Jira make timeout on finding service dependencies after server reboot

[Xarkam]

Hi!

After a reboot server for kernel update, mi JIRA instance cannot restart.

The plugin system give me mass timeout

2016-05-10 16:10:34,425 JIRA-Bootstrap INFO      [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup begun
2016-05-10 16:19:36,935 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.administration.atlassian-admin-quicksearch-jira, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:19:37,146 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira' never resolved service '&sal-app-properties-import' with filter '(objectClass=com.atlassian.sal.api.ApplicationProperties)'
2016-05-10 16:19:37,146 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira' never resolved service '&sal-request-factory-import' with filter '(objectClass=com.atlassian.sal.api.net.RequestFactory)'
2016-05-10 16:19:37,146 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira' never resolved service '&sal-locale-resolver-import' with filter '(objectClass=com.atlassian.sal.api.message.LocaleResolver)'
2016-05-10 16:19:37,146 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira' never resolved service '&sal-i18n-resolver-import' with filter '(objectClass=com.atlassian.sal.api.message.I18nResolver)'
2016-05-10 16:19:37,146 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira' never resolved service '&sal-user-manager-import' with filter '(objectClass=com.atlassian.sal.api.user.UserManager)'
2016-05-10 16:19:37,175 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.administration.atlassian-admin-quicksearch-jira'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.administration.atlassian-admin-quicksearch-jira' has timed out waiting for (|(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.ApplicationProperties))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:37,184 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.administration.atlassian-admin-quicksearch-jira, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.administration.atlassian-admin-quicksearch-jira' has timed out waiting for (|(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.ApplicationProperties))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:37,185 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.administration.atlassian-admin-quicksearch-jira], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.sal.api.ApplicationProperties)] (from bean [&sal-app-properties-import]), Dependency on [(objectClass=com.atlassian.sal.api.net.RequestFactory)] (from bean [&sal-request-factory-import]), Dependency on [(objectClass=com.atlassian.sal.api.message.LocaleResolver)] (from bean [&sal-locale-resolver-import]), Dependency on [(objectClass=com.atlassian.sal.api.message.I18nResolver)] (from bean [&sal-i18n-resolver-import]), Dependency on [(objectClass=com.atlassian.sal.api.user.UserManager)] (from bean [&sal-user-manager-import])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.administration.atlassian-admin-quicksearch-jira' has timed out waiting for (|(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.ApplicationProperties))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:37,186 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.failure-cache-plugin, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:19:46,950 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.atlassian-failure-cache-plugin' never resolved service '&threadLocalDelegateExecutorFactory' with filter '(objectClass=com.atlassian.sal.api.executor.ThreadLocalDelegateExecutorFactory)'
2016-05-10 16:19:46,951 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.atlassian-failure-cache-plugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.failure-cache-plugin' has timed out waiting for (objectClass=com.atlassian.sal.api.executor.ThreadLocalDelegateExecutorFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,951 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.failure-cache-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.failure-cache-plugin' has timed out waiting for (objectClass=com.atlassian.sal.api.executor.ThreadLocalDelegateExecutorFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,971 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.failure-cache-plugin], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.sal.api.executor.ThreadLocalDelegateExecutorFactory)] (from bean [&threadLocalDelegateExecutorFactory])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.failure-cache-plugin' has timed out waiting for (objectClass=com.atlassian.sal.api.executor.ThreadLocalDelegateExecutorFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,972 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:19:46,972 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.templaterenderer.atlassian-template-renderer-velocity1.6-plugin' never resolved service '&templateContextFactory' with filter '(objectClass=com.atlassian.templaterenderer.TemplateContextFactory)'
