Container starts successfully and works, but ShinyProxy says "Container did not respond in time"

attached · June 29, 2023, 4:39pm

When trying to run a MRE for the other post in this forum, I came across a strange problem I could not fix myself.

The problem also appears identically when using the shinyproxy example images. So I guess it has nothing todo with the specific app.

The code can be found here (including instructions on what to do):

I have an image that works and looks nice.
I can also start ShinyProxy on port 3839 on the host machine with the following command:

docker run --publish 3839:8080 -v /var/run/docker.sock:/var/run/docker.sock --rm shinyproxy:latest

Looks good, too. Now when I want to start the app, ShinyProxy manages to start the app container instance (I can see this when looking at docker ps), and when opening the app container instance in a separate window it also works perfectly! But within the app window in ShinyProxy, the app will not appear and show an error instead (logs):

Container did not respond in time

github.com

NilsOle/shinyproxy_debugging/blob/main/output.txt

  .   ____          _            __ _ _
 /\\ / ___'_ __ _ _(_)_ __  __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
 \\/  ___)| |_)| | | | | || (_| |  ) ) ) )
  '  |____| .__|_| |_|_| |_\__, | / / / /
 =========|_|==============|___/=/_/_/_/
 :: Spring Boot ::                (v2.7.6)

2023-06-29 16:18:32.198  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode
2023-06-29 16:18:32.201  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data Redis repositories in DEFAULT mode.
2023-06-29 16:18:32.236  INFO 1 --- [           main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 25 ms. Found 0 Redis repository interfaces.
2023-06-29 16:18:32.316  INFO 1 --- [           main] faultConfiguringBeanFactoryPostProcessor : No bean named 'errorChannel' has been explicitly defined. Therefore, a default PublishSubscribeChannel will be created.
2023-06-29 16:18:32.323  INFO 1 --- [           main] faultConfiguringBeanFactoryPostProcessor : No bean named 'integrationHeaderChannelRegistry' has been explicitly defined. Therefore, a default DefaultHeaderChannelRegistry will be created.
2023-06-29 16:18:32.560  INFO 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.integration.config.IntegrationManagementConfiguration' of type [org.springframework.integration.config.IntegrationManagementConfiguration] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2023-06-29 16:18:32.567  INFO 1 --- [           main] trationDelegate$BeanPostProcessorChecker : Bean 'integrationChannelResolver' of type [org.springframework.integration.support.channel.BeanFactoryChannelResolver] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2023-06-29 16:18:32.813  WARN 1 --- [           main] io.undertow.websockets.jsr               : UT026010: Buffer pool was not set on WebSocketDeploymentInfo, the default pool will be used
2023-06-29 16:18:32.840  INFO 1 --- [           main] io.undertow.servlet                      : Initializing Spring embedded WebApplicationContext
2023-06-29 16:18:32.840  INFO 1 --- [           main] w.s.c.ServletWebServerApplicationContext : Root WebApplicationContext: initialization completed in 1532 ms
2023-06-29 16:18:32.877  INFO 1 --- [           main] e.o.c.service.IdentifierService          : ShinyProxy runtimeId:                   a30ce10c-2fdd-40db-b7ae-4ef0b95dbcaf
2023-06-29 16:18:32.918  INFO 1 --- [           main] e.o.c.service.IdentifierService          : ShinyProxy instanceID (hash of config): 409de63418f47314ca2a7ef65a1c915ba227119e

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output of docker ps after clicking on the app:

# docker ps
CONTAINER ID   IMAGE               COMMAND                  CREATED              STATUS              PORTS                                       NAMES
066e1a6e8616   testapp             "R -e 'shiny::runApp…"   18 seconds ago       Up 17 seconds       0.0.0.0:20100->3838/tcp                     cool_chatelet
08144db01812   shinyproxy:latest   "java -jar /opt/shin…"   About a minute ago   Up About a minute   0.0.0.0:3839->8080/tcp, :::3839->8080/tcp   silly_bartik

What am I doing wrong?

ShinyProxy manages to successfully start the app container instance and there is no R error since I can interact with that very same app container instance without problems, but ShinyProxy would not connect to it.

Thanks for help.

tdekoninck · June 30, 2023, 6:41am

Hi

When you run shinyproxy in a container, you have to create a bridge network and specify this as a setting to the app. See https://github.com/openanalytics/shinyproxy-config-examples/tree/master/02-containerized-docker-engine and https://github.com/openanalytics/shinyproxy-config-examples/blob/master/02-containerized-docker-engine/application.yml#L25

attached · June 30, 2023, 10:40am

Thanks, that solved the problem. For those coming here from Google / ChatGPT:

Make sure you have created a docker network with sudo docker network create sp-example-net (for example)
In application.yml, add internal-networking: true to the docker section of the proxy settings, as well as container-network: sp-example-net to the container-network property of your app section
Start with sudo docker run --publish 8080:8080 -v /var/run/docker.sock:/var/run/docker.sock:ro --rm --group-add $(getent group docker | cut -d: -f3) --net sp-example-net shinyproxy:latest