Develop Reference

java: Error initializing PCKS11 provider getting IOException C_GetFunctionList == NULL

I'm trying to write a Java application for digitally signing documents using a bit4Id miniLector token.
I'm in a Linux development environment.
The token is correctly installed, I can sign my documents also with the app downloaded from the manufacturer, but I have to write a new one for other purposes. The driver used is located at
/usr/lib/x86_64-linux-gnu/engines-1.1/pkcs11.so
I'm stuck with this error:
/usr/lib/jvm/jdk1.8.0_111/bin/java ...
Exception in thread "main" java.security.ProviderException: Initialization failed
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:376)
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:103)
at com.itextpdf.samples.signatures.chapter02.C2_01_SignHelloWorld.main
(C2_01_SignHelloWorld.java:83)
Caused by: java.io.IOException: ERROR: C_GetFunctionList == NULL
at sun.security.pkcs11.wrapper.PKCS11.connect(Native Method)
at sun.security.pkcs11.wrapper.PKCS11.<init>(PKCS11.java:138)
at sun.security.pkcs11.wrapper.PKCS11.getInstance(PKCS11.java:151)
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:313)
... 2 more
The provider is listed in $JAVA_HOME/jre/lib/security/java.security file as:
security.provider.10=sun.security.pkcs11.SunPKCS11
The code behaving this way is this:
String configFile = "/opt/bar/cfg/pkcs11.cfg";
Provider provider = new sun.security.pkcs11.SunPKCS11(configFile); <-- line 83
The needed libraries are all imported by my IDE and I have no compile/link errors.
I didn't find this exact type of error in hours of googling.
If you need any further information let me know, any kind help is very appreciated, thanks.
For visual clarity I add all missing information with respect to the original question here below
Updates
Content of the pkcs11.cfg file:
$ cat /opt/bar/cfg/pkcs11.cfg
name="bit4id miniLector-EVO"
library=/usr/lib/x86_64-linux-gnu/engines-1.1/pkcs11.so

Ok, I got it.
The problem is the driver.
Replacing
/usr/lib/x86_64-linux-gnu/engines-1.1/pkcs11.so
with
/opt/Firma4NG/System/Firma4NG_Linux/Firma4/drivers/mu-x64/libbit4xpki.so
that is one of the manufacturer's driver, now I can go further and, for example, dumping all info about the card:
Information for provider SunPKCS11-bit4id miniLector-EVO
Library info:
cryptokiVersion: 2.20
manufacturerID: bit4id srl
flags: 0
libraryDescription: bit4id PKCS#11
libraryVersion: 1.02
...
This question can be closed.

Replacement of renderRequest.getParameter("param") in Liferay 7.x

When I'm using below code getting warning that it's deprecated
renderRequest.getParameter("param")
Then I used
renderRequest.getRenderParameters().getValue("param")
as this was suggested by v3.0. But after that getting bellow error at run time
2020-11-19 02:58:02.537 ERROR [http-nio-8080-exec-6][render_portlet_jsp:131] null
java.lang.UnsupportedOperationException: Requires 3.0 opt-in
at com.liferay.portlet.internal.PortletRequestImpl.getRenderParameters(PortletRequestImpl.java:520)
at com.training.portlet.MyPortlet5.doView(MyPortlet5.java:61)
at com.liferay.portal.kernel.portlet.LiferayPortlet.doDispatch(LiferayPortlet.java:303)
at com.liferay.portal.kernel.portlet.bridges.mvc.MVCPortlet.doDispatch(MVCPortlet.java:478)
at javax.portlet.GenericPortlet.render(GenericPortlet.java:291)
at com.liferay.portal.kernel.portlet.bridges.mvc.MVCPortlet.render(MVCPortlet.java:302)
at com.liferay.portlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:127)
at com.liferay.portlet.ScriptDataPortletFilter.doFilter(ScriptDataPortletFilter.java:58)
at com.liferay.portlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:124)
at com.liferay.portal.kernel.portlet.PortletFilterUtil.doFilter(PortletFilterUtil.java:71)
at com.liferay.portal.kernel.servlet.PortletServlet.service(PortletServlet.java:115)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)
at org.eclipse.equinox.http.servlet.internal.registration.EndpointRegistration.service(EndpointRegistration.java:153)
at org.eclipse.equinox.http.servlet.internal.servlet.ResponseStateHandler.processRequest(ResponseStateHandler.java:62)
at org.eclipse.equinox.http.servlet.internal.context.DispatchTargets.doDispatch(DispatchTargets.java:120)
at org.eclipse.equinox.http.servlet.internal.servlet.RequestDispatcherAdaptor.include(RequestDispatcherAdaptor.java:48)
at com.liferay.portlet.internal.InvokerPortletImpl.invoke(InvokerPortletImpl.java:573)
at com.liferay.portlet.internal.InvokerPortletImpl.invokeRender(InvokerPortletImpl.java:670)
at com.liferay.portlet.internal.InvokerPortletImpl.render(InvokerPortletImpl.java:362)
at

