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Nexus orientdb can't load jna library #5

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bhamail opened this issue Dec 22, 2019 · 0 comments
Open

Nexus orientdb can't load jna library #5

bhamail opened this issue Dec 22, 2019 · 0 comments

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@bhamail
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bhamail commented Dec 22, 2019 •
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I've seen error messages like the one below when running recent versions of Nexus Repository Manager on a raspberrypi:

2019-12-22 13:57:24,722-0500 WARN  [jetty-main-1]  *SYSTEM org.sonatype.nexus.features.internal.FeaturesWrapper - Problem starting reference:file:system/net/java/dev/jna/jna-platform/4.5.0/jna-platform-4.5.0.jar
org.osgi.framework.BundleException: Unable to resolve com.sun.jna.platform [197](R 197.0): missing requirement [com.sun.jna.platform [197](R 197.0)] osgi.wiring.bundle; (&(osgi.wiring.bundle=com.sun.jna)(bundle-version>=4.5.0)) [caused by: Unable to resolve com.sun.jna [13](R 13.0): missing requirement [com.sun.jna [13](R 13.0)] osgi.native; (|(&(osgi.native.osname~=win32)(osgi.native.processor~=x86))(&(osgi.native.osname~=win32)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=win)(osgi.native.processor~=x86))(&(osgi.native.osname~=win)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=wince)(osgi.native.processor~=arm))(&(osgi.native.osname~=sunos)(osgi.native.processor~=x86))(&(osgi.native.osname~=sunos)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=sunos)(osgi.native.processor~=sparc))(&(osgi.native.osname~=sunos)(osgi.native.processor~=sparcv9))(&(osgi.native.osname~=aix)(osgi.native.processor~=ppc))(&(osgi.native.osname~=aix)(osgi.native.processor~=ppc64))(&(osgi.native.osname~=linux)(osgi.native.processor~=ppc))(&(osgi.native.osname~=linux)(osgi.native.processor~=ppc64))(&(osgi.native.osname~=linux)(osgi.native.processor~=ppc64le))(&(osgi.native.osname~=linux)(osgi.native.processor~=x86))(&(osgi.native.osname~=linux)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=linux)(osgi.native.processor~=arm))(&(osgi.native.osname~=linux)(osgi.native.processor~=armel))(&(osgi.native.osname~=linux)(osgi.native.processor~=aarch64))(&(osgi.native.osname~=linux)(osgi.native.processor~=ia64))(&(osgi.native.osname~=linux)(osgi.native.processor~=sparcv9))(&(osgi.native.osname~=linux)(osgi.native.processor~=mips64el))(&(osgi.native.osname~=linux)(osgi.native.processor~=s390x))(&(osgi.native.osname~=freebsd)(osgi.native.processor~=x86))(&(osgi.native.osname~=freebsd)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=openbsd)(osgi.native.processor~=x86))(&(osgi.native.osname~=openbsd)(osgi.native.processor~=x86-64))(&(osgi.native.osname~=macosx)(|(osgi.native.processor~=x86)(osgi.native.processor~=x86-64)(osgi.native.processor~=ppc))))] Unresolved requirements: [[com.sun.jna.platform [197](R 197.0)] osgi.wiring.bundle; (&(osgi.wiring.bundle=com.sun.jna)(bundle-version>=4.5.0))]
	at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4149)
	at org.apache.felix.framework.Felix.startBundle(Felix.java:2119)
	at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:998)
	at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:984)
	at org.sonatype.nexus.features.internal.FeaturesWrapper.startBundle(FeaturesWrapper.java:260)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at org.sonatype.nexus.features.internal.FeaturesWrapper.fastInstallFeature(FeaturesWrapper.java:184)
	at org.sonatype.nexus.features.internal.FeaturesWrapper.invoke(FeaturesWrapper.java:128)
	at com.sun.proxy.$Proxy1.installFeatures(Unknown Source)
	at org.sonatype.nexus.bootstrap.osgi.BootstrapListener.installNexusEdition(BootstrapListener.java:271)
	at org.sonatype.nexus.bootstrap.osgi.BootstrapListener.contextInitialized(BootstrapListener.java:125)
	at org.eclipse.jetty.server.handler.ContextHandler.callContextInitialized(ContextHandler.java:957)
	at org.eclipse.jetty.servlet.ServletContextHandler.callContextInitialized(ServletContextHandler.java:553)
	at org.eclipse.jetty.server.handler.ContextHandler.startContext(ContextHandler.java:922)
	at org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:365)
	at org.eclipse.jetty.webapp.WebAppContext.startWebapp(WebAppContext.java:1497)
	at org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1459)
	at org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:852)
	at org.eclipse.jetty.servlet.ServletContextHandler.doStart(ServletContextHandler.java:278)
	at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:545)
	at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:167)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:110)
	at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
	at com.codahale.metrics.jetty9.InstrumentedHandler.doStart(InstrumentedHandler.java:101)
	at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:167)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:119)
	at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
	at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:167)
	at org.eclipse.jetty.server.Server.start(Server.java:418)
	at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:110)
	at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
	at org.eclipse.jetty.server.Server.doStart(Server.java:382)
	at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
	at org.sonatype.nexus.bootstrap.jetty.JettyServer$JettyMainThread.run(JettyServer.java:274)

