A fatal error occured during initialisation. JIRA has been locked. com.atlassian.jira.InfrastructureException: Error occurred while starting Plugin Manager. Unable to install bundle

[Perfit IT]

I have upgrade JIRA from 6.4 to 7.0 I followed exactly the documentation but I can not get JIRA to startup.

BTW I have tried most of the solution of tickets that have similar error no luck. please I need help thanks

here is the log of catalina.out file:

A fatal error occured during initialisation. JIRA has been locked.
com.atlassian.jira.InfrastructureException: Error occurred while starting Plugin Manager. Unable to install bundle
at com.atlassian.jira.ComponentManager$PluginSystem.start(ComponentManager.java:685)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:196)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:168)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:35)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$175(DefaultJiraLauncher.java:136)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$14/180980507.run(Unknown Source)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:356)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:226)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:126)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$173(DefaultJiraLauncher.java:92)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$1/497718868.run(Unknown Source)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:34)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:90)
at com.atlassian.jira.startup.LauncherContextListener.contextInitialized(LauncherContextListener.java:84)
... 5 filtered
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to install bundle
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.installBundle(FelixOsgiContainerManager.java:585)
at com.atlassian.plugin.osgi.factory.OsgiPluginUninstalledHelper.install(OsgiPluginUninstalledHelper.java:49)
at com.atlassian.plugin.osgi.factory.OsgiPlugin.installInternal(OsgiPlugin.java:386)
at com.atlassian.plugin.impl.AbstractPlugin.install(AbstractPlugin.java:502)
at com.atlassian.plugin.manager.DefaultPluginManager.addPlugins(DefaultPluginManager.java:1175)
at com.atlassian.jira.plugin.JiraPluginManager.earlyStartup(JiraPluginManager.java:112)
at com.atlassian.jira.plugin.JiraPluginManager.start(JiraPluginManager.java:100)
at com.atlassian.jira.ComponentManager$PluginSystem.start(ComponentManager.java:675)
... 22 more
Caused by: org.osgi.framework.BundleException: Could not create bundle object.
at org.apache.felix.framework.Felix.installBundle(Felix.java:2952)
at org.apache.felix.framework.BundleContextImpl.installBundle(BundleContextImpl.java:165)
at org.apache.felix.framework.BundleContextImpl.installBundle(BundleContextImpl.java:138)
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager$BundleRegistration.install(FelixOsgiContainerManager.java:767)
at com.atlassian.plugin.osgi.container.felix.FelixOsgiContainerManager.installBundle(FelixOsgiContainerManager.java:581)
Caused by: java.lang.IllegalArgumentException: Unable to parse header: com.atlassian.greenhopper.api.*;resolution:optional
at org.apache.felix.framework.util.manifestparser.ManifestParser.parseStandardHeader(ManifestParser.java:1734)
at org.apache.felix.framework.util.manifestparser.ManifestParser.<init>(ManifestParser.java:170)
at org.apache.felix.framework.BundleRevisionImpl.<init>(BundleRevisionImpl.java:118)
at org.apache.felix.framework.BundleImpl.createRevision(BundleImpl.java:1199)
at org.apache.felix.framework.BundleImpl.<init>(BundleImpl.java:96)
... 34 more
2016-06-16 09:36:48,838 localhost-startStop-1 INFO [c.a.jira.upgrade.ConsistencyCheckImpl] Checking JIRA consistency
2016-06-16 09:36:48,861 localhost-startStop-1 ERROR [c.a.jira.upgrade.ConsistencyCheckImpl] An error occurred during the consistency check
java.lang.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:638)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:129)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.getServices(ConsistencyCheckImpl.java:175)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.ensureSingleService(ConsistencyCheckImpl.java:521)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkMailListenerAndService(ConsistencyCheckImpl.java:381)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkDataConsistency(ConsistencyCheckImpl.java:229)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.checkConsistency(ConsistencyCheckImpl.java:218)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.initialise(ConsistencyCheckImpl.java:182)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$175(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$14/180980507.run(Unknown Source)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:356)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:226)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:126)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$173(DefaultJiraLauncher.java:92)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$1/497718868.run(Unknown Source)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:34)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:90)
at com.atlassian.jira.startup.LauncherContextListener.contextInitialized(LauncherContextListener.java:84)
... 5 filtered
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2016-06-16 09:36:52,256 localhost-startStop-1 ERROR [c.a.jira.startup.JiraStartupLogger] Cannnot obtain JIRA system information
java.lang.IllegalStateException: It is illegal to call the ServiceManager before all components are loaded. Please use interface com.atlassian.jira.extension.Startable to get notified when JIRA has started.
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:638)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:129)
at com.atlassian.jira.startup.JiraSystemInfo.obtainServices(JiraSystemInfo.java:611)
at com.atlassian.jira.startup.JiraStartupLogger.printStartedMessage(JiraStartupLogger.java:149)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.printJIRAStartupMessage(ConsistencyCheckImpl.java:198)
at com.atlassian.jira.upgrade.ConsistencyCheckImpl.initialise(ConsistencyCheckImpl.java:186)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$175(DefaultJiraLauncher.java:137)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$14/180980507.run(Unknown Source)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:356)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:226)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:126)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$173(DefaultJiraLauncher.java:92)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$1/497718868.run(Unknown Source)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:34)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:90)
at com.atlassian.jira.startup.LauncherContextListener.contextInitialized(LauncherContextListener.java:84)
... 5 filtered
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2016-06-16 09:36:52,268 localhost-startStop-1 INFO [c.a.jira.startup.JiraStartupLogger]