This issue was because my portlet module was using portlet API v2.0 by default and getRenderParameters() is available since v3.0. So, when explicitly I mentioned in component class to use v3.0 and did Gradle refresh the issue got fix.
I could fix this issue by adding
"javax.portlet.version=3.0"
in portlet's component class.
#Component(
immediate = true,
property = {
"javax.portlet.version=3.0",
"com.liferay.portlet.display-category=category.app",
"com.liferay.portlet.instanceable=true",
"javax.portlet.init-param.template-path=/",
"javax.portlet.resource-bundle=content.Language",
"javax.portlet.security-role-ref=power-user,user",
"javax.portlet.init-param.view-template=/myportlet5/view.jsp",
"javax.portlet.name=" + MyModuleMainPortletKeys.MY_PORTLET5
},
service = Portlet.class

GraalVM native image with micronaut and aws sdk-v2

I have an issue when building a GraalVM native image using micronaut and aws sdk-v2. Before detailing the error I want to note that before using the sdk-v2 the native image was built correctly.
Once I updated to aws sdk-v2 (via micronaut dependency as):
...
implementation "io.micronaut.aws:micronaut-aws-sdk-v2:2.0.2"
...
I get an error when the trying to built the image
Fatal error:java.lang.NoSuchMethodError
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603)
at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006)
at com.oracle.svm.hosted.NativeImageGenerator.run(NativeImageGenerator.java:480)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.buildImage(NativeImageGeneratorRunner.java:349)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.build(NativeImageGeneratorRunner.java:508)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.main(NativeImageGeneratorRunner.java:114)
at com.oracle.svm.hosted.NativeImageGeneratorRunner$JDK9Plus.main(NativeImageGeneratorRunner.java:537)
Caused by: java.lang.NoSuchMethodError: 'void io.micronaut.core.graal.AutomaticFeatureUtils.initializeAtBuildTime(org.graalvm.nativeimage.hosted.Feature$BeforeAnalysisAccess, java.lang.String)'
at io.micronaut.aws.sdk.v2.graal.AwsSdkAutomaticFeature.beforeAnalysis(AwsSdkAutomaticFeature.java:41)
at com.oracle.svm.hosted.NativeImageGenerator.lambda$runPointsToAnalysis$7(NativeImageGenerator.java:693)
at com.oracle.svm.hosted.FeatureHandler.forEachFeature(FeatureHandler.java:70)
at com.oracle.svm.hosted.NativeImageGenerator.runPointsToAnalysis(NativeImageGenerator.java:693)
at com.oracle.svm.hosted.NativeImageGenerator.doRun(NativeImageGenerator.java:555)
at com.oracle.svm.hosted.NativeImageGenerator.lambda$run$0(NativeImageGenerator.java:468)
at java.base/java.util.concurrent.ForkJoinTask$AdaptedRunnableAction.exec(ForkJoinTask.java:1407)
at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020)
at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656)
at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594)
at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)
Error: Image build request failed with exit status 1
com.oracle.svm.driver.NativeImage$NativeImageError: Image build request failed with exit status 1
at com.oracle.svm.driver.NativeImage.showError(NativeImage.java:1558)
at com.oracle.svm.driver.NativeImage.build(NativeImage.java:1308)
at com.oracle.svm.driver.NativeImage.performBuild(NativeImage.java:1269)
at com.oracle.svm.driver.NativeImage.main(NativeImage.java:1228)
at com.oracle.svm.driver.NativeImage$JDK9Plus.main(NativeImage.java:1740)
...
My assumption was that micronaut must be doing some reflection internally and that is making the build process to fail.
I have added the following json file to set a reflection configuartion
[
{
"name" : "io.micronaut.core.graal.AutomaticFeatureUtils",
"allDeclaredConstructors" : true,
"allPublicConstructors" : true,
"allDeclaredMethods" : true,
"allPublicMethods" : true
},
{
"name":"io.micronaut.core.graal.AutomaticFeatureUtils",
"methods":[{"name":"initializeAtBuildTime","parameterTypes":["org.graalvm.nativeimage.hosted.Feature$BeforeAnalysisAccess","java.lang.String[]"] }]
}
]
However the error persists. Not sure if it is due to the fact that AutomaticFeatureUtils.initializeAtBuildTime is expecting a varargs of strings and however in the stacktrace I can see just one String being passed, or the error is not related to reflection at all.
No matter what I try, that method is not found when building the image.
Any idea on what I may be missing here?
Thanks!!