And eventually Nexus Repository Manager fails to start, logging an error like this:

2019-12-22 13:58:38,364-0500 ERROR [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseServerImpl - Failed transition: NEW -> STARTED
java.lang.reflect.InvocationTargetException: null
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:45)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:77)
	at com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
	at org.sonatype.nexus.internal.orient.DatabaseServerImpl$$EnhancerByGuice$$71c8a538.start(<generated>)
	at org.sonatype.nexus.internal.orient.OrientBootstrap.doStart(OrientBootstrap.java:78)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.internal.orient.OrientBootstrap$$EnhancerByGuice$$221620cd.CGLIB$start$4(<generated>)
	at org.sonatype.nexus.internal.orient.OrientBootstrap$$EnhancerByGuice$$221620cd$$FastClassByGuice$$c04bff7f.invoke(<generated>)
	at com.google.inject.internal.cglib.proxy.$MethodProxy.invokeSuper(MethodProxy.java:228)
	at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:76)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:77)
	at com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
	at org.sonatype.nexus.internal.orient.OrientBootstrap$$EnhancerByGuice$$221620cd.start(<generated>)
	at org.sonatype.nexus.extender.NexusLifecycleManager.startComponent(NexusLifecycleManager.java:199)
	at org.sonatype.nexus.extender.NexusLifecycleManager.to(NexusLifecycleManager.java:111)
	at org.sonatype.nexus.extender.NexusContextListener.moveToPhase(NexusContextListener.java:312)
	at org.sonatype.nexus.extender.NexusContextListener.frameworkEvent(NexusContextListener.java:209)
	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1431)
	at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoClassDefFoundError: com/sun/jna/Platform
	at com.orientechnologies.common.jna.ONative.instance(ONative.java:30)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaultDiskCacheSize(OMemoryAndLocalPaginatedEnginesInitializer.java:167)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaults(OMemoryAndLocalPaginatedEnginesInitializer.java:77)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.initialize(OMemoryAndLocalPaginatedEnginesInitializer.java:62)
	at com.orientechnologies.orient.core.engine.local.OEngineLocalPaginated.startup(OEngineLocalPaginated.java:56)
	at com.orientechnologies.orient.core.Orient.startEngine(Orient.java:930)
	at com.orientechnologies.orient.core.Orient.loadStorage(Orient.java:523)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:173)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:154)
	at com.orientechnologies.orient.server.OSystemDatabase.init(OSystemDatabase.java:151)
	at com.orientechnologies.orient.server.OSystemDatabase.<init>(OSystemDatabase.java:44)
	at com.orientechnologies.orient.server.OServer.initSystemDatabase(OServer.java:1309)
	at com.orientechnologies.orient.server.OServer.activate(OServer.java:367)
	at org.sonatype.nexus.internal.orient.DatabaseServerImpl.doStart(DatabaseServerImpl.java:202)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at org.sonatype.nexus.internal.orient.OrientBootstrap.doStart(OrientBootstrap.java:78)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	... 7 common frames omitted
Caused by: java.lang.ClassNotFoundException: com.sun.jna.Platform not found by com.orientechnologies.orientdb-core [196]
	at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1639)
	at org.apache.felix.framework.BundleWiringImpl.access$200(BundleWiringImpl.java:80)
	at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:2053)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 30 common frames omitted
2019-12-22 13:58:38,378-0500 ERROR [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.OrientBootstrap - Failed transition: NEW -> STARTED
java.lang.reflect.InvocationTargetException: null
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:45)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:77)
	at com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55)
	at org.sonatype.nexus.internal.orient.OrientBootstrap$$EnhancerByGuice$$221620cd.start(<generated>)
	at org.sonatype.nexus.extender.NexusLifecycleManager.startComponent(NexusLifecycleManager.java:199)
	at org.sonatype.nexus.extender.NexusLifecycleManager.to(NexusLifecycleManager.java:111)
	at org.sonatype.nexus.extender.NexusContextListener.moveToPhase(NexusContextListener.java:312)
	at org.sonatype.nexus.extender.NexusContextListener.frameworkEvent(NexusContextListener.java:209)
	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1431)
	at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoClassDefFoundError: com/sun/jna/Platform
