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Install4J version unpacking fails

We are using Install4J version for creating an installer. During install, install4j throws the below exception during unpacking. Because of this the jar files bundled is getting extracted partially (size and cheksum both doesn't match) and the application is not working.
How to debug this issue ?
I started install with the flag
-Dinstall4j.debug=true -Dinstall4j.logToStderr=true
but it's not giving much information and we use Java 8 and Ubuntu
java.io.IOException: null ref
at com.sun.java.util.jar.pack.NativeUnpack.getNextFile(Native Method)
at com.sun.java.util.jar.pack.NativeUnpack.run(NativeUnpack.java:215)
at com.sun.java.util.jar.pack.NativeUnpack.run(NativeUnpack.java:247)
at com.sun.java.util.jar.pack.UnpackerImpl.unpack(UnpackerImpl.java:138)
at com.sun.java.util.jar.pack.UnpackerImpl.unpack(UnpackerImpl.java:174)
at com.install4j.runtime.installer.helper.Unpacker.unpack(Unpacker.java:55)
at com.install4j.runtime.installer.InstallerContextImpl.unpackAdditionalUserFiles(InstallerContextImpl.java:265)
at com.install4j.runtime.installer.InstallerContextImpl.checkStart(InstallerContextImpl.java:230)
at com.install4j.runtime.installer.controller.Controller.start(Controller.java:59)
at com.install4j.runtime.installer.Installer.runInProcess(Installer.java:41)
at com.install4j.runtime.installer.Installer.main(Installer.java:28)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)
[INFO] com.install4j.runtime.beans.actions.misc.RequestPrivilegesAction [ID 13]: Execute action

The Pack200 decompression fails for one of the JAR files in the "Installer->Custom Code & Resources" list.
You may need to unjar it and jar it again.
Contact support#ej-technologies.com for a build that prints the name of the file where the unpacking fails.

SonarQube analysis of Java module fails in Jenkins

I have created a Jenkins project to run SonarQube analysis of my product code. The workspace contains multiple modules (some in Nodejs i.e. Javascript) and some in Java. My sonar properties looks like
sonar.projectKey=product-key
sonar.projectName=product-name
sonar.projectVersion=1.0
sonar.sources=./nodejsmodule1,./nodejsmodule2
sonar.sourceEncoding=UTF-8
This works perfectly without issue and gives me a nice SonarQube dashboard. However, if I change the sonar.sources property to:
sonar.sources=./nodejsmodule1,./nodejsmodule2,./java-module-name/src/main/java
the Jenkins build fails with the following error:
ERROR: Error during Sonar runner execution
org.sonar.runner.impl.RunnerException: Unable to execute Sonar
at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:91)
at org.sonar.runner.impl.BatchLauncher$1.run(BatchLauncher.java:75)
at java.security.AccessController.doPrivileged(Native Method)
at org.sonar.runner.impl.BatchLauncher.doExecute(BatchLauncher.java:69)
at org.sonar.runner.impl.BatchLauncher.execute(BatchLauncher.java:50)
at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:102)
at org.sonar.runner.api.Runner.execute(Runner.java:100)
at org.sonar.runner.Main.executeTask(Main.java:70)
at org.sonar.runner.Main.execute(Main.java:59)
at org.sonar.runner.Main.main(Main.java:53)
Caused by: java.lang.NoSuchMethodError: org.sonar.api.resources.Project.getPom()Lorg/apache/maven/project/MavenProject;
at org.sonar.plugins.surefire.api.SurefireUtils.getReportsDirectoryFromPluginConfiguration(SurefireUtils.java:56)
at org.sonar.plugins.surefire.api.SurefireUtils.getReportsDirectory(SurefireUtils.java:39)
at org.sonar.plugins.surefire.SurefireSensor.analyse(SurefireSensor.java:63)
at org.sonar.batch.phases.SensorsExecutor.executeSensor(SensorsExecutor.java:58)
at org.sonar.batch.phases.SensorsExecutor.execute(SensorsExecutor.java:50)
at org.sonar.batch.phases.PhaseExecutor.execute(PhaseExecutor.java:98)
at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:192)
at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:100)
at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:85)
at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:258)
at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:253)
at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:243)
at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:100)
at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:85)
at org.sonar.batch.bootstrap.GlobalContainer.executeAnalysis(GlobalContainer.java:153)
at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:110)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:76)
at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:87)
... 9 more
When I use
sonar.sources=./nodejsmodule1,./nodejsmodule2,./java-module-name/pom.xml
The error goes away. The multi-language analysis happens. The events widget on the SonarQube dashboard for the project shows that Java and JavaScript profiles got used during the analysis. But the code analysis results don't contain anything about Java. JavaScript analysis results show up. Doesn't matter in which order I specify the sonar.sources values (i.e. JavaScript followed by Java or Java followed by JavaScript). I looked at other StackOverflow questions (e.g. Sonar analysing Maven 3 and multi language project using JENKINS). Clearly, they are specifying the location of the classes file as well. Maybe the java code is getting compiled during the Jenkins build step for SonarQube analysis so they can point to the target/classes location. When I try this (i.e. sonar.binaries=./java-module-name/target/classes), the build fails.
Based on http://docs.sonarqube.org/display/SONAR/Analyzing+with+SonarQube+Scanner+for+Maven#AnalyzingwithSonarQubeScannerforMaven-AnalyzingaMulti-languageProject, I also tried sonar.sources=./java-module-name/src,./java-module-name/pom.xml. But that brings back the exception. The exception also happens for sonar.sources=./java-module-name,./java-module-name/pom.xml, sonar.sources=./java-module-name/src/main,./java-module-name/pom.xml and sonar.sources=./java-module-name/src/main/java,./java-module-name/pom.xml.
What am I doing wrong?