This error is not related to reflection.
Feature and AutomaticFeature are GraalVM native image concepts that allow programmatic configuration for the native iamge, more details can be found for example in the javadoc: https://github.com/oracle/graal/blob/master/sdk/src/org.graalvm.nativeimage/src/org/graalvm/nativeimage/hosted/Feature.java#L59
The error you show happens during the image generation, this is a normal java process, which doesn't need to have reflection configured etc. Those are the configuration for the runtime behavior.
What the error says is that AwsSdkAutomaticFeature (source tries to call void io.micronaut.core.graal.AutomaticFeatureUtils.initializeAtBuildTime(org.graalvm.nativeimage.hosted.Feature$BeforeAnalysisAccess, java.lang.String) but there's no such method. Most probable cause is the version mismatch between the dependency and the core micronaut library that contain graal support.

beanshell - Deadlock issue

Has anyone got any experience of having deadlocks with beanshell? This is something we have been encountering recently in our production system where script execution is blocking other threads, due to it's lock on classloading via tomcat. The following is the stacktrace for the lock owner in thread dump:
"Thread-64" : 150 : BLOCKED : cpu=37812500000 : cpuLoad= 0.0
BlockedCount:93354 BlockedTime:-1 LockName:java.lang.Object#219d66b6 LockOwnerID:151 LockOwnerName:Thread-65
WaitedCount:13 WaitedTime:-1 InNative:false IsSuspended:false at org.apache.catalina.webresources.AbstractSingleArchiveResourceSet.getArchiveEntries(AbstractSingleArchiveResourceSet.java:66)
at org.apache.catalina.webresources.AbstractArchiveResourceSet.getResource(AbstractArchiveResourceSet.java:262)
at org.apache.catalina.webresources.StandardRoot.getResourceInternal(StandardRoot.java:281)
at org.apache.catalina.webresources.Cache.getResource(Cache.java:62)
at org.apache.catalina.webresources.StandardRoot.getResource(StandardRoot.java:216)
at org.apache.catalina.webresources.StandardRoot.getClassLoaderResource(StandardRoot.java:225)
at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:2173)
at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:811)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1260)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1119)
at java.lang.Class.forName0(Class.java:-2)
at java.lang.Class.forName(Class.java:348)
at bsh.classpath.ClassManagerImpl.classForName(null:-1)
at bsh.NameSpace.classForName(null:-1)
at bsh.NameSpace.getImportedClassImpl(null:-1)
at bsh.NameSpace.getClassImpl(null:-1)
at bsh.NameSpace.getClass(null:-1)
at bsh.Name.consumeNextObjectField(null:-1)
at bsh.Name.toObject(null:-1)
at bsh.BSHAmbiguousName.toObject(null:-1)
at bsh.BSHAmbiguousName.toObject(null:-1)
at bsh.BSHPrimaryExpression.eval(null:-1)
at bsh.BSHPrimaryExpression.eval(null:-1)
at bsh.BSHVariableDeclarator.eval(null:-1)
at bsh.BSHTypedVariableDeclaration.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at my.package.MyClassFile(MyClassFile:2332)
I see that Groovy is a more popular choice for Java scripting, but I haven't seen many posts where it says that bsh can cause deadlocks.
It would be good to get some ideas from SO users.
Regards,

