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Startup Errors

Chris Woelkers - NOAA Affiliate
I have an installation of Geonetwork on CentOS.
It starts fine but gives a few errors and I am wondering what they mean.

Here is the relevant output from journalctl.

Jan 09 20:00:16 crow2 systemd[1]: Started Apache Tomcat Web
Application Container.
Jan 09 20:00:16 crow2 systemd[1]: Starting Apache Tomcat Web
Application Container...
Jan 09 20:00:16 crow2 server[369]: Java virtual machine used:
/usr/lib/jvm/jre/bin/java
Jan 09 20:00:16 crow2 server[369]: classpath used:
/usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar
Jan 09 20:00:16 crow2 server[369]: main class used:
org.apache.catalina.startup.Bootstrap
Jan 09 20:00:16 crow2 server[369]: flags used:
Jan 09 20:00:16 crow2 server[369]: options used:
-Dcatalina.base=/var/lib/tomcats/geonetwork
-Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs=
-Djava.io.tmpdir=/var/cache/tomcat/temp
-Djava.util.logging.config.file=/var/lib/tomcats/geonetwork/conf/log
Jan 09 20:00:16 crow2 server[369]: arguments used: start
Jan 09 20:00:16 crow2 server[369]: Jan 09, 2017 8:00:16 PM
org.apache.catalina.core.AprLifecycleListener init
Jan 09 20:00:16 crow2 server[369]: INFO: The APR based Apache Tomcat
Native library which allows optimal performance in production
environments was not found on the java.library.path:
/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.coyote.AbstractProtocol init
Jan 09 20:00:17 crow2 server[369]: INFO: Initializing ProtocolHandler
["http-bio-8080"]
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.coyote.AbstractProtocol init
Jan 09 20:00:17 crow2 server[369]: INFO: Initializing ProtocolHandler
["ajp-bio-8009"]
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.startup.Catalina load
Jan 09 20:00:17 crow2 server[369]: INFO: Initialization processed in 447 ms
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.core.StandardService startInternal
Jan 09 20:00:17 crow2 server[369]: INFO: Starting service Catalina
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.core.StandardEngine startInternal
Jan 09 20:00:17 crow2 server[369]: INFO: Starting Servlet Engine:
Apache Tomcat/7.0.54
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.startup.HostConfig deployWAR
Jan 09 20:00:17 crow2 server[369]: INFO: Deploying web application
archive /var/lib/tomcats/geonetwork/webapps/geonetwork.war
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.loader.WebappClassLoader validateJarFile
Jan 09 20:00:17 crow2 server[369]: INFO:
validateJarFile(/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar)
- jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending
class: javax/servlet/Servlet.class
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.loader.WebappClassLoader validateJarFile
Jan 09 20:00:17 crow2 server[369]: INFO:
validateJarFile(/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/lib/javax.servlet-api-3.1.0.jar)
- jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending
class: javax/servlet/Servlet.class
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.loader.WebappClassLoader validateJarFile
Jan 09 20:00:17 crow2 server[369]: INFO:
validateJarFile(/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/lib/jsp-api-2.1-6.1.14.jar)
- jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending
class: javax/el/Expression.class
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.loader.WebappClassLoader validateJarFile
Jan 09 20:00:17 crow2 server[369]: INFO:
validateJarFile(/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/lib/servlet-api-2.5-20081211.jar)
- jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending
class: javax/servlet/Servlet.class
Jan 09 20:00:17 crow2 server[369]: Jan 09, 2017 8:00:17 PM
org.apache.catalina.loader.WebappClassLoader validateJarFile
Jan 09 20:00:17 crow2 server[369]: INFO:
validateJarFile(/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/lib/servlet-api-2.5-6.1.14.jar)
- jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending
class: javax/servlet/Servlet.class
Jan 09 20:00:33 crow2 server[369]: Jan 09, 2017 8:00:33 PM
org.apache.catalina.core.ApplicationContext log
Jan 09 20:00:33 crow2 server[369]: INFO: No Spring
WebApplicationInitializer types detected on classpath
Jan 09 20:00:46 crow2 server[369]: 2017-01-09 20:00:46,818 ERROR
[org.hibernate.tool.hbm2ddl.SchemaUpdate] - HHH000299: Could not
complete schema update
Jan 09 20:00:46 crow2 server[369]: java.lang.NullPointerException
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.tool.hbm2ddl.DatabaseMetadata.getTableMetadata(DatabaseMetadata.java:158)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.cfg.Configuration.generateSchemaUpdateScriptList(Configuration.java:1202)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:212)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:178)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:522)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:850)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:843)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.boot.registry.classloading.internal.ClassLoaderServiceImpl.withTccl(ClassLoaderServiceImpl.java:398)
Jan 09 20:00:46 crow2 server[369]: at