**********************************************************************************
JIRA 7.0.0 build: 70107 started. You can now access JIRA through your web browser.
**********************************************************************************

2016-06-16 09:36:52,426 localhost-startStop-1 WARN [c.a.jira.startup.JiraStartupLogger]

********************************************************************************************************************************************************************************************************
WARNING: JIRA's brute force password protection is not enabled. You should have <elevatedsecurityguard class="com.atlassian.jira.security.login.JiraElevatedSecurityGuard"/> in seraph-config.xml. Not having this configuration can cause known security risks. For more information please see https://confluence.atlassian.com/display/JIRA/.
********************************************************************************************************************************************************************************************************
<elevatedsecurityguard class="com.atlassian.jira.security.login.JiraElevatedSecurityGuard"/>
2016-06-16 09:36:52,469 localhost-startStop-1 ERROR [c.a.jira.upgrade.UpgradeLauncher] Skipping, JIRA is locked.
2016-06-16 09:36:52,471 localhost-startStop-1 INFO [c.a.jira.scheduler.JiraSchedulerLauncher] JIRA Scheduler not started: JIRA startup checklist failed.
2016-06-16 09:36:53,636 localhost-startStop-1 ERROR [c.a.j.s.services.analytics.JiraStartStopAnalyticHelper] Error trying to grab analytics from [com.atlassian.jira.service.services.analytics.start.WorkflowAnalyticTask]
java.lang.NullPointerException
at com.atlassian.jira.workflow.DefaultWorkflowSchemeManager.getActiveWorkflowNames(DefaultWorkflowSchemeManager.java:457)
at com.atlassian.jira.workflow.OSWorkflowManager.getSchemeActiveWorkflows(OSWorkflowManager.java:189)
at com.atlassian.jira.workflow.OSWorkflowManager.getActiveWorkflows(OSWorkflowManager.java:171)
at com.atlassian.jira.service.services.analytics.start.WorkflowAnalyticTask.getAnalytics(WorkflowAnalyticTask.java:40)
at com.atlassian.jira.service.services.analytics.JiraStartStopAnalyticHelper.getOnStartUsageStats(JiraStartStopAnalyticHelper.java:50)
at com.atlassian.jira.startup.AnalyticsLauncher.start(AnalyticsLauncher.java:30)
at com.atlassian.jira.startup.ActiveServicesLauncher.start(ActiveServicesLauncher.java:63)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$175(DefaultJiraLauncher.java:140)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$14/180980507.run(Unknown Source)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:356)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:226)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:126)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$173(DefaultJiraLauncher.java:92)
at com.atlassian.jira.startup.DefaultJiraLauncher$$Lambda$1/497718868.run(Unknown Source)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:34)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:90)
at com.atlassian.jira.startup.LauncherContextListener.contextInitialized(LauncherContextListener.java:84)
... 5 filtered
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2016-06-16 09:36:54,457 localhost-startStop-1 INFO [c.a.j.index.ha.DefaultIndexRecoveryManager] Latest index date: {2016-06-15 23:48:04}, Latest DB date: {2016-06-15 23:48:04}
2016-06-16 09:36:58,676 localhost-startStop-1 INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 426 MiB. Committed: 1187 MiB. Max: 2474 MiB
Non-heap memory : Used: 112 MiB. Committed: 114 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 538 MiB. Committed: 1301 MiB. Max: 3738 MiB
---------------------------------------------------------------------------------
2016-06-16 09:36:59,088 localhost-startStop-1 ERROR [c.a.j.web.dispatcher.JiraWebworkActionDispatcher]

