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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
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RStudio crashes when an external FS is mounted to the user content directory #9

Closed minorsecond closed 5 years ago

minorsecond commented 5 years ago

Mounting an NFS share to ~/ShinyStudio/content/users/username causes RStudio to crash when it's is being started. I'm not sure if there is a better way to do this than what I am doing, or if it is even possible. Is it?

The error message follows.

`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:118)
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:213)
at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:109)
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)`
fresh2dev commented 5 years ago

I haven’t tested ShinyStudio under this scenario, but I’m sure we can get it to work.

For starters, most setup issues can be resolved by ensuring the executing user has ownership over all pertinent files. You can use sudo chown -R $USER:$USER ./ShinyStudio to do this.

If that doesn’t work, please capture and post logs emitted from the RStudio container. Trick is, you only have a few seconds to copy the logs before ShinyProxy destroys the container.

fresh2dev commented 5 years ago

Did you ever make any progress with this?

fresh2dev commented 5 years ago

Please let me know if you have any remaining issues.