The error only shows up when you include Java sources? So maybe you are using some outdated plugins on your 5.2, which are triggered on Java analysis and use the no longer available getPom() method.
org.sonar.api.resources.Project.getPom() is no longer available in SQ 5.2.
See Project.class in 5.2
The stacktrace points to surefire. Which version are you using?

Tomcat8 & waffle integeration

We are currently using waffle for authenticating our web based application build using java/j2ee. We are in the process of migrating the application to use Tomcat 8.We were initially using java 6 & tomcat 6 and the authentication worked fine. Now after the migration to java 8 & tomcat 8, We are unable to load the login page of the application. Im getting the below error.
org.apache.tomcat.util.digester.Digester startElement
SEVERE: Begin event threw error
java.lang.NoSuchFieldError: FQN
at waffle.apache.WaffleAuthenticatorBase.<init>(WaffleAuthenticatorBase.java:44)
at waffle.apache.MixedAuthenticator.<init>(MixedAuthenticator.java:45)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
Im currently using waffle-tomcat8-1.7.3.jar file for the authentication.Please help us in resolving this issue. Any help on this is much appreciated.

Make sure you include all dependencies for Waffle:
Package Waffle JARs, including waffle-jna.jar, guava-18.0.jar,
jna-4.1.0.jar, jna-platform-4.1.0.jar, slf4j*.jar and
waffle-tomcat-6.jar in the application's lib directory or copy them to
Tomcat's lib.
https://github.com/dblock/waffle/blob/master/Docs/tomcat/TomcatSingleSignOnValve.md
Did you try also the newer 1.8 release?
http://mvnrepository.com/artifact/com.github.dblock.waffle/waffle-tomcat8/1.8.0

java newrelic agent throwing classnotfound exception

I am trying to install newrelic on a linux machine with tomcat 7. This installation does not have a catalina.sh so cannot use the newrelic installer.
I tried the manula approach of adding the newrelic.jar to the javaagent like:
CATALINA_OPTS="$CATALINA_OPTS -javaagent:/usr/share/tomcat7/newrelic/newrelic.jar"
But whenever I start the tomcat I get the following classnotfoundexception:
Unable to start New Relic agent: javax.xml.transform.TransformerFactoryConfigurationError: Provider org.apache.xalan.processor.TransformerFactoryImpl not found
javax.xml.transform.TransformerFactoryConfigurationError: Provider org.apache.xalan.processor.TransformerFactoryImpl not found
at javax.xml.transform.TransformerFactory.newInstance(TransformerFactory.java:106)
at com.newrelic.agent.extension.dom.ExtensionDomParser.getTransformerFactory(ExtensionDomParser.java:360)
at com.newrelic.agent.extension.dom.ExtensionDomParser.fixNamespace(ExtensionDomParser.java:337)
at com.newrelic.agent.extension.dom.ExtensionDomParser.parseDocument(ExtensionDomParser.java:167)
at com.newrelic.agent.extension.dom.ExtensionDomParser.readFile(ExtensionDomParser.java:152)
at com.newrelic.agent.extension.ExtensionParsers$3.parse(ExtensionParsers.java:46)
at com.newrelic.agent.extension.JarExtension.<init>(JarExtension.java:59)
at com.newrelic.agent.extension.JarExtension.<init>(JarExtension.java:104)
at com.newrelic.agent.extension.ExtensionService.initializeBuiltInExtensions(ExtensionService.java:388)
at com.newrelic.agent.extension.ExtensionService.doStart(ExtensionService.java:145)
at com.newrelic.agent.service.AbstractService.start(AbstractService.java:54)
at com.newrelic.agent.service.ServiceManagerImpl.doStart(ServiceManagerImpl.java:124)
at com.newrelic.agent.service.AbstractService.start(AbstractService.java:54)
at com.newrelic.agent.Agent.premain(Agent.java:208)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:622)
at com.newrelic.bootstrap.BootstrapAgent.premain(BootstrapAgent.java:117)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:622)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(InstrumentationImpl.java:343)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(InstrumentationImpl.java:358)
Caused by: java.lang.ClassNotFoundException: org/apache/xalan/processor/TransformerFactoryImpl
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:270)
at javax.xml.transform.FactoryFinder.getProviderClass(FactoryFinder.java:124)
at javax.xml.transform.FactoryFinder.newInstance(FactoryFinder.java:179)
I have tried everything I could for this, but nothing works. I have even added the xalan jar manually to the tomcat lib but no luck

You need to make sure you have xalan.jar installed. If it is installed, it may be in the wrong place. You probably need it at the container level, here is a blog post that discusses this issue (tomcat5 but most of the advice should still apply).
http://doookstechstuff.blogspot.com/2010/04/how-to-fix-tomcat5-on-rhel5.html

Make sure that the location where you put the xalan.jar is in the classpath and that the user account you're running tomcat under has access to it. If you have dropped it in the tomcat /lib folder make sure the perms for the .jar file match the other objects in the folder.
Let us know if this helps. If you need additional information it might be best to create a ticket with New Relic Support (http://support.newrelic.com).

Error running ADF Morena application?

I develop an application in ADF. Scanning documents using Morena 6. When I test on my PC everything works ok but when I switch on the GlassFish application server and start scanning the document I receive an error.
Caused by: java.lang.UnsatisfiedLinkError: SK.gnome.twain.TwainManager.listSources()[LSK/gnome/twain/TwainSource;
at SK.gnome.twain.TwainManager.listSources(Native Method)
at SK.gnome.twain.TwainManager.selectSource(TwainManager.java:163)
at beans.ImageBean.skenirajDokument(ImageBean.java:571)

Could it be that your Morena jar file is not cross platform? http://docs.oracle.com/javase/7/docs/api/java/lang/UnsatisfiedLinkError.html