******************************************
JIRA startup failed, JIRA has been locked.
******************************************

[crf]

Reading through the log, I see two separate problem reports.  The first is that it had trouble reading one of the plugin bundle manifests:

Caused by: java.lang.IllegalArgumentException: Unable to parse header: com.atlassian.greenhopper.api.*;resolution:optional
at org.apache.felix.framework.util.manifestparser.ManifestParser.parseStandardHeader(ManifestParser.java:1734)

This looks like somebody tried to include import instructions in the plugin's manifest but didn't specify the actual header or that the indentation in the manifest isn't correct (the rules for how they have to be indented are pretty strange).  Maybe this is a custom plugin?  I can't tell for certain from the information here.  Maybe there is an earlier error in the logs that will tell you which one?

The second error is the one that actually locked JIRA and it looks to be a race condition during the system startup, where components have been initialized in an unexpected order that isn't tolerated well.  However, this may just be a side-effect of the unexpected failure initializing the plugin that was reported above.

1. If you really are trying 7.0.0, you probably shouldn't be.  It almost always makes sense to use the latest bugfix release in preference to the .0, as we may have found and fixed important bugs that it introduced.
2. Something like this which involves troubleshooting logs and upgrade failures is usually best handled with a Support Request.

[Nic Brough -Adaptavist-]

At a glance, it mentions "greenhopper" - could this be the result of an attempt to upgrade from 6 to 7 where the GH/Agile add-on for 6.x was copied into the plugins directory of a "JIRA 7 Core" installation, instead of upgrading to JIRA 7 Software?

(Just a thought, haven't tried it myself, although I have seen someone forcibly install the Agile add-on in 7 and then complain that it doesn't work...)

[crf]

Possibly.  Another data point not visible to you is that a customer reported seeing this exact stack trace with Portfolio as the apparent culprit.  Either way, contacting support is probably the best action to take for stack traces / locking during an upgrade attempt.

[Nic Brough -Adaptavist-]

Interesting, I'll try to keep that in mind!

I know that an add-on appearing to be the cause is not always the right pointer - add-on X could be reporting all the errors and lead us to think it's that, but the errors may be because add-on Y is doing bad things and causing X to fail.  This is a flaw in the way programming languages build and report things rather than a coding error.

But, yes, reach for support if this happens, they're very helpful.

[Yogesh Mude[Jira]]

try to delete .lock file from  JIRA Home directory and restart again.

[crf]

JIRA being "locked" has nothing to do with a lock file.  It has to do with JIRA locking users out to prevent any additional damage when it detects that something has gone seriously wrong.

[Nic Brough -Adaptavist-]

Very true - I've seen this a couple of times.

JIRA fails to start, and tells you about the lock file.  If you stop it, fix the root problem and restart it, it works.  If you remove the lock file and restart it, it can quite easily damage your database.

Never remove a lock file until you know exactly why it was put there and made it safe.