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This unfortunately seems to be a problem with ANTS Profiler 4. It has to do with the way NUnit shadow copies the assemblies, which means we have issues finding the pdbs. We'll be looking into it for an upcoming patch release.
For the time being, an easy workaround is to turn off 'Enable shadow copying' in Tools->Options in the NUnit GUI runner UI. Then the pdbs stay-put, and we can line-level profile fine.
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I am profiling the NUnit GUI runner (2.4.8) that is running a test in my assembly. My assemblies are compiled against .NET 3.5. Ants 3 does not have a problem profiling this exact setup at the line level.