R markdown report not generating from shiny app

[AmyMikhail]

Problem statement:

The shiny app launches, but when clicking the generate report button it only produces a copy of the inputs. The r markdown report is not generated.

[PaulC91]

Hi Amy.

This will be due to an id mis-match on the download handler between the UI and the server. outputId = "rapport" in the UI and output$report in the server.

A mistake I have made many times!

Best,
Paul

[AmyMikhail]

Thanks @PaulC91 - after correcting this I have another error though with regards to the filepath to the temporary file:

Warning in normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="C:\Users\AMikhail\AppData\Local\Temp\Rtmp4KKxBw/ELISAQCrapport.Rmd": The system cannot find the file specified
Warning: Error in abs_path: The file 'C:\Users\AMikhail\AppData\Local\Temp\Rtmp4KKxBw/ELISAQCrapport.Rmd' does not exist.
  [No stack trace available]

Any ideas?

[PaulC91]

hm not sure why the temp file isn't being recognised, but it's not strictly necessary so maybe try passing just "ELISAQCrapport.Rmd" as the input to rmarkdown::render.

Another thing I just noticed is that the output_file argument of the render function needs to be file in this case which is passed as the argument of the content function in the download handler. So try:

rmarkdown::render(input = "ELISAQCrapport.Rmd", 
                  output_file = file,
                  params = params,
                  envir = new.env(parent = globalenv()))

[AmyMikhail]

It is strange but when I tried removing the temp file creation and saving the file in exactly the same place as the .Rmd is, it still can´t find it:

Warning in normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="ELISAQCrapport.RMD": The system cannot find the file specified
Warning: Error in abs_path: The file 'ELISAQCrapport.RMD' does not exist.
  [No stack trace available]

I get this error even if I avoid changing the name of the .html output - not sure why.