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Prepare a 64bit setup.exe from basic msi project Installshield 2009 premier

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I'm deploying 64bit dlls, exes by setting each component's 64bit component = yes and setting "General Information->Summary INformation Stream->Template Summary = x64;1033". All things are ok, but the produced setup.exe when i run it, from task manager i notice its a 32 bit exe. How to make it a 64bit exe?

Why I wanna do it: In custom action i called some methods of managed dll(64bit) and wrote some registries to Software/MyApp, the matter is setup.exe(32bit) loads the dll which eventually writes to Software/Wow6432Node/MyApp. Yes I can replace the dlls with 64bit exes but can't we make the setup.exe a 64bit one?

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The "bit-ness" (e.g. 32-bit or 64-bit) of an exe is determined at compile time. If you have the source code for setup.exe you could recompile, targeting it to a 64-bit platform. Other than recompiling, there really isn't a way to make it 64-bit.