RStudio in ShinyProxy (Container unresponsive)

bogdan · September 12, 2021, 2:44pm

Hi

I read the comments of this topic (A proxy for RStudio Server like ShinyProxy) - it didn’t help.

I will try to describe my situation:

System:
Windows + WSL2 + Ubuntu 20.04 + Docker Desktop (Expose daemon on tcp: // localhost: 2375 without TLS -> ON)

What has been done and is working:

Created the /opt/R folder
Rstudio

Created the /opt/R/rstudio folder

Dockerfile for rstudio:
```
FROM rocker/rstudio

RUN install2.r --error --skipinstalled \
    renv

RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
```
Now if I write the commands:
docker build -t rstudio .
and
docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH = true rstudio

Then the server (itself, without shinyproxy) starts up!

ShinyProxy

Created a folder /opt/R/shiny-proxy

Dockerfile for shinyproxy

FROM openjdk:11-jre

RUN mkdir -pv /opt/R/shiny-proxy
RUN cd /opt/R/shiny-proxy && wget https://www.shinyproxy.io/downloads/shinyproxy-2.5.0.jar

EXPOSE 8080

WORKDIR /opt/R/shiny-proxy
CMD ["java", "-noverify", "-jar", "shinyproxy-2.5.0.jar", "--spring.jmx.enabled=false", "--spring.config.location=./config/application.yml"]

Docker-compose (in /opt/R)

version: '2'

services:
   shiny-proxy:
      build:
         context: ./shiny-proxy/
      image: shiny-proxy
      container_name: shiny-proxy-1
      restart: on-failure
      environment:
         R_USER_PASSWORD: pass
      volumes:
        - /var/run/docker.sock:/var/run/docker.sock
        - ./shiny-proxy/config:/opt/R/shiny-proxy/config
      ports:
        - "8080:3838"

And I fill in the application.yml file

server:
   forward-headers-strategy: native

proxy:
  title: "Analyst module"
  template-path: ./templates
  landing-page: /
  heartbeat-rate: 10000
  heartbeat-timeout: 60000
  port: 3838
  authentication: simple
  container-wait-time: 30000

docker:
   internal-networking: true
 
admin-groups: admin

users:
 - name: ruser
   password: pwd
   groups: admin

 specs:
 - id: "SEPARATOR_DEV"
   display-name: "Develop"
   logo-url: "code"
   
 - id: "rstudio"
   access-groups: [admin]
   display-name: "RStudio IDE"
   logo-url: "r project"
   description: "RStudio"
   container-image: rstudio
   port: 8787
   container-volumes: [ "/home/#{proxy.userId}:/home/#{proxy.userId}" ]
   container-env:
     USER: "#{proxy.userId}"
     DISABLE_AUTH: true
     WWW_ROOT_PATH: "#{proxySpec.containerSpecs[0].env.get('SHINYPROXY_PUBLIC_PATH')}"

ShinyProxy has started successfully!

But RStudio doesn’t want to run in it!!!

shiny-proxy-1  | 2021-09-12 14:38:43.265  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (2/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:38:45.267  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (3/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:38:47.268  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (4/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:38:49.269  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (5/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:39:01.282  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (6/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:39:03.283  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (7/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:39:05.285  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (8/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:39:07.286  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (9/15): http://7428710c6983:8787
shiny-proxy-1  | 2021-09-12 14:39:09.287  WARN 1 --- [  XNIO-1 task-2] e.o.shinyproxy.ShinyProxyTestStrategy    : Container unresponsive, trying again (10/15): http://7428710c6983:8787

Question: What do I need to write to make it work?

tdekoninck · September 13, 2021, 6:53am

Hi

When using ShinyProxy with Docker and internal networking, you have to create a dedicated Docker network. See https://github.com/openanalytics/shinyproxy-config-examples/tree/master/02-containerized-docker-engine
Make sure to edit your application.yml file to include the container-network: sp-example-net option for every app (see the repo).

bogdan · September 13, 2021, 8:54am

Creating your own docker-network didn’t help.

Solved the problem with colleagues. We created an .env-file, wrote the COMPOSE_PROJECT_NAME=test variable to it

Further in the docker-compose indicated: SHINY_PROXY_DOCKER_NETWORK: ${COMPOSE_PROJECT_NAME}_default

And in application.yml after port: 8787:
container-network: ${SHINY_PROXY_DOCKER_NETWORK}

Erwann_SCAON · January 20, 2022, 1:32pm

Same here still stuck while trying to figure out how to run RStudio in ShinyProxy.

Everything went fine for creating the image based on an renv.lock file.
I can access RStudio easily when launched with docker run.
But it’s still tricky to me how to configure the application.yml file.
I read a bunch of online posts but still fail (being stuck with ShinyProxy 2.3.0 surely do not help to try to launch an image based on rocker/rstudio:4.1.0).

Any updated guidelines on this topic ?

Best regards

tdekoninck · January 20, 2022, 8:08am

Hi @Erwann_SCAON

I just did a test with ShinyProxy 2.3.0 and the rocker/rstudio:3.2.0 docker image, and everything works fine here.

Here is a minimal application.yml file that you can start with:

proxy:
  title: Open Analytics Shiny Proxy
  logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
  landing-page: /
  heartbeat-rate: 10000
  heartbeat-timeout: 60000
  port: 8080
  authentication: simple
  admin-groups: scientists
  users:
  - name: jack
    password: password
    groups: scientists
  docker:
    cert-path: /home/none
    url: http://localhost:2375
    port-range-start: 20000
  specs:
  - id: rstudio
    container-image: rocker/rstudio:3.2.0
    container-env:
      DISABLE_AUTH: true
    port: 8787

I would advise to start testing with this configuration and then applying your modifications on top of it. Let us know if you get stuck somewhere and then we can further discuss.
Please note that we have a demo with rstudio: https://github.com/openanalytics/shinyproxy-rstudio-ide-demo . This version is only compatible with 2.5.0 and 2.6.0, but you can use older version of Rstudio as described here: https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/tree/1.2.1335__3.6.0

Erwann_SCAON · January 20, 2022, 1:33pm

Thanks for your reply, I’ll try it.

Ps: My previous post had a typo, I’m trying to use rocker/rstudio:4.1.0 (not 3.2.0)

tdekoninck · January 24, 2022, 7:41am

Hi @Erwann_SCAON

With RStudio 4.1.0 you will have to use at least ShinyProxy 2.5.0. There may be some workarounds to make it work with 2.3.1, but I guess that would be more effort than using ShinyProxy 2.5.0

gacolitti · March 16, 2022, 8:27pm

I don’t think there is an RStudio 4.1.0.

See https://support.rstudio.com/hc/en-us/articles/200716783-RStudio-IDE-Release-History