I have a .Rmd along with a .sql file that is read by the .Rmd file that I’m trying to deploy in ShinyProxy. I am able to run this from within RStudio on my Mac.
The application loads, I can see it in ShinyProxy, but when I click on the application, it launches, then says please wait, then the error java.lang.StackOverflowError. I tried increasing the stack size with the JAVA_OPTS in the Dockerfile.
I do see this in shinyproxy.log:
java.lang.reflect.InvocationTargetException: null
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_322]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_322]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_322]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_322]
at org.glassfish.jersey.client.ClientExecutorProvidersConfigurator.lookupManagedExecutorService(ClientExecutorProvidersConfigurator.java:152) [jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.ClientExecutorProvidersConfigurator.(ClientExecutorProvidersConfigurator.java:49) [jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.ClientConfig$State.initRuntime(ClientConfig.java:442) [jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.internal.util.collection.Values$LazyValueImpl.get(Values.java:317) ~[jersey-common-2.30.1.jar!/:na]
at org.glassfish.jersey.client.ClientConfig.getRuntime(ClientConfig.java:807) ~[jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.ClientRequest.getClientRuntime(ClientRequest.java:219) ~[jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.ClientRequest.getInjectionManager(ClientRequest.java:610) ~[jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.JerseyWebTarget.onBuilder(JerseyWebTarget.java:364) ~[jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.JerseyWebTarget.request(JerseyWebTarget.java:207) ~[jersey-client-2.30.1.jar!/:na]
at org.glassfish.jersey.client.JerseyWebTarget.request(JerseyWebTarget.java:36) ~[jersey-client-2.30.1.jar!/:na]
at com.spotify.docker.client.DefaultDockerClient.createContainer(DefaultDockerClient.java:743) ~[docker-client-8.15.3.jar!/:8.15.3]
at com.spotify.docker.client.DefaultDockerClient.createContainer(DefaultDockerClient.java:724) ~[docker-client-8.15.3.jar!/:8.15.3]
at eu.openanalytics.containerproxy.backend.docker.DockerEngineBackend.startContainer(DockerEngineBackend.java:99) ~[containerproxy-0.8.10.jar!/:0.8.10]
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.doStartProxy(AbstractContainerBackend.java:163) ~[containerproxy-0.8.10.jar!/:0.8.10]
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:129) ~[containerproxy-0.8.10.jar!/:0.8.10]
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:279) ~[containerproxy-0.8.10.jar!/:0.8.10]
at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:150) ~[classes!/:2.6.0]
at eu.openanalytics.shinyproxy.controllers.AppController.startApp(AppController.java:91) ~[classes!/:2.6.0]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_322]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_322]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_322]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_322]
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:190) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:138) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:105) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:878) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:792) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:943) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:517) ~[jakarta.servlet-api-4.0.4.jar!/:4.0.4]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) ~[spring-webmvc-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:584) ~[jakarta.servlet-api-4.0.4.jar!/:4.0.4]
at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:129) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.keycloak.adapters.springsecurity.filter.KeycloakPreAuthActionsFilter.doFilter(KeycloakPreAuthActionsFilter.java:96) ~[keycloak-spring-security-adapter-13.0.1.jar!/:13.0.1]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at eu.openanalytics.containerproxy.util.AppRecoveryFilter.doFilter(AppRecoveryFilter.java:63) ~[containerproxy-0.8.10.jar!/:0.8.10]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at eu.openanalytics.shinyproxy.AuthenticationRequiredFilter.doFilter(AuthenticationRequiredFilter.java:71) ~[classes!/:2.6.0]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:118) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:158) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at eu.openanalytics.containerproxy.util.AppRecoveryFilter.doFilter(AppRecoveryFilter.java:63) ~[containerproxy-0.8.10.jar!/:0.8.10]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:155) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.keycloak.adapters.springsecurity.filter.KeycloakPreAuthActionsFilter.doFilter(KeycloakPreAuthActionsFilter.java:96) ~[keycloak-spring-security-adapter-13.0.1.jar!/:13.0.1]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:117) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:92) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:77) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178) ~[spring-security-web-5.3.9.RELEASE.jar!/:5.3.9.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.springframework.boot.actuate.metrics.web.servlet.WebMvcMetricsFilter.doFilterInternal(WebMvcMetricsFilter.java:97) ~[spring-boot-actuator-2.3.12.RELEASE.jar!/:2.3.12.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.2.15.RELEASE.jar!/:5.2.15.RELEASE]
