* Pandoc Error with Rmarkdown and Shiny
@ 2017-08-25 8:24 Andrew Scotchmer
[not found] ` <1c67925b-ebef-4e18-ba6d-477292e07160-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 2+ messages in thread
From: Andrew Scotchmer @ 2017-08-25 8:24 UTC (permalink / raw)
To: pandoc-discuss
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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
[not found] ` <1c67925b-ebef-4e18-ba6d-477292e07160-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2017-08-25 14:15 ` John MacFarlane
0 siblings, 0 replies; 2+ messages in thread
From: John MacFarlane @ 2017-08-25 14:15 UTC (permalink / raw)
To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw
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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> [3]https://groups.google.com/d/msgid/pandoc-discuss/1c67925b-ebef-4e18-
> ba6d-477292e07160%40googlegroups.com.
> For more options, visit [4]https://groups.google.com/d/optout.
>
>References
>
> 1. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> 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
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2017-08-25 8:24 Pandoc Error with Rmarkdown and Shiny Andrew Scotchmer
[not found] ` <1c67925b-ebef-4e18-ba6d-477292e07160-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2017-08-25 14:15 ` John MacFarlane
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