2016-05-10 16:19:46,972 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.templaterenderer.atlassian-template-renderer-velocity1.6-plugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin' has timed out waiting for (objectClass=com.atlassian.templaterenderer.TemplateContextFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,972 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin' has timed out waiting for (objectClass=com.atlassian.templaterenderer.TemplateContextFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,987 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.templaterenderer.TemplateContextFactory)] (from bean [&templateContextFactory])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-velocity16-plugin' has timed out waiting for (objectClass=com.atlassian.templaterenderer.TemplateContextFactory)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,987 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.templaterenderer.atlassian-template-renderer-api, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:19:46,988 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.templaterenderer.api' never resolved service '&i18nResolver' with filter '(objectClass=com.atlassian.sal.api.message.I18nResolver)'
2016-05-10 16:19:46,988 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.templaterenderer.api'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-api' has timed out waiting for (objectClass=com.atlassian.sal.api.message.I18nResolver)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:46,995 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.templaterenderer.atlassian-template-renderer-api, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-api' has timed out waiting for (objectClass=com.atlassian.sal.api.message.I18nResolver)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:19:47,004 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.templaterenderer.atlassian-template-renderer-api], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.sal.api.message.I18nResolver)] (from bean [&i18nResolver])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.templaterenderer.atlassian-template-renderer-api' has timed out waiting for (objectClass=com.atlassian.sal.api.message.I18nResolver)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,814 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.auiplugin, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:22:19,815 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.auiplugin' never resolved service '&darkFeatureManager' with filter '(objectClass=com.atlassian.sal.api.features.DarkFeatureManager)'
2016-05-10 16:22:19,815 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.auiplugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.auiplugin' has timed out waiting for (objectClass=com.atlassian.sal.api.features.DarkFeatureManager)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,815 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.auiplugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.auiplugin' has timed out waiting for (objectClass=com.atlassian.sal.api.features.DarkFeatureManager)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,821 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.auiplugin], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.sal.api.features.DarkFeatureManager)] (from bean [&darkFeatureManager])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.auiplugin' has timed out waiting for (objectClass=com.atlassian.sal.api.features.DarkFeatureManager)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,822 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.applinks-basicauth-plugin, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&localeResolver' with filter '(objectClass=com.atlassian.sal.api.message.LocaleResolver)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&xsrfTokenValidator' with filter '(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&loginUriProvider' with filter '(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&requestFactory' with filter '(objectClass=com.atlassian.sal.api.net.RequestFactory)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&typeAccessor' with filter '(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&templateRenderer' with filter '(objectClass=com.atlassian.templaterenderer.TemplateRenderer)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&webSudoManager' with filter '(objectClass=com.atlassian.sal.api.websudo.WebSudoManager)'
2016-05-10 16:22:19,822 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&applicationProperties' with filter '(objectClass=com.atlassian.sal.api.ApplicationProperties)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&xsrfTokenAccessor' with filter '(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenAccessor)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&userManager' with filter '(objectClass=com.atlassian.sal.api.user.UserManager)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&jaxbJsonMarshaller' with filter '(objectClass=com.atlassian.plugins.rest.common.json.JaxbJsonMarshaller)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&authenticationConfigurationManager' with filter '(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&i18nResolver' with filter '(objectClass=com.atlassian.sal.api.message.I18nResolver)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&applicationLinkService' with filter '(objectClass=com.atlassian.applinks.api.ApplicationLinkService)'