	at com.orientechnologies.common.jna.ONative.instance(ONative.java:30)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaultDiskCacheSize(OMemoryAndLocalPaginatedEnginesInitializer.java:167)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaults(OMemoryAndLocalPaginatedEnginesInitializer.java:77)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.initialize(OMemoryAndLocalPaginatedEnginesInitializer.java:62)
	at com.orientechnologies.orient.core.engine.local.OEngineLocalPaginated.startup(OEngineLocalPaginated.java:56)
	at com.orientechnologies.orient.core.Orient.startEngine(Orient.java:930)
	at com.orientechnologies.orient.core.Orient.loadStorage(Orient.java:523)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:173)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:154)
	at com.orientechnologies.orient.server.OSystemDatabase.init(OSystemDatabase.java:151)
	at com.orientechnologies.orient.server.OSystemDatabase.<init>(OSystemDatabase.java:44)
	at com.orientechnologies.orient.server.OServer.initSystemDatabase(OServer.java:1309)
	at com.orientechnologies.orient.server.OServer.activate(OServer.java:367)
	at org.sonatype.nexus.internal.orient.DatabaseServerImpl.doStart(DatabaseServerImpl.java:202)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at org.sonatype.nexus.internal.orient.OrientBootstrap.doStart(OrientBootstrap.java:78)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	... 7 common frames omitted
Caused by: java.lang.ClassNotFoundException: com.sun.jna.Platform not found by com.orientechnologies.orientdb-core [196]
	at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1639)
	at org.apache.felix.framework.BundleWiringImpl.access$200(BundleWiringImpl.java:80)
	at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:2053)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 30 common frames omitted
2019-12-22 13:58:38,383-0500 ERROR [FelixStartLevel]  *SYSTEM Felix - Framework listener delivery error.
java.lang.NoClassDefFoundError: com/sun/jna/Platform
	at com.orientechnologies.common.jna.ONative.instance(ONative.java:30)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaultDiskCacheSize(OMemoryAndLocalPaginatedEnginesInitializer.java:167)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.configureDefaults(OMemoryAndLocalPaginatedEnginesInitializer.java:77)
	at com.orientechnologies.orient.core.engine.OMemoryAndLocalPaginatedEnginesInitializer.initialize(OMemoryAndLocalPaginatedEnginesInitializer.java:62)
	at com.orientechnologies.orient.core.engine.local.OEngineLocalPaginated.startup(OEngineLocalPaginated.java:56)
	at com.orientechnologies.orient.core.Orient.startEngine(Orient.java:930)
	at com.orientechnologies.orient.core.Orient.loadStorage(Orient.java:523)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:173)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.<init>(ODatabaseDocumentTx.java:154)
	at com.orientechnologies.orient.server.OSystemDatabase.init(OSystemDatabase.java:151)
	at com.orientechnologies.orient.server.OSystemDatabase.<init>(OSystemDatabase.java:44)
	at com.orientechnologies.orient.server.OServer.initSystemDatabase(OServer.java:1309)
	at com.orientechnologies.orient.server.OServer.activate(OServer.java:367)
	at org.sonatype.nexus.internal.orient.DatabaseServerImpl.doStart(DatabaseServerImpl.java:202)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at org.sonatype.nexus.internal.orient.OrientBootstrap.doStart(OrientBootstrap.java:78)
	at org.sonatype.nexus.common.stateguard.StateGuardLifecycleSupport.start(StateGuardLifecycleSupport.java:67)
	at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
	at org.sonatype.nexus.common.stateguard.StateGuard$TransitionImpl.run(StateGuard.java:193)
	at org.sonatype.nexus.common.stateguard.TransitionsInterceptor.invoke(TransitionsInterceptor.java:56)
	at org.sonatype.nexus.extender.NexusLifecycleManager.startComponent(NexusLifecycleManager.java:199)
	at org.sonatype.nexus.extender.NexusLifecycleManager.to(NexusLifecycleManager.java:111)
	at org.sonatype.nexus.extender.NexusContextListener.moveToPhase(NexusContextListener.java:312)
	at org.sonatype.nexus.extender.NexusContextListener.frameworkEvent(NexusContextListener.java:209)
	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1431)
	at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: com.sun.jna.Platform not found by com.orientechnologies.orientdb-core [196]
	at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1639)
	at org.apache.felix.framework.BundleWiringImpl.access$200(BundleWiringImpl.java:80)
	at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:2053)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 30 common frames omitted

