Shiny Server missing charts generated by R markdown file

Question

I have an R markdown file which I'd like to be available on my corporate Shiny Server.

According to R Markdown: The Definitive Guide I can add runtime: shiny to the YAML metadata at the top of the Rmd file to turn it into a Shiny document. I have done this and it works. If I click "Run Document" in RStudio it will run the Rmd and I will see the report with no problems.

My project is located in the ShinyApps directory where the Shiny Server is looking for apps to serve. When I hit the URL for this project I get the report without any charts. I just get broken image icons where the charts should be. (I am using RStudio Server so it is the exact same files being accessed by RStudio and Shiny Server).

R version 3.4.3, Shiny Server version 1.5.6.875

UPDATE: I have reproduced the behaviour with the simplest possible example. I created a new RStudio project - just a plain project - called TEST located in my ShinyApps directory. Then I created a new R Markdown file, which I called TEST.Rmd. This file is pre-populated with example RMarkdown using the cars and pressure built-in datasets. I changed the YAML header to include runtime: shiny. The RStudio "knit" button is replaced by the "Run Document" button, as expected, and clicking this runs the document and works as expected. Attempting to view the page via the Shiny Server has the same issue whereby the plot is not included; a broken image icon takes its place.

UPDATE 2: As requested, here is the Markdown file. It is literally the sample file generated by RStudio with the addition of runtime: shiny in the YAML header.

---
title: "Test RMarkdown"
author: "Michael Henry"
date: "4/6/2020"
output: html_document
runtime: shiny
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

UPDATE 3: So I went hunting around the server looking for a log file for Shiny Server. I do not have any administrator privileges so I've never looked for this before, but I found a log file which included this: /lib64/libpango-1.0.so.0: undefined symbol: g_log_structured_standard. It turns out there is a bug in RHEL which has a fix available so I have put a request in with my administrator to apply the fix. I will report back after this has been applied as to whether it resolved my issue.

UPDATE 4: It turns out my RHEL server is up-to-date; it already has the version of glib2 suggested by the bugfix. The fact that I am still getting this error is therefore something that my administrator is going to escalate to Red Hat.

UPDATE 5: The Red Hat support suggested there was another glib2 so file lying around and it turned out that this was the case. Removing this file resolved the issue!

Answer 1

So, I think you might need to add some extra code to make the markdown application run as you expect in the Shiny Server environment

try wrapping the charts and plots with the following:

renderPlot({})

This gives the server an order to both run the plot and then make it available to the Shiny document. Shiny is a weird thing to straight up R programmers.

You are basically computing and creating things in an R environment and handing them off to a Javascript/HTML one which needs to know in its own language what to do. That renderPlot({}) tells the JS component how to promote the R output to your page.

You can see from this section of the reference document you linked to what the format is and how it is promoted to the page by Shiny.

If you are still stuck after doing this, reach back out and I will try to help trouble shoot!