There's a fix for one dead lock in GUI does not start in Java 8 found in Beanshell (almost latest) version 2.0b5.
You can open a new issue in Beanshell project.
It may be connected to ClassManagerImpl:
Bsh has a multi-tiered class loading architecture. No class loader is
created unless/until a class is generated, the classpath is modified,
or a class is reloaded.
Note: we may need some synchronization in here

Changes to a Lotus Domino xpages java application do not propagate to the server

Using Lotus Domino 8.5.2 Fixpack 3
The title sums it up. I have an xpages application that uses java. It seems that any java changes I make, never become visible on the server. It sounds a dead ringer for a cache issue of some kind. The application runs on the server and I see System.out.println statements in the server log, but do not any of the changes I've made to those statements or any new ones I've added.
The code is set to Rebuild Automatically. Still, it never looks like the server sees the changes. Is there some special way I need to build the database (aside from the typical Rebuild All)? Do I need to reset or restart some process on the domino server for it to see the changes?
Any thoughts or ideas would be greatly appreciated.
EDIT 1
I'm returning to this project and, hence, this question. The specific error message I'm getting is:
[6815810:00012-05659] 03/19/2013 09:27:01 HTTP JVM: Managedbean Calendar could not be created Can't instantiate class: 'calendar.CalendarServices'.. java.lang.ClassNotFoundException: class java.lang.ClassNotFoundException: calendar.CalendarServices. For more detailed inform
ation, please consult error-log-0
[6815810:00012-05659] 03/19/2013 09:27:01 HTTP JVM: xml located in /local/notesdata/domino/workspace/logs
[6815810:00012-05659] 03/19/2013 09:27:01 HTTP JVM: com.ibm.xsp.exception.EvaluationExceptionEx: Error while executing JavaScript action expression
I've tried unchecking automatic build and doing a clean --> rebuild all. I've tried signing the nsf again. I've ensured that I'm on the acl. And, as recommended, I've tried the
restart task http
Command via live console. No matter what I do I'm getting this error. The odd thing is that this project is just a copy --> paste (with rename) of another one that works fine. So, the project works...until I change and recompile...
The log that exception above points to wasn't very helpful. It reads:
<CommonBaseEvent creationTime="2013-03-05T09:01:03.254-06:00" globalInstanceId="EL0a04a8b800013d3af27da200000008" msg="Managedbean Calendar could not be created Can&apos;t instantiate class: &apos;calendar.CalendarServices&apos;.. java.lang.ClassNotFoundException: class java.lang.ClassNotFoundException: calendar.CalendarServices" severity="50" version="1.0.1">
<extendedDataElements name="CommonBaseEventLogRecord:level" type="noValue">
<children name="CommonBaseEventLogRecord:name" type="string">
<values>SEVERE</values>
</children>
</extendedDataElements>
<extendedDataElements name="CommonBaseEventLogRecord:sourceClassName" type="string">
<values>com.sun.faces.application.ApplicationAssociate</values>
</extendedDataElements>
<extendedDataElements name="CommonBaseEventLogRecord:sourceMethodName" type="string">
<values>createAndMaybeStoreManagedBeans</values>
</extendedDataElements>