I think this is because the native arm library is missing from this version of jna.
One workaround that appears to help is to download a newer version of jna, and add the directory with the jna jars to the endorse dirs path. For example:

  1. Download jna jars to a new folder: /opt/sonatype/jna/
    I made the jars executable just in case, but I'm not sure that is needed, or even if the jan-platform.jar is needed.
/opt/sonatype/jna $ ls -alh
total 4.1M
drwxr-xr-x 2 root root 4.0K Dec 22 13:41 .
drwxr-xr-x 5 root root 4.0K Dec 22 13:38 ..
-rwxr-xr-x 1 root root 1.5M Oct 30 12:37 jna-5.5.0.jar
-rwxr-xr-x 1 root root 2.6M Oct 30 12:38 jna-platform-5.5.0.jar
  1. Edit the Nexus config to include this new directory in the endorsed dirs list:
cat /opt/sonatype/nexus3/bin/nexus.vmoptions

-Xms350m
-Xmx350m
-XX:MaxDirectMemorySize=350m
-XX:+UnlockDiagnosticVMOptions
-XX:+LogVMOutput
-XX:LogFile=/opt/sonatype/sonatype-work/nexus3/log/jvm.log
-XX:-OmitStackTraceInFastThrow
-Djava.net.preferIPv4Stack=true
-Dkaraf.home=.
-Dkaraf.base=.
-Dkaraf.etc=etc/karaf
-Djava.util.logging.config.file=etc/karaf/java.util.logging.properties
-Dkaraf.data=/opt/sonatype/sonatype-work/nexus3
-Dkaraf.log=/opt/sonatype/sonatype-work/nexus3/log
-Djava.io.tmpdir=/opt/sonatype/sonatype-work/nexus3/tmp
-Dkaraf.startLocalConsole=false
#
# additional vmoptions needed for Java9+
#
# --add-reads=java.xml=java.logging
# --add-exports=java.base/org.apache.karaf.specs.locator=java.xml,ALL-UNNAMED
# --patch-module=java.base=lib/endorsed/org.apache.karaf.specs.locator-4.2.6.jar
# --patch-module=java.xml=lib/endorsed/org.apache.karaf.specs.java.xml-4.2.6.jar
# --add-opens=java.base/java.security=ALL-UNNAMED
# --add-opens=java.base/java.net=ALL-UNNAMED
# --add-opens=java.base/java.lang=ALL-UNNAMED
# --add-opens=java.base/java.util=ALL-UNNAMED
# --add-opens=java.naming/javax.naming.spi=ALL-UNNAMED
# --add-opens=java.rmi/sun.rmi.transport.tcp=ALL-UNNAMED
# --add-exports=java.base/sun.net.www.protocol.http=ALL-UNNAMED
# --add-exports=java.base/sun.net.www.protocol.https=ALL-UNNAMED
# --add-exports=java.base/sun.net.www.protocol.jar=ALL-UNNAMED
# --add-exports=jdk.xml.dom/org.w3c.dom.html=ALL-UNNAMED
# --add-exports=jdk.naming.rmi/com.sun.jndi.url.rmi=ALL-UNNAMED
#
# comment out this vmoption when using Java9+
#
#-Djava.endorsed.dirs=lib/endorsed
-Djava.endorsed.dirs=lib/endorsed:/opt/sonatype/jna
  1. Stop and restart Nexus Repository Manager

The Setup instructions: Step 3 have been updated to reflect the need for a newer jna version. Please follow those steps.
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@bhamail