org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:842)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:60)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:343)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:318)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1637)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1574)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1054)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:829)
Jan 09 20:00:46 crow2 server[369]: at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:538)
Jan 09 20:00:46 crow2 server[369]: at
jeeves.config.springutil.JeevesContextLoaderListener.contextInitialized(JeevesContextLoaderListener.java:111)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4973)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5467)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1083)
Jan 09 20:00:46 crow2 server[369]: at
org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1880)
Jan 09 20:00:46 crow2 server[369]: at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
Jan 09 20:00:46 crow2 server[369]: at
java.util.concurrent.FutureTask.run(FutureTask.java:266)
Jan 09 20:00:46 crow2 server[369]: at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
Jan 09 20:00:46 crow2 server[369]: at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
Jan 09 20:00:46 crow2 server[369]: at java.lang.Thread.run(Thread.java:745)
Jan 09 20:01:08 crow2 server[369]: 2017-01-09 20:01:08,132 WARN
[geonetwork.data.directory] -     - Data directory properties is not
set. Use geonetwork.dir or geonetwork.dir properties.
Jan 09 20:01:08 crow2 server[369]: 2017-01-09 20:01:08,132 WARN
[geonetwork.data.directory] -     - Data directory provided could not
be used. Using default location:
/var/lib/tomcats/geonetwork/webapps/geonetwork/WEB-INF/data
Jan 09 20:01:09 crow2 server[369]: 2017-01-09 20:01:09,200 WARN
[geonetwork.schemamanager] - Cannot resolve
http://www.w3.org/2001/xml.xsd: will append last component to current
path (not sure it will help though!)
Jan 09 20:01:09 crow2 server[369]: 2017-01-09 20:01:09,665 WARN
[geonetwork.schemamanager] - WARNING: gco:Record is a global element
without a type - assuming a string
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,231 WARN
[geonetwork.schemamanager] - WARNING: gco:Record is a global element
without a type - assuming a string
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,396 WARN
[geonetwork.schemamanager] - WARNING: gco:Record is a global element
without a type - assuming a string
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,402 WARN
[geonetwork.schemamanager] - WARNING: schema-substitutions.xml has
wiped out XSD substitution list for gml:VerticalDatum
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,405 WARN
[geonetwork.schemamanager] - WARNING: schema-substitutions.xml has
wiped out XSD substitution list for gml:CoordinateSystemAxis
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,406 WARN
[geonetwork.schemamanager] - WARNING: schema-substitutions.xml has
wiped out XSD substitution list for gml:VerticalCS
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,409 WARN
[geonetwork.schemamanager] - WARNING: schema-substitutions.xml has
wiped out XSD substitution list for gml:CoordinateSystemAxis
Jan 09 20:01:11 crow2 server[369]: 2017-01-09 20:01:11,764 WARN
[geonetwork.schemamanager] - Cannot resolve
http://www.w3.org/2001/03/xml.xsd: will append last component to
current path (not sure it will help though!)
Jan 09 20:01:14 crow2 server[369]: 2017-01-09 20:01:14,312 WARN
[geonetwork.lucene] - Stopwords file with incorrect ISO 639-2 language
as filename: README
Jan 09 20:01:17 crow2 server[369]: Jan 09, 2017 8:01:17 PM
org.apache.catalina.core.ApplicationContext log
Jan 09 20:01:17 crow2 server[369]: INFO: Initializing Spring
FrameworkServlet 'spring'
Jan 09 20:01:25 crow2 server[369]: Jan 09, 2017 8:01:25 PM
org.apache.catalina.startup.HostConfig deployWAR
Jan 09 20:01:25 crow2 server[369]: INFO: Deployment of web application
archive /var/lib/tomcats/geonetwork/webapps/geonetwork.war has
finished in 68,634 ms
Jan 09 20:01:25 crow2 server[369]: Jan 09, 2017 8:01:25 PM
org.apache.coyote.AbstractProtocol start
Jan 09 20:01:25 crow2 server[369]: INFO: Starting ProtocolHandler
["http-bio-8080"]
Jan 09 20:01:25 crow2 server[369]: Jan 09, 2017 8:01:25 PM
org.apache.coyote.AbstractProtocol start
Jan 09 20:01:25 crow2 server[369]: INFO: Starting ProtocolHandler
["ajp-bio-8009"]
Jan 09 20:01:25 crow2 server[369]: Jan 09, 2017 8:01:25 PM
org.apache.catalina.startup.Catalina start
Jan 09 20:01:25 crow2 server[369]: INFO: Server startup in 68740 ms
Jan 09 20:03:56 crow2 server[369]: 2017-01-09 20:03:56,786 WARN
[geonetwork.resources] - Resource not found images/logos/favicon.png,
default resource returned: /images/logos/favicon.png
Jan 09 20:03:56 crow2 server[369]: 2017-01-09 20:03:56,792 WARN
[geonetwork.resources] - Resource not found images/logos/favicon.png,
default resource returned: /images/logos/favicon.png
Jan 09 20:03:57 crow2 server[369]: 2017-01-09 20:03:57,288 WARN
[geonetwork.thesaurus] - No thesaurus found for concept scheme
http://geonetwork-opensource.org/inspire-theme (lang=eng)

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