<extendedDataElements name="CommonBaseEventLogRecord:Exception" type="string">
<values>javax.faces.FacesException: Can&apos;t instantiate class: &apos;calendar.CalendarServices&apos;.. java.lang.ClassNotFoundException: class java.lang.ClassNotFoundException: calendar.CalendarServices
at com.sun.faces.config.ManagedBeanFactory.newInstance(ManagedBeanFactory.java:234)
at com.sun.faces.application.ApplicationAssociate.createAndMaybeStoreManagedBeans(ApplicationAssociate.java:291)
at com.sun.faces.el.VariableResolverImpl.resolveVariable(VariableResolverImpl.java:135)
at com.ibm.xsp.el.VariableResolverImpl.resolveVariable(VariableResolverImpl.java:71)
at com.ibm.xsp.javascript.ServerSideLocalObject.resolveVariable(ServerSideLocalObject.java:97)
at com.ibm.xsp.javascript.ServerSideLocalObject.resolveAttribute(ServerSideLocalObject.java:73)
at com.ibm.xsp.javascript.AbstractLocalObject._get(AbstractLocalObject.java:119)
at com.ibm.xsp.javascript.AbstractLocalObject.getPropertyReference(AbstractLocalObject.java:101)
at com</values>
<values>.ibm.jscript.engine.ProgramContext.findGlobalScopeIdentifier(ProgramContext.java:143)
at com.ibm.jscript.engine.ProgramContext.findIdentifier(ProgramContext.java:134)
at com.ibm.jscript.ASTTree.ASTIdentifier.interpret(ASTIdentifier.java:105)
at com.ibm.jscript.ASTTree.ASTMember.interpret(ASTMember.java:106)
at com.ibm.jscript.ASTTree.ASTCall.interpret(ASTCall.java:88)
at com.ibm.jscript.ASTTree.ASTArgumentList.interpretArguments(ASTArgumentList.java:63)
at com.ibm.jscript.types.FBSObject.call(FBSObject.java:153)
at com.ibm.jscript.ASTTree.ASTCall.interpret(ASTCall.java:175)
at com.ibm.jscript.ASTTree.ASTIf.interpret(ASTIf.java:85)
at com.ibm.jscript.ASTTree.ASTTry.interpret(ASTTry.java:109)
at com.ibm.jscript.ASTTree.ASTProgram.interpret(ASTProgram.java:119)
at com.ibm.jscript.ASTTree.ASTProgram.interpretEx(ASTProgram.java:139)
at com.ibm.jscript.JSExpression._interpretExpression(JSExpression.java:435)</values>
<values>
at com.ibm.jscript.JSExpression.access$1(JSExpression.java:424)
at com.ibm.jscript.JSExpression$2.run(JSExpression.java:414)
at java.security.AccessController.doPrivileged(AccessController.java:284)
at com.ibm.jscript.JSExpression.interpretExpression(JSExpression.java:410)
at com.ibm.jscript.JSExpression.evaluateValue(JSExpression.java:251)
at com.ibm.jscript.JSExpression.evaluateValue(JSExpression.java:234)
at com.ibm.xsp.javascript.JavaScriptInterpreter.interpret(JavaScriptInterpreter.java:220)
at com.ibm.xsp.binding.javascript.JavaScriptMethodBinding.invoke(JavaScriptMethodBinding.java:111)
at com.ibm.xsp.component.UIViewRootEx.invokePhaseMethodBinding(UIViewRootEx.java:1705)
at com.ibm.xsp.controller.FacesControllerImpl.invokePhaseMethodBinding(FacesControllerImpl.java:444)
at com.ibm.xsp.controller.FacesControllerImpl.access$0(FacesControllerImpl.java:438)
at com.ibm.xsp.controller.FacesControllerImpl$</values>
<values>ViewPhaseListener.afterPhase(FacesControllerImpl.java:506)
at com.sun.faces.lifecycle.LifecycleImpl.phase(LifecycleImpl.java:218)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:120)
at com.ibm.xsp.controller.FacesControllerImpl.render(FacesControllerImpl.java:264)
at com.ibm.xsp.webapp.FacesServlet.serviceView(FacesServlet.java:219)
at com.ibm.xsp.webapp.FacesServletEx.serviceView(FacesServletEx.java:193)
at com.ibm.xsp.webapp.FacesServlet.service(FacesServlet.java:154)
at com.ibm.xsp.webapp.FacesServletEx.service(FacesServletEx.java:137)
at com.ibm.xsp.webapp.DesignerFacesServlet.service(DesignerFacesServlet.java:86)
at com.ibm.designer.runtime.domino.adapter.ComponentModule.invokeServlet(ComponentModule.java:538)
at com.ibm.domino.xsp.module.nsf.NSFComponentModule.invokeServlet(NSFComponentModule.java:1151)
at com.ibm.designer.runtime.domino.adapter.ComponentModule$AdapterInvoker.invokeServl</values>
<values>et(ComponentModule.java:803)
at com.ibm.designer.runtime.domino.adapter.ComponentModule$ServletInvoker.doService(ComponentModule.java:758)
at com.ibm.designer.runtime.domino.adapter.ComponentModule.doService(ComponentModule.java:527)
at com.ibm.domino.xsp.module.nsf.NSFComponentModule.doService(NSFComponentModule.java:1135)
at com.ibm.domino.xsp.module.nsf.NSFService.doServiceInternal(NSFService.java:523)
at com.ibm.domino.xsp.module.nsf.NSFService.doService(NSFService.java:352)
at com.ibm.designer.runtime.domino.adapter.LCDEnvironment.doService(LCDEnvironment.java:304)
at com.ibm.designer.runtime.domino.adapter.LCDEnvironment.service(LCDEnvironment.java:261)
at com.ibm.domino.xsp.bridge.http.engine.XspCmdManager.service(XspCmdManager.java:291)
Caused by: java.security.PrivilegedActionException: java.lang.ClassNotFoundException: class java.lang.ClassNotFoundException: calendar.CalendarServices
at java.security.AccessController</values>
<values>.doPrivileged(AccessController.java:255)
at com.sun.faces.config.ManagedBeanFactory.newInstance(ManagedBeanFactory.java:216)
... 51 more
Caused by: java.lang.ClassNotFoundException: class java.lang.ClassNotFoundException: calendar.CalendarServices
at java.beans.Beans.instantiate(Beans.java:194)
at java.beans.Beans.instantiate(Beans.java:75)
at com.sun.faces.config.ManagedBeanFactory$1.run(ManagedBeanFactory.java:222)
at java.security.AccessController.doPrivileged(AccessController.java:251)
... 52 more
</values>
</extendedDataElements>
<sourceComponentId component="Expeditor 6.2" componentIdType="ProductName" instanceId="" location="<server here>" locationType="Hostname" subComponent="com.sun.faces.application.ApplicationImpl" threadId="0" componentType="http://www.w3.org/2001/XMLSchema-instance"/>
<situation categoryName="ReportSituation">
<situationType xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ReportSituation" reasoningScope="INTERNAL" reportCategory="LOG"/>
</situation>
</CommonBaseEvent>
As ever, penny for your thoughts.
Also, thank you all for your feedback. I'm sorry I've been away for a bit and neglected this question. I really would like to figure this out.

You didn't mention Project -> Clean so try that first.
I had once similar problem that was caused by an underscore in class or package name.
If the problem exists also for XPages then it's a a general build problem. This can occur at least when developers with different Designer and/or ExtLib versions modify the application. When I had this problem the only way to fix it was to create a new application and copy paste everything there. In our case the other developer never had the problem.

This is just silly. My src folder wasn't on the build path. That was causing all the issues.