Rendering a PDF from an RMarkdown document in a Shiny app only works once

[k96nb01]

I have a Markdown document that I would like to run from a Shiny app. Here is an example Markdown document that reproduces the problem:

---
title: "Test Markdown report"
subtitle: "Report date: `r as.integer(format(Sys.time(), '%m'))`/`r as.integer(format(Sys.time(), '%d'))`/`r format(Sys.time(), '%Y')`"
output:
  pdf_document: default
params:
  MRN_patient: "01234"
  First_name_donor: "ABCD123"
urlcolor: blue
fontsize: 9pt
header-includes:
  \usepackage{titling}
  \setlength{\droptitle}{-10em}
  \usepackage{caption}
  \usepackage{helvet}
  \renewcommand{\familydefault}{\sfdefault}
  \usepackage{fancyhdr}
  \pagestyle{fancy}
  \setlength{\headheight}{13.59999pt}
  \fancyhead[L]{Deceased donor assessment report}
  \fancyhead[R]{`r as.integer(format(Sys.time(), '%m'))`/`r as.integer(format(Sys.time(), '%d'))`/`r format(Sys.time(), '%Y')`}
---

\vspace{-20truemm}
\captionsetup[table]{labelformat=empty}

```{r include=FALSE}
library(DBI)
library(odbc)
library(tidyverse)
library(kableExtra)
library(lubridate)
library(stringi)

(table <- tribble(
  ~recipient, ~donor,
  "John",   "123456789"
))

Patient: r table$recipient, r table$donor       MRN: 123456789       ABO: A
Donor: r table$ABCD999       DOB: 1/1/1900      

#Table of typing
kbl(table, booktabs = TRUE, , caption = "Typing") %>% kable_styling(full_width = T) %>% column_spec(1, width = "2cm") %>% kable_styling(latex_options = "hold_position")

I have used these instructions: Shiny - Generating downloadable reports (rstudio.com) to construct a Shiny app to render this parameterized report:

library(shiny)

ui = fluidPage(
    textInput("MRN", "Patient MRN"),
    textInput("DonorID", "Donor ID"),
    downloadButton("report", "Generate report")
  )

server = function(input, output) {
    output$report <- downloadHandler(
      filename = "report.pdf",
      content = function(file) {
        # Copy the report file to a temporary directory before processing it, in
        # case we don't have write permissions to the current working dir (which
        # can happen when deployed).
        tempReport <- file.path(tempdir(), "temp.rmd")
        file.copy("test_RMarkdown.rmd", tempReport, overwrite = TRUE)
        
        # Set up parameters to pass to Rmd document
        params <- list(
          MRN_patient = input$MRN,
          First_name_donor = input$DonorID
          )
        
        # Knit the document, passing in the `params` list, and eval it in a
        # child of the global environment (this isolates the code in the document
        # from the code in this app).
        rmarkdown::render(tempReport, output_file = file,
                          params = params,
                          envir = new.env(parent = globalenv())
        
        )
        
      }
    )
  }


# Run the application 
shinyApp(ui = ui, server = server)

This works beautifully, the first time. If I try to generate another report from the Shiny app, it doesn't work, and I get this error message:

! LaTeX Error: Environment tabu undefined.

Warning: Error in : LaTeX failed to compile C:\Users\BrowNich\AppData\Local\Temp\Rtmpg9bnRg\file489843723ddc.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See file489843723ddc.log for more info.
  [No stack trace available]

This would appear to be similar to the issue described here: r - Why does rendering a pdf from rmarkdown require closing rstudio between renders? - Stack Overflow

However, my code already contains the envir = new.env(parent = globalenv()) argument in render, and if I change to envir = new.env() I still get the same error. Closing RStudio and opening again gets it to work, but only for the first time again.

Not sure what I'm doing wrong?

[k96nb01]

I figured it out. The problem was with the kableextra package not loading properly the second time, and I used the following instructions to fix it: r - Why does rendering a pdf from rmarkdown require closing rstudio between renders? - Stack Overflow

Specifically, I added the following to the YAML header:

 \usepackage{booktabs}
  \usepackage{longtable}
  \usepackage{array}
  \usepackage{multirow}
  \usepackage{wrapfig}
  \usepackage{float}
  \usepackage{colortbl}
  \usepackage{pdflscape}
  \usepackage{tabu}
  \usepackage{threeparttable}
  \usepackage[normalem]{ulem}

The linked website suggested adding \usepackage[table]{xcolor}, but that caused conflicts, so I went without it. Now I can generate pdf reports all day!

[cderv]

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