Why shinyApp does not render Rmarkdown file as in RStudio

I'm struggling to understand why shinyApp does not render a Rmarkdown file as done by RStudio, even when Rmarkdown is explicitly defined in app.R.

The Rmd file below has been written in RStudio, and when the "Run document" button is clicked an HTML document is generated with a friendly web of the application, the sidebar, pages, and plots. However, if this is hosted together with an app.R file in shiny-server, some errors are returned and the file rendered lacks of the structure of the original document (eg. sidebar, pages, etc..). This can be generated also by running Rscript --vanilla app.R and going to localhost:port.

Here are the files I'm using:

example.Rmd

---
title: "Example file"
runtime: shiny
theme: simplex
vertical_layout: fill
output:
  flexdashboard::flex_dashboard:
    orientation: rows
---

```{r setup, include=FALSE}
library(shiny)
library(tidyverse)
library(plotly)
```

Sidebar {.sidebar}
======================================================================

**Options**

```{r opt_general, echo = FALSE}
selectInput("opt_cyl",
            label = "Select cyl",
            choices = mtcars %>% .$cyl %>% unique %>% sort,
            multiple = TRUE,
            selected = "4")

sliderInput("opt_qsec", label = "Qsec", min = mtcars$qsec %>% min, max = mtcars$qsec %>% max, value = mtcars$qsec %>% max, step = 0.01)
```

**More options**

```{r opt_dist, echo = FALSE}
checkboxInput("opt_log", label = "Log scale (qsec)", value = FALSE)
```

Explore
======================================================================

```{r global, echo=FALSE}
 mtcars$cyl <- as.character(mtcars$cyl)
 ```

 ```{r reactive_global, echo=FALSE}
rcars <- reactive({
   C <- dplyr::filter(mtcars, cyl==input$opt_cyl, qsec <= input$opt_qsec)
  return(C)
})
 ```

Row
------------------------

### One nice plot

```{r plot1a, echo = FALSE}
    uiOutput("r1a")

output$r1a <- renderUI({
  plotlyOutput("p1a")
})

output$p1a <- renderPlotly({
  P <- mtcars %>% ggplot() + geom_point(aes(x=cyl, y=qsec))
  ggplotly(P)
})
```

### Another nice plot

```{r plot1b, echo = FALSE}
uiOutput("r1b")

output$r1b <- renderUI({
  plotlyOutput("p1b")
})

output$p1b <- renderPlotly({
  P <- rcars() %>% ggplot() + geom_point(aes(x=cyl, y=qsec))
  ggplotly(P)
})
```

Row
------------------------

### Second row plot

```{r plot2, echo = FALSE}
uiOutput("r2")

output$r2 <- renderUI({
  plotlyOutput("p2")
})

output$p2 <- renderPlotly({
  C <- rcars()
  if (input$opt_log) C$qsec <- log(C$qsec)
  P <- C %>% ggplot() + geom_point(aes(x=mpg, y=qsec))
  ggplotly(P)
})
```

About
======================================================================

Some nice README

The corresponding app.R file is:

library(shiny)
library(knitr)

ui <- shinyUI(
  fluidPage(
    uiOutput('markdown')
  )
)

server <-function (input, output) {
  output$markdown <- renderUI({
    HTML(markdown::markdownToHTML(knit('example.Rmd', quiet = TRUE)))
  })
}

shinyApp(ui, server)

The error returned in the log file is:

Listening on http://127.0.0.1:44229
Warning: Error in : Result must have length 32, not 0
125:
Warning: Error in : Result must have length 32, not 0
100:

Does someone can give me a pointer on why this is happening? Thank you

PS: Just in case anyone is interested, I did asked this first on stack overflow and offered a bounty (see https://stackoverflow.com/questions/56192753/shinyapp-not-rendering-rmarkdown-file-as-rstudio). Hope I can find guidance here because I'm truly lost.

This question has been finally answered in Stack Overflow, but I do not understand completely the answer. Why it works, and why my original code didn't. Do you know what I was doing wrong?

Furthermore, I can still see some differences between the local application and the remote one. In the real app (not the example) errors are handled with:

if (someting_bad) stop("error_message")

So that "error_message" is printed whenever something_bad happens. But at the shinyapps.io site all these messages are replaced by "An error has occurred. Check your logs or contact the app author for clarification.". Why this difference?

SO is correct. If you are trying to "run" a shiny app, the RMarkdown document can not be "render"ed once. It must be continuously "run"ning. If you'd like to embed a shiny app (or running rmarkdown document) within another shiny application, I'd suggest using an iframe in the outer application.

stop is a last resort. If you have known errors, try using shiny::validate or notifications (or similar functions) to produce messages for your users to read.

Thank you very much for your help and for pointing out these "best practices" :slight_smile:

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