pandoc version 1.12.3 or higher is required and was not found (R shiny)

I have a problem generating a pdf report from my app shiny which is hosted on a server.

the app works fine but when I press the button to download the report, I get this error :

 pandoc version 1.12.3 or higher is required and was not found.

The proble is that if I type pandoc -v I get:

 pandoc 1.12.3.3
 Compiled with texmath 0.6.6, highlighting-kate 0.5.6.1.
Syntax highlighting is supported for the following languages:
    actionscript, ada, apache, asn1, asp, awk, bash, bibtex, boo, c, changelog,
    clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css, curry, d,
    diff, djangotemplate, doxygen, doxygenlua, dtd, eiffel, email, erlang,
    fortran, fsharp, gnuassembler, go, haskell, haxe, html, ini, java, javadoc,
    javascript, json, jsp, julia, latex, lex, literatecurry, literatehaskell,
    lua, makefile, mandoc, markdown, matlab, maxima, metafont, mips, modelines,
    modula2, modula3, monobasic, nasm, noweb, objectivec, objectivecpp, ocaml,
    octave, pascal, perl, php, pike, postscript, prolog, python, r,
    relaxngcompact, restructuredtext, rhtml, roff, ruby, rust, scala, scheme,
    sci, sed, sgml, sql, sqlmysql, sqlpostgresql, tcl, texinfo, verilog, vhdl,
    xml, xorg, xslt, xul, yacc, yaml
 Default user data directory: /home/daniele/.pandoc
 Copyright (C) 2006-2013 John MacFarlane
 Web:  http://johnmacfarlane.net/pandoc
 This is free software; see the source for copying conditions.  There is no
 warranty, not even for merchantability or fitness for a particular purpose.

So I suppose I have the right version for that. TexLive is also installed and the path is in $PATH.

Server.R

library(shiny)
library(drsmooth)
library(shinyBS)
library(knitr)
library(xtable)
library(rmarkdown)

shinyServer(function(input, output,session) { 

 output$downloadReport <- downloadHandler(
filename = function() {
  paste('report', sep = '.','pdf')
},

content = function(file) {
  src <- normalizePath('report.Rmd')

  # temporarily switch to the temp dir, in case you do not have write
  # permission to the current working directory
  owd <- setwd(tempdir())
  on.exit(setwd(owd))
  file.copy(src, 'report.Rmd')

  library(rmarkdown)
  out <- render('report.Rmd')
  file.rename(out, file)
})

output$tb <- renderUI({
             p(h4("Report")),
            "Dowload a the report of your analysis in a pdf format",
            tags$br(),downloadButton('downloadReport',label="Download report"),
            tags$em("This option will be available soon")
     })
})

* report.Rmd* does not contain any sort of calculation, it's only text. The pdf generation works fine on my local version (MacOS) but not on the server.

I'm here to give other information if needed.

Solution 1:

Go into RStudio and find the system environment variable for RSTUDIO_PANDOC

Sys.getenv("RSTUDIO_PANDOC")

Then put that in your R script prior to calling the render command.

Sys.setenv(RSTUDIO_PANDOC="--- insert directory here ---")

This worked for me after I'd been struggling to find how rmarkdown finds pandoc. I had to check github to look at the source.

Solution 2:

Another option so that this works for all your R scripts is to define this variable globally.

On Debian/Ubuntu, add the following line to your .bashrc file:

export RSTUDIO_PANDOC=/usr/lib/rstudio/bin/pandoc

On macOS, add the following to your .bash_profile file:

export RSTUDIO_PANDOC=/Applications/RStudio.app/Contents/MacOS/pandoc

On Windows (using Git Bash), add the following to your .bashrc file:

export RSTUDIO_PANDOC="/c/Program Files/RStudio/bin/pandoc/"

Solution 3:

The easiest way I solved this issue is to pass the Sys.setenv(..) command inside the crontab command prior to calling the RMarkdown::render. You need to separate the two commands with a semicolon:

R -e "Sys.setenv(RSTUDIO_PANDOC='/usr/lib/rstudio-server/bin/pandoc'); rmarkdown::render('File.Rmd', output_file='output.html')"

(Remember that the rstudio-server path differs from the non-server version)

Solution 4:

For those not using RStudio, you may just need to install pandoc on your system. For me it was

sudo pacman -S pandoc

and it worked (Arch Linux).

Solution 5:

I'm using Arch Linux, and RStudio as well.. the only thing that worked for me was:

sudo pacman -S pandoc