StackOverFlowError when using SAXReader after Java security update - java

Running a Mac (OS X 10.8.1). We were upgraded to the latest Java security update 1.6.0_35-b10-428 and since then our main app doesn't launch in Eclipse.
The Exception below is thrown when starting up Openfire 3.6.4. Pretty much where the openfire.xml config is parsed is when the error occurs:
private void buildDoc(Reader in) throws IOException {
try {
SAXReader xmlReader = new SAXReader();
xmlReader.setEncoding("UTF-8");
document = xmlReader.read(in);
}
catch (Exception e) {
Log.error("Error reading XML properties", e);
System.out.println("NOOO");
e.printStackTrace();
throw new IOException(e.getMessage());
}
finally {
if (in != null) {
in.close();
}
}
}
Exception thrown:
Exception in thread "main" java.lang.StackOverflowError
at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:52)
at java.nio.ByteBuffer.wrap(ByteBuffer.java:350)
at java.nio.ByteBuffer.wrap(ByteBuffer.java:373)
at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:237)
at java.lang.StringCoding.encode(StringCoding.java:272)
at java.lang.String.getBytes(String.java:946)
at java.io.UnixFileSystem.getBooleanAttributes0(Native Method)
at java.io.UnixFileSystem.getBooleanAttributes(UnixFileSystem.java:228)
at java.io.File.exists(File.java:733)
at sun.misc.URLClassPath$FileLoader.getResource(URLClassPath.java:999)
at sun.misc.URLClassPath.getResource(URLClassPath.java:169)
at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at org.dom4j.DocumentFactory.createDocument(DocumentFactory.java:102)
at org.dom4j.DocumentFactory.createDocument(DocumentFactory.java:122)
at org.dom4j.io.SAXContentHandler.createDocument(SAXContentHandler.java:830)
at org.dom4j.io.SAXContentHandler.getDocument(SAXContentHandler.java:164)
at org.dom4j.io.SAXContentHandler.comment(SAXContentHandler.java:428)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.comment(AbstractSAXParser.java:667)
at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.comment(XMLDTDValidator.java:978)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:479)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
at org.dom4j.io.SAXReader.read(SAXReader.java:465)
at org.dom4j.io.SAXReader.read(SAXReader.java:365)
at org.jivesoftware.util.XMLProperties.buildDoc(XMLProperties.java:471)
at org.jivesoftware.util.XMLProperties.<init>(XMLProperties.java:114)
at org.jivesoftware.util.XMLProperties.<init>(XMLProperties.java:63)
at org.jivesoftware.util.JiveGlobals.loadSetupProperties(JiveGlobals.java:832)
at org.jivesoftware.util.JiveGlobals.getXMLProperty(JiveGlobals.java:282)
at org.jivesoftware.util.JiveGlobals.isSetupMode(JiveGlobals.java:791)
at org.jivesoftware.util.JiveGlobals.getProperty(JiveGlobals.java:529)
at org.jivesoftware.openfire.XMPPServer.initialize(XMPPServer.java:300)
at org.jivesoftware.openfire.XMPPServer.start(XMPPServer.java:419)
at org.jivesoftware.openfire.XMPPServer.<init>(XMPPServer.java:163)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at java.lang.Class.newInstance0(Class.java:355)
at java.lang.Class.newInstance(Class.java:308)
at org.jivesoftware.openfire.starter.ServerStarter.start(ServerStarter.java:106)
at org.jivesoftware.openfire.starter.ServerStarter.main(ServerStarter.java:51)
Edit: Added Xss1m as suggested, but whilst the application got further I'm seeing the same error. Here's my startup args:
here's my startup args:
-DopenfireHome="${workspace_loc:openfire}/target/openfire" -Djava.net.preferIPv4Stack=true -Xms32m -Xmx512m -Xss1m -XX:ThreadStackSize=128 -XX:PermSize=72m -XX:MaxPermSize=96m -XX:+PrintGCDetails -Xloggc:/tmp/gc.log -XX:+HeapDumpOnOutOfMemoryError
Edit2:
Seems the below amendments work:
amending -Xss128k to -Xss1m and removing -XX:ThreadStackSize=128


Did you try increasing stack size? You can do it by specifying -Xss1m when starting JVM. In the example JVM will allocate 1 Megabyte for stack for each thread. Be careful not to use too big a value as it will be multiplied by the number of threads in your application.
To change configuration in Eclipse, please follow these steps (copied from here).
Open the Run Configuration for your application (Run/Run Configurations..., then look for the applications entry in 'Java application').
The arguments tab has a text box Vm arguments, enter -Xss1m (or a bigger parameter for the maximum stack size). The default value is 512 kByte.
EDIT:
It looks like it's a common issue. Security patch probably introduced another method call to the chain and all projects that used to fit into the stack don't fit anymore.