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.FilterHandler.handleRequest(FilterHandler.java:84) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:68) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.handlers.PathHandler.handleRequest(PathHandler.java:104) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at eu.openanalytics.containerproxy.util.ProxyMappingManager$ProxyPathHandler.handleRequest(ProxyMappingManager.java:160) ~[containerproxy-0.8.10.jar!/:0.8.10]
at io.undertow.servlet.handlers.RedirectDirHandler.handleRequest(RedirectDirHandler.java:68) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:117) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.handlers.SameSiteCookieHandler.handleRequest(SameSiteCookieHandler.java:97) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.SendErrorPageHandler.handleRequest(SendErrorPageHandler.java:52) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:269) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:78) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:133) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:130) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:249) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:78) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:99) ~[undertow-servlet-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.Connectors.executeRootHandler(Connectors.java:387) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:841) ~[undertow-core-2.2.8.Final.jar!/:2.2.8.Final]
at org.jboss.threads.ContextClassLoaderSavingRunnable.run(ContextClassLoaderSavingRunnable.java:35) ~[jboss-threads-3.1.0.Final.jar!/:3.1.0.Final]
at org.jboss.threads.EnhancedQueueExecutor.safeRun(EnhancedQueueExecutor.java:2019) ~[jboss-threads-3.1.0.Final.jar!/:3.1.0.Final]
at org.jboss.threads.EnhancedQueueExecutor$ThreadBody.doRunTask(EnhancedQueueExecutor.java:1558) ~[jboss-threads-3.1.0.Final.jar!/:3.1.0.Final]
at org.jboss.threads.EnhancedQueueExecutor$ThreadBody.run(EnhancedQueueExecutor.java:1449) ~[jboss-threads-3.1.0.Final.jar!/:3.1.0.Final]
at org.xnio.XnioWorker$WorkerThreadFactory$1$1.run(XnioWorker.java:1280) ~[xnio-api-3.8.4.Final.jar!/:3.8.4.Final]
at java.lang.Thread.run(Thread.java:750) ~[na:1.8.0_322]
Caused by: javax.naming.NoInitialContextException: Need to specify class name in environment or system property, or as an applet parameter, or in an application resource file: java.naming.factory.initial
at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:673) ~[na:1.8.0_322]
at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:313) ~[na:1.8.0_322]
at javax.naming.InitialContext.getURLOrDefaultInitCtx(InitialContext.java:350) ~[na:1.8.0_322]
at javax.naming.InitialContext.lookup(InitialContext.java:417) ~[na:1.8.0_322]
… 143 common frames omitted
Dockerfile:
FROM openanalytics/r-shiny
MAINTAINER Tim M.Schendzielorz “tim.schendzielorz@googlemail.com”
ENV JAVA_OPTS “-Xms4G -Xmx8G -Xss2G”
RUN export JAVA_OPTS
ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
RUN export JAVA_HOME
Install Java for rJava
Install OpenJDK-8
RUN apt-get update &&
apt-get install -y default-jdk &&
apt-get install -y default-jre &&
apt-get install -y ant &&
apt-get clean;
Install dependency libraries
RUN apt-get update && apt-get install -y
libxml2-dev
libudunits2-dev
libssh2-1-dev
libcurl4-openssl-dev
libsasl2-dev
libv8-dev
&& rm -rf /var/lib/apt/lists/*
install needed R packages
RUN R -e “install.packages(c(‘tidyverse’, ‘flexdashboard’, ‘knitr’, ‘plotly’, ‘shiny’, ‘rJava’, ‘RJDBC’, ‘dplyr’, ‘readr’, ‘DT’, ‘lubridate’), dependencies = TRUE, repo=‘http://cran.r-project.org’)”
make directory and copy Rmarkdown flexdashboard file in it
RUN mkdir -p /prmc
COPY prmc/PRMC.Rmd /prmc/PRMC.Rmd
COPY prmc/prmc.sql /prmc/prmc.sql
COPY prmc/ojdbc8.jar /prmc/ojdbc8.jar
make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /prmc
expose port on Docker container
EXPOSE 3838
run flexdashboard as localhost and on exposed port in Docker container
CMD [“R”, “-e”, “rmarkdown::run(’/prmc/PRMC.Rmd’, shiny_args = list(port = 3838, host = ‘0.0.0.0’))”]
Application.xml:
proxy:
title: Open Analytics Shiny Proxy
title: SKCC Open Analytics ShinyProxy
logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
logo-url: https://ewebapp01pa.jefferson.edu/includes/images/logo-2014.jpg
landing-page: /
heartbeat-rate: 10000
heartbeat-timeout: 60000
port: 8081
authentication: keycloak
admin-groups: admin
useForwardHeaders: true
Example: ‘simple’ authentication configuration
users:
- name: jack
password: password
groups: scientists, admin
- name: jeff
password: password
groups: mathematicians
keycloak authentication
keycloak:
auth-server-url: https://XX.XXX.XXX.XXX/auth
realm: shinyproxy
public-client: true
resource: shinyproxy
credentials-secret: XXXXXXXXXXXXXXXXXXXXXXXXXX
use-resource-role-mappings: false
Docker configuration
docker:
url: http://localhost:2375
port-range-start: 20000
specs:
- id: 01_hello
display-name: Hello Application
description: Application which demonstrates the basics of a Shiny app
container-cmd: [“R”, “-e”, “shinyproxy::run_01_hello()”]
container-image: openanalytics/shinyproxy-demo
access-groups: [scientists, mathematicians, analyze, admin]
- id: 06_tabsets
display-name: 06_tabsets
description: Application 06_tabsets demonstration
container-cmd: [“R”, “-e”, “shinyproxy::run_06_tabsets()”]
container-image: openanalytics/shinyproxy-demo
access-groups: []
- id: euler
display-name: Euler’s number
container-cmd: [ “R”, “-e”, “shiny::runApp(’/root/euler’)” ]
container-image: openanalytics/shinyproxy-template
access-groups: scientists
- id: prmc
display-name: PRMC
description: PRMC Dashboard
docker-cmd: [“R”, “-e rmarkdown::run(’/prmc/PRMC.Rmd’)”]
container-image: prmc_dashboard
access-groups: [scientists, mathematicians, analyze, admin]
logging:
file:
name: shinyproxy.log
level:
root: DEBUG