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rdockershinyflexdashboard

Dockerized flexdashboard app won't run in localhost

I am attempting to create a Dockerized Flexdashboard app. I am able to run it locally, but not in the localhost. I can, however, run shiny apps just fine within the same docker image. Interestingly, the error message in the localhost says 'Not Found' for the Flexdashboard app which is different than when a page doesn't exist at all ('Page Not Found').

How can I Dockerize a Flexdashboard app?

MWE

dir.create("testshinydocker")
dir.create("testshinydocker/apps")
dir.create("testshinydocker/apps/kmeans")
dir.create("testshinydocker/apps/kmeansflex")

cat(readLines("https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/server.R"),
    file = "testshinydocker/apps/kmeans/server.R", sep = "\n")

cat(readLines("https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/ui.R"),
    file = "testshinydocker/apps/kmeans/ui.R", sep = "\n")

cat(
  c('FROM rocker/shiny:latest\n',

  "RUN  echo 'install.packages(c(\"flexdashboard\"), \\",
  "repos='$MRAN', \\",
  "dependencies=TRUE)' > /tmp/packages.R \\",
  "  && Rscript /tmp/packages.R\n",

  'EXPOSE 3838\n',
  'COPY apps /srv/shiny-server/\n',
  'CMD ["/usr/bin/shiny-server.sh"]\n'),
  file = "testshinydocker/Dockerfile",
  sep = "\n"
)

cat(readLines("https://raw.githubusercontent.com/rstudio/flexdashboard/master/examples/11_shiny-kmeans-clustering/dashboard.Rmd"),
    file = "testshinydocker/apps/kmeansflex/kmeans2.Rmd", sep = "\n")

shiny::runApp('testshinydocker/apps/kmeans')

rmarkdown::run("testshinydocker/apps/kmeansflex/kmeans2.Rmd")

Docker code (run in Powershell)

cd {path to testshinydocker directory}
docker build -t myapp .
docker run --rm -d -p 3838:3838 myapp

localhost URLs

Shiny app works enter image description here

Flexdashbord app 'Not Found' enter image description here

Nonexistent dinosaurs page 'Page not Found' enter image description here

Solution

  • This is likely a result of a bug in the rmarkdown package being used in your image (rmoarkdown v. 1.18) and is related to this: https://github.com/rstudio/rmarkdown/issues/1731 and https://github.com/rstudio/rmarkdown/issues/1714. I'm guessing http://localhost:3838/kmeansflex/kmeans2.Rmd does indeed work.

    Here's how you could test this. Make a shiny app in the apps folder to see what version of rmarkdown is being run. Make a folder in apps called 'rmarkdown'. Then put the following simple ui.R and server.R scripts in there to build a shiny app (we know shiny apps render for you) to determine what version of rmarkdown you have:

    The ui.R script

    fluidPage( 
  hr(),
  fluidRow(column(3, verbatimTextOutput("value")))   
)

    The server.r script

    function(input, output) {
​  output$value <- renderPrint({ utils::packageVersion('rmarkdown') })
}

    Then docker build and re-docker run and go to http://localhost:3838/rmarkdown/ in the browser. It should take you to the screen and display the version of rmarkdown you have. If it is 1.18 that's the culprit.

    enter image description here

    Potential Solution

    If the rmarkdown installed is version 1.18 a possible solution would be to install rmarkdown from github in your Dockerfile so that you'd get a newer version without this bug and all is well. Here's what that would look like in your Dockerfile:

    FROM rocker/shiny:latest

# apt-get and system utilities
RUN apt-get update && apt-get install -y \
    libssl-dev \
    libsodium-dev

RUN  echo 'install.packages(c("flexdashboard", "remotes", "openssl"), \
repos='$MRAN', \
dependencies=TRUE)' > /tmp/packages.R \
  && Rscript /tmp/packages.R

RUN Rscript -e 'remotes::install_github("rstudio/rmarkdown")' 

COPY apps /srv/shiny-server/


EXPOSE 3838

CMD ["/usr/bin/shiny-server.sh"]