seq(1,nrow(tatilocalesapuestas),2), background="#F9F9F9") %>% 
 
 footnote(
  general="Elaboración propia",
  general_title = "Nota: ",
  threeparttable = T
  )

DATAFRAME: tablalocales.R


structure(list(`Locales por Titular` = c(1, 2, 3, 4, 5, 6, 7, 
8, 9, 11, 12, 13, 14, 15, 18, 28, 39, 54), Titulares = c(21L, 
12L, 3L, 2L, 1L, 4L, 3L, 2L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 
1L, 1L), `% Titulares` = c(34.4262295081967, 19.672131147541, 
4.91803278688525, 3.27868852459016, 1.63934426229508, 6.55737704918033, 
4.91803278688525, 3.27868852459016, 1.63934426229508, 4.91803278688525, 
1.63934426229508, 3.27868852459016, 1.63934426229508, 1.63934426229508, 
1.63934426229508, 1.63934426229508, 1.63934426229508, 1.63934426229508
), Locales = c(21, 24, 9, 8, 5, 24, 21, 16, 9, 33, 12, 26, 14, 
15, 18, 28, 39, 54), `% Locales` = c(5.58510638297872, 6.38297872340426, 
2.3936170212766, 2.12765957446809, 1.32978723404255, 6.38297872340426, 
5.58510638297872, 4.25531914893617, 2.3936170212766, 8.77659574468085, 
3.19148936170213, 6.91489361702128, 3.72340425531915, 3.98936170212766, 
4.78723404255319, 7.4468085106383, 10.3723404255319, 14.3617021276596
), `Acumulado Locales` = c(21, 45, 54, 62, 67, 91, 112, 128, 
137, 170, 182, 208, 222, 237, 255, 283, 322, 376), `Acumulado Titulares` = c(21L, 
33L, 36L, 38L, 39L, 43L, 46L, 48L, 49L, 52L, 53L, 55L, 56L, 57L, 
58L, 59L, 60L, 61L), `Acumulado Locales %` = c(5.58510638297872, 
11.968085106383, 14.3617021276596, 16.4893617021277, 17.8191489361702, 
24.2021276595745, 29.7872340425532, 34.0425531914894, 36.436170212766, 
45.2127659574468, 48.4042553191489, 55.3191489361702, 59.0425531914894, 
63.031914893617, 67.8191489361702, 75.2659574468085, 85.6382978723404, 
100), `Acumulado Titulares %` = c(34.4262295081967, 54.0983606557377, 
59.0163934426229, 62.2950819672131, 63.9344262295082, 70.4918032786885, 
75.4098360655738, 78.6885245901639, 80.327868852459, 85.2459016393443, 
86.8852459016393, 90.1639344262295, 91.8032786885246, 93.4426229508197, 
95.0819672131148, 96.7213114754098, 98.3606557377049, 100)), row.names = c(NA, 
-18L), class = "data.frame")

UPDATE: It's a known bug:

Error when loading kableExtra in markdown file after updating to R 4.3.0

There are two options:

Leave the YAML of the rmarkdown document with a single output.
Update the kableExtra package in your development version devtools::install_github("kupietz/kableExtra")

Is that the `sessionInfo` from your interactive session? Or from your markdown document? Make sure you load all the same libraries in your markdown document. Do you have `library(kableExtra)` in there? That seems to be where the `footnote` function comes from. It's easier to help you if you include a simple [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input that can be used to test and verify possible solutions. — MrFlick, May 30 '23 at 19:27
The only way I can reproduce this error (assuming `kableExtra`) is to fashion a document where `library(kableExtra)` is _not_ executed within the document itself. Since you say you have it in the `.rmd` file itself, it might be that it is within an `if` block that is not called, in a code-block that is not `eval`ed, or something else. Unfortunately, I don't know if there's much we can do without more of a reproducible question; are you able to provide a minimal `.rmd` file (without real data) in the question the reproduces the failure? — r2evans, May 30 '23 at 19:56
I have added the necessary code to be able to reproduce. And the data. (Thanks for your time.) — José Carlos, May 31 '23 at 17:37
It is a known bug. https://stackoverflow.com/questions/76118194/error-when-loading-kableextra-in-markdown-file-after-updating-to-r-4-3-0 — José Carlos, Jun 02 '23 at 17:53

error running knitr kable with .pdf output after updating Rstudio

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