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.applinks.applinks-basicauth-plugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.applinks.applinks-basicauth-plugin' has timed out waiting for (|(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)(objectClass=com.atlassian.applinks.api.ApplicationLinkService)(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.websudo.WebSudoManager)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenAccessor)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)(objectClass=com.atlassian.sal.api.ApplicationProperties)(objectClass=com.atlassian.templaterenderer.TemplateRenderer)(objectClass=com.atlassian.plugins.rest.common.json.JaxbJsonMarshaller))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,823 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.applinks-basicauth-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.applinks.applinks-basicauth-plugin' has timed out waiting for (|(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)(objectClass=com.atlassian.applinks.api.ApplicationLinkService)(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.websudo.WebSudoManager)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenAccessor)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)(objectClass=com.atlassian.sal.api.ApplicationProperties)(objectClass=com.atlassian.templaterenderer.TemplateRenderer)(objectClass=com.atlassian.plugins.rest.common.json.JaxbJsonMarshaller))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,887 Spring DM Context Creation Timer ERROR      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Unable to create application context for [com.atlassian.applinks.applinks-basicauth-plugin], unsatisfied dependencies: Dependency on [(objectClass=com.atlassian.sal.api.message.LocaleResolver)] (from bean [&localeResolver]), Dependency on [(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)] (from bean [&xsrfTokenValidator]), Dependency on [(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)] (from bean [&loginUriProvider]), Dependency on [(objectClass=com.atlassian.sal.api.net.RequestFactory)] (from bean [&requestFactory]), Dependency on [(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)] (from bean [&typeAccessor]), Dependency on [(objectClass=com.atlassian.templaterenderer.TemplateRenderer)] (from bean [&templateRenderer]), Dependency on [(objectClass=com.atlassian.sal.api.websudo.WebSudoManager)] (from bean [&webSudoManager]), Dependency on [(objectClass=com.atlassian.sal.api.ApplicationProperties)] (from bean [&applicationProperties]), Dependency on [(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenAccessor)] (from bean [&xsrfTokenAccessor]), Dependency on [(objectClass=com.atlassian.sal.api.user.UserManager)] (from bean [&userManager]), Dependency on [(objectClass=com.atlassian.plugins.rest.common.json.JaxbJsonMarshaller)] (from bean [&jaxbJsonMarshaller]), Dependency on [(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)] (from bean [&authenticationConfigurationManager]), Dependency on [(objectClass=com.atlassian.sal.api.message.I18nResolver)] (from bean [&i18nResolver]), Dependency on [(objectClass=com.atlassian.applinks.api.ApplicationLinkService)] (from bean [&applicationLinkService])
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.applinks.applinks-basicauth-plugin' has timed out waiting for (|(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)(objectClass=com.atlassian.applinks.api.ApplicationLinkService)(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)(objectClass=com.atlassian.sal.api.net.RequestFactory)(objectClass=com.atlassian.sal.api.message.I18nResolver)(objectClass=com.atlassian.sal.api.message.LocaleResolver)(objectClass=com.atlassian.sal.api.websudo.WebSudoManager)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenAccessor)(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)(objectClass=com.atlassian.sal.api.user.UserManager)(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)(objectClass=com.atlassian.sal.api.ApplicationProperties)(objectClass=com.atlassian.templaterenderer.TemplateRenderer)(objectClass=com.atlassian.plugins.rest.common.json.JaxbJsonMarshaller))
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
        at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
2016-05-10 16:22:19,887 Spring DM Context Creation Timer WARN      [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.applinks-cors-plugin, config=osgibundle:/META-INF/spring/*.xml)]
2016-05-10 16:22:19,888 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&localeResolver' with filter '(objectClass=com.atlassian.sal.api.message.LocaleResolver)'
2016-05-10 16:22:19,888 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&xsrfTokenValidator' with filter '(objectClass=com.atlassian.sal.api.xsrf.XsrfTokenValidator)'
2016-05-10 16:22:19,888 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&loginUriProvider' with filter '(objectClass=com.atlassian.sal.api.auth.LoginUriProvider)'
2016-05-10 16:22:19,888 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&requestFactory' with filter '(objectClass=com.atlassian.sal.api.net.RequestFactory)'
2016-05-10 16:22:19,888 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&typeAccessor' with filter '(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)'
2016-05-10 16:22:19,889 Spring DM Context Creation Timer ERROR      [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-cors-plugin' never resolved service '&templateRenderer' with filter '(objectClass=com.atlassian.templaterenderer.TemplateRenderer)'

I have no idea what causes this problem.

And I suspect the same problem with my other instance of confluence and Bitbucket server.
I have no acces to jira. 

Any help is welcome.

ps.: I have not others errors in my logs.

[Xarkam · Accepted solution]

Hi, after a complete shutdown and restart of my server, all my Atlassian applications running normaly.