Pandoc Error with Rmarkdown and Shiny

Pandoc Error with Rmarkdown and Shiny

[Andrew Scotchmer]

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Hi

I have a simple R shiny app.  Whenever I try and download the table I 
created I get the following error:

pandoc: Cannot decode byte '\xfe': 
Data.Text.Internal.Encoding.Fusion.streamUtf8: Invalid UTF-8 stream 
Warning: Error in : pandoc document conversion failed with error 1 Stack 
trace (innermost first): 
    53: pandoc_convert
     52: convert
    51: rmarkdown::render 
    50: download$func [/home/scotcan1/Webshot/app.R#50]
      1: shiny::runApp 
Error : pandoc document conversion failed with error 1

I don't know what this means.   Here is my R/Shiny script and Rmarkdown.

*R:*
library(shiny)
library(DT)
data(iris)
ui <- fluidPage(
  
  titlePanel("|Species Table"),
  
  sidebarLayout(
    sidebarPanel(
      selectInput("specs",
                  "Number of bins:",
                  unique(iris$Species)),
      downloadButton("download", "Download Report")
    ),
    
    mainPanel(
      tableOutput("specTable")
    )
    
  )
  
)
server <- function(input, output) {
  
  subSpec <- function(x){
    testdat <- iris[iris$Species == x, ]
    return(testdat[1:10,])
  }
  
  reactiveFunction <- reactive({ subSpec(input$specs) })
  
  
  output$reactiveTable <- renderDataTable({ reactiveFunction() }, rownames = 
FALSE)
  
  output$specTable <- renderUI({
    dataTableOutput("reactiveTable")
    
  })
  
  
  
  output$download <- downloadHandler(
    filename <- "report_file.html",
    
    content <- function(file){
      write.csv(reactiveFunction(), "test_csv.csv", row.names = FALSE)
      params <- list(data = reactiveFunction())
      rmarkdown::render(filename, output_file = file)
    }
  )
}
shinyApp(ui = ui, server = server)



*Rmarkdown:*
---
title: "Untitled"
output: html_document
params:
  data: NA
---

```{r, echo=FALSE}
data(iris)
library(DT)
datatable(params$data)
```



Any help to interpret the error appreciated.

Andrew

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Re: Pandoc Error with Rmarkdown and Shiny

[John MacFarlane]

Pandoc expects its input to be UTF-8 encoded text, and
complains in this way if it is not.

Probably your script is using a different text encoding
for the downloaded report_file.html.  (Or, if this is
downloaded, perhaps it's not UTF-8 encoded on the server.)
You need to make sure it's UTF-8 encoded before passing
it to pandoc or rmarkdown::render.  (I speak without
knowing what rmarkdown::render does, but I assume it
just calls pandoc and doesn't do any encoding.)

+++ Andrew Scotchmer [Aug 25 17 01:24 ]:
>   Hi
>   I have a simple R shiny app.  Whenever I try and download the table I
>   created I get the following error:
>   pandoc: Cannot decode byte '\xfe':
>   Data.Text.Internal.Encoding.Fusion.streamUtf8: Invalid UTF-8 stream
>   Warning: Error in : pandoc document conversion failed with error 1
>   Stack trace (innermost first):
>       53: pandoc_convert
>        52: convert
>       51: rmarkdown::render
>       50: download$func [/home/scotcan1/Webshot/app.R#50]
>         1: shiny::runApp
>   Error : pandoc document conversion failed with error 1
>   I don't know what this means.   Here is my R/Shiny script and
>   Rmarkdown.
>   R:
>   library(shiny)
>   library(DT)
>   data(iris)
>   ui <- fluidPage(
>
>     titlePanel("|Species Table"),
>
>     sidebarLayout(
>       sidebarPanel(
>         selectInput("specs",
>                     "Number of bins:",
>                     unique(iris$Species)),
>         downloadButton("download", "Download Report")
>       ),
>
>       mainPanel(
>         tableOutput("specTable")
>       )
>
>     )
>
>   )
>   server <- function(input, output) {
>
>     subSpec <- function(x){
>       testdat <- iris[iris$Species == x, ]
>       return(testdat[1:10,])
>     }
>
>     reactiveFunction <- reactive({ subSpec(input$specs) })
>
>
>     output$reactiveTable <- renderDataTable({ reactiveFunction() },
>   rownames = FALSE)
>
>     output$specTable <- renderUI({
>       dataTableOutput("reactiveTable")
>
>     })
>
>
>
>     output$download <- downloadHandler(
>       filename <- "report_file.html",
>
>       content <- function(file){
>         write.csv(reactiveFunction(), "test_csv.csv", row.names = FALSE)
>         params <- list(data = reactiveFunction())
>         rmarkdown::render(filename, output_file = file)
>       }
>     )
>   }
>   shinyApp(ui = ui, server = server)
>   Rmarkdown:
>   ---
>   title: "Untitled"
>   output: html_document
>   params:
>     data: NA
>   ---
>   ```{r, echo=FALSE}
>   data(iris)
>   library(DT)
>   datatable(params$data)
>   ```
>   Any help to interpret the error appreciated.
>   Andrew
>
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>
>References
>
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>   2. mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   3. https://groups.google.com/d/msgid/pandoc-discuss/1c67925b-ebef-4e18-ba6d-477292e07160-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org?utm_medium=email&utm_source=footer
>   4. https://groups.google.com/d/optout