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I think that is a classpath issue.
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See
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I used Intellij Idea 12 Community edition. I am trying to create test case for my class by creating test case. When i run my test case it says
java.lang.NoClassDefFoundError: org/hamcrest/SelfDescribing
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at org.junit.internal.builders.JUnit4Builder.runnerForClass(JUnit4Builder.java:10)
at org.junit.runners.model.RunnerBuilder.safeRunnerForClass(RunnerBuilder.java:59)
at org.junit.internal.builders.AllDefaultPossibilitiesBuilder.runnerForClass(AllDefaultPossibilitiesBuilder.java:26)
at org.junit.runners.model.RunnerBuilder.safeRunnerForClass(RunnerBuilder.java:59)
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at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:63)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:120)
Caused by: java.lang.ClassNotFoundException: org.hamcrest.SelfDescribing
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 25 more
How would i run test case in Intellij. I included the junit4.11 jar file to my module

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add junit.jar to your project dependence.
you may also need to add hamcrest.jar in addition.
Open File->Project Structure,Click Modules->Dependences,add junit.jar.

Latest version of hamcrest-all is available at:
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If you come across this (and a few other threads) on this error and adding the jar to dependencies doesn't work, you will need to add to the general java classpath.
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Adding all the hamcrest jars to Library/Java/Extensions finally fixed the problem when nothing else would.

Having issues trying to run a standalone Java 6 program which is packaged in a war file and deployed under tomcat 7

The issue is that when I run it via Eclipse Juno by clicking on it and "Run as Java Application" it works,
but it needs to be to run in a Linux shell script or at least from the Linux shell.
I need it to append all the jar files from $CATALINA_HOME/webapps/myapp/WEB-INF/lib to my classpath.
Here's my code:
package com.myapp.client;
public class ClientApp {
public static void main(String args[]) {
System.out.println("Hi Client");
}
}
When I cd into $CATALINA_HOME/webapps/myapp/WEB-INF/classes/com/myapp/client issue the following command:
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I receive this exception:
Exception in thread "main" java.lang.NoClassDefFoundError: ClientApp (wrong name: com/myapp/client/ClientApp)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: ClientApp. Program will exit
When I go to my home dir (/home/devuser) and type this in, it still doesn't work:
java -classpath "/home/devuser/DevTools/apache-tomcat-7.0.32/webapps/myapp/WEB-INF/lib/*:." $CATALINA_HOME/webapps/myapp/WEB-INF/classes/com.myapp.ClientApp
Exception in thread "main" java.lang.NoClassDefFoundError: /home/devuser/DevTools/apache-tomcat-7/0/32/webapps/myapp/WEB-INF/classes/com/myapp/ClientApp
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at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: /home/devuser/DevTools/apache-tomcat-7.0.32/webapps/myapp/WEB-INF/classes/com.myapp.ClientApp. Program will exit.
Thank you for taking the time to read this... Would appreciate it if someone could assist me.

All of your libraries and classes need to be in your classpath, then the next argument is the path to your class.
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java.lang.StackOverflowError
at java.util.Vector.addElement(Vector.java:572)
at java.lang.ClassLoader.addClass(ClassLoader.java:166)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at org.apache.cxf.bus.spring.SpringBusFactory.createBus(SpringBusFactory.java:102)
at org.apache.cxf.bus.spring.SpringBusFactory.createBus(SpringBusFactory.java:91)
at org.apache.cxf.bus.spring.SpringBusFactory.createBus(SpringBusFactory.java:69)
at org.apache.cxf.bus.spring.SpringBusFactory.createBus(SpringBusFactory.java:58)
at org.apache.cxf.BusFactory.getDefaultBus(BusFactory.java:99)
at org.apache.cxf.BusFactory.createThreadBus(BusFactory.java:165)
at org.apache.cxf.BusFactory.getThreadDefaultBus(BusFactory.java:155)
at org.apache.cxf.BusFactory.getThreadDefaultBus(BusFactory.java:140)
at org.apache.cxf.endpoint.AbstractEndpointFactory.getBus(AbstractEndpointFactory.java:83)
at org.apache.cxf.jaxrs.AbstractJAXRSFactoryBean.getBus(AbstractJAXRSFactoryBean.java:89)
at org.apache.cxf.jaxrs.AbstractJAXRSFactoryBean.createEndpointInfo(AbstractJAXRSFactoryBean.java:133)
at org.apache.cxf.jaxrs.AbstractJAXRSFactoryBean.createEndpoint(AbstractJAXRSFactoryBean.java:216)
at org.apache.cxf.jaxrs.client.JAXRSClientFactoryBean.createWebClient(JAXRSClientFactoryBean.java:195)
at org.apache.cxf.jaxrs.client.WebClient.create(WebClient.java:90)

It turns out that the threads on my production environment have been configured with a very small stack size, so there genuinely is not enough space to do the recursive class loading. D'oh.

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