Hi Tiago,

This is one of those cases when you have to declare the header files to 
add_library(...) as well. In that case AUTOMOC should work fine. At least it 
does for us, in a very similar setup.

http://acode-browser.usatlas.bnl.gov/lxr/source/atlas/graphics/VP1/VP1Gui/CMakeLists.txt

Cheers,
            Attila

> On 11 May 2016, at 07:14, Tiago Macarios <tiagomacar...@gmail.com> wrote:
> 
> Hi,
> 
> I am having trouble using AUTOMOC with a project where header files and 
> source files are in different sub-directories. I wrote a detailed stack 
> overflow question here:
> http://stackoverflow.com/questions/37151163/cmake-automoc-with-files-on-