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These errors usually mean that you are either converting an app that is referencing a swc via RSL instead of linking it into the codebase. Or it could be a flex app built in debug mode, which If I remember correctly was an issue in the last release of the packager.

Can you be more specific, where do I see "RSL" and if I have swc's there?

I opened my project properties are set to merged into code.  I do not have a debug perspective open - flash perspective only.   I also added to project properties - flex compiler: -compiler.include-libraries

How do I get rid of this error?

Exception in thread "main" java.lang.Error: Unable to find named traits: mx.collections.errors::ItemPendingError
    at adobe.abc.Domain.resolveTypeName(Domain.java:195)
    at adobe.abc.Domain.resolveTypeName(Domain.java:112)
    at adobe.abc.GlobalOptimizer$InputAbc.resolveTypeName(GlobalOptimizer.ja va:274)
    at adobe.abc.GlobalOptimizer$InputAbc.readCode(GlobalOptimizer.java:983)
    at adobe.abc.GlobalOptimizer$InputAbc.readBody(GlobalOptimizer.java:531)
    at adobe.abc.GlobalOptimizer$InputAbc.readAbc(GlobalOptimizer.java:404)
    at adobe.abc.GlobalOptimizer$InputAbc.readAbc(GlobalOptimizer.java:280)
    at adobe.abc.LLVMEmitter.generateBitcode(LLVMEmitter.java:160)
    at com.adobe.air.ipa.AOTCompiler.convertAbcToLlvmBitcode(AOTCompiler.jav a:329)
    at com.adobe.air.ipa.AOTCompiler.GenerateMacBinary(AOTCompiler.java:600)
    at com.adobe.air.ipa.IPAOutputStream.compileRootSwf(IPAOutputStream.java :196)
    at com.adobe.air.ipa.IPAOutputStream.finalizeSig(IPAOutputStream.java:35 5)
    at com.adobe.air.ADTPackager.createPackage(ADTPackager.java:65)
    at com.adobe.air.ipa.IPAPackager.createPackage(IPAPackager.java:165)
    at com.adobe.air.ADTEntrypoint.parseArgsAndGo(ADTEntrypoint.java:132)
    at com.adobe.air.ipa.PFI.parseArgsAndGo(PFI.java:152)
    at com.adobe.air.ADTEntrypoint.run(ADTEntrypoint.java:68)
    at com.adobe.air.ipa.PFI.main(PFI.java:112)

I did finally resolve this - in my case it was not due to the RSL.

The key was how I was compiling.    I was compiling using flash builder, but the secret is to compile using command line.

From this thread: http://forums.adobe.com/thread/731171

Basically you use amxmlc to compile your mxml file created in flash builder.   That creates an swf you can then use PFI builder to create an ipa.

I use the batch files from this page to create the ipa: http://iphoneflashdev.blogspot.com/2010/09/i-promise-this-is-last-post -about-this.html

any issues, more info in this thread:  http://forums.adobe.com/thread/617244

So I create a flex project, AIR, then I add in the required files - icons directory, app.xml, Default.png.    Make sure the application tags are "<s:Application".

From there, use amxmlc to create my swf, then use the batch files via Run->External Tools->...  to create my ipa.

At least in my copy, the RSL settings are correct.