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fresh2dev / ShinyStudio

A fully Dockerized, self-hosted development environment for teams. Develop where you serve.
https://hub.docker.com/r/dm3ll3n/shinystudio
MIT License
242 stars 40 forks source link

Error accessing RStudio and VS Code #7

Closed Jazelle759 closed 5 years ago

Jazelle759 commented 5 years ago

Hi, sorry to bother but I am new to using linux and docker so please bear with me here. I unable to access either RStudio or VS Code when I tried using ShinyStudio on a new DigitalOcean droplet (Ubuntu 16.04.6 x64).

I installed Docker and Docker Compose before setting up accordingly using 

# Clone this repository.
git clone https://github.com/dm3ll3n/ShinyStudio

# Enter the new directory.
cd ShinyStudio

# Setup and run.
./control.sh setup

All settings are the default.

I tried logging in as superadmin and admin at http://178.128.90.83:8080 but am unable to access both RStudio or VS Code.

The error I get when I try to open R Studio image

The error I get when I try to open VS Code

Error
Status code: 500

Message: Container did not respond in time

Stack Trace: 
eu.openanalytics.containerproxy.ContainerProxyException: Container did not respond in time
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:115)
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:213)
at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:100)
at eu.openanalytics.shinyproxy.controllers.AppController.startApp(AppController.java:68)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:870)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:776)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:881)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:855)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:129)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:200)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at io.undertow.servlet.handlers.FilterHandler.handleRequest(FilterHandler.java:84)
at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62)
at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:64)
at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36)
at io.undertow.server.handlers.PathHandler.handleRequest(PathHandler.java:94)
at eu.openanalytics.containerproxy.util.ProxyMappingManager$ProxyPathHandler.handleRequest(ProxyMappingManager.java:159)
at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:131)
at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46)
at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64)
at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60)
at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77)
at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:292)
at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:81)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:138)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:135)
at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48)
at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:272)
at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:81)
at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:104)
at io.undertow.server.Connectors.executeRootHandler(Connectors.java:336)
at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:830)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Output of docker images command

REPOSITORY                          TAG                 IMAGE ID            CREATED             SIZE
shinystudio_rstudio_rshiny_vscode   latest              ae206cbbb0c2        2 days ago          4.58GB
shinystudio_shinyproxy              latest              643db9596b2a        2 days ago          503MB
shinystudio_influxdb                latest              9b1de10472e1        2 days ago          258MB
rocker/verse                        latest              597f520c26ed        3 days ago          3.2GB
influxdb                            latest              f0656e147345        2 weeks ago         258MB
openjdk                             8-jre               b5ee13f1fc07        2 weeks ago         443MB
hello-world                         latest              fce289e99eb9        4 months ago        1.84kB

Docker Version

Client:
 Version:           18.09.6
 API version:       1.39
 Go version:        go1.10.8
 Git commit:        481bc77
 Built:             Sat May  4 02:35:27 2019
 OS/Arch:           linux/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          18.09.6
  API version:      1.39 (minimum version 1.12)
  Go version:       go1.10.8
  Git commit:       481bc77
  Built:            Sat May  4 01:59:36 2019
  OS/Arch:          linux/amd64
  Experimental:     false

docker container ls output

CONTAINER ID        IMAGE                    COMMAND                  CREATED             STATUS              PORTS                    NAMES
6618efeb52bb        shinystudio_shinyproxy   "/opt/shinyproxy/sta…"   2 days ago          Up 2 days           0.0.0.0:8080->8080/tcp   shinystudio_shinyproxy_run_f6fd64fa9bcd
37b9f3ff1a05        shinystudio_influxdb     "/entrypoint.sh infl…"   2 days ago          Up 2 days           0.0.0.0:8886->8086/tcp   shinystudio_influxdb_1
fresh2dev commented 5 years ago

Are you, by chance, running the setup with the "root" account? It should be run with a non-root account with sudoer access. If that doesn't apply here, please obtain and post the logs from the container that is spawned after invoking RStudio. This container will only exist for a short period before ShinyProxy removes it, so you must be quick. Find the running container ID, then run docker logs -f <CONTAINER> to watch the RStudio logs. Paste 'em here and we can investigate further.

Jazelle759 commented 5 years ago

I was using "root" account. I have used a non-root account with sudoer access and re-set up and it seems to be working. Thanks! Why is it that "root" account can't be used?

fresh2dev commented 5 years ago

The user account is created in each container when the container is spawned. The "root" account cannot be re-created.