RMarkdown and pandoc

[Bob Tao]

I wonder if there is a better way to handle the rmarkdown/pandoc issue. For example, include pandoc in the markdown installation somehow, or better configuration.

1. I have run into problems when using rmarkdown. For example, I could work on our RStudio server through a browser and run Shiny application that calls rmarkdown::render and all is fine. 
2. Strangely I could not do KnitPDF in the same window where I could run Shiny app ("pandoc version 1.12.3 or higher is required and was not found". is there a way to config which pandoc to use? Sys.getenv('RSTUDIO_PANDOC') is showing pandoc is the latest version)
   
3. When the code is deployed so others can use it, it failed, and complained "pandoc version 1.12.3 or higher is required and was not found"
4. If I start R from command line on the linux server,  rmarkdown::render works fine.
   
5. I could login the same server, but could not run "Rscript -e "rmarkdown::render('x.Rmd')" the error is show below:
   

Error in stri_trans_nfc(str) : 
  The requested ICU resource file cannot be found. Possible problem: ICU data ha
s not been downloaded yet. Call `stri_install_check()`. (U_FILE_ACCESS_ERROR)
Calls: <Anonymous> ... <Anonymous> -> stri_wrap -> stri_trans_nfc -> .Call

Execution halted

[Yihui Xie]

For the pandoc issue, the bottom line is: as long as you are in the
RStudio world (e.g. RStudio IDE, RStudio Server, Shiny Server, ...),
you should be fine, otherwise you have to make sure the pandoc
executable can be found via the PATH variable of your system.

For the stringi issue, I think the simplest solution is to reinstall
it: install.packages('stringi')

Regards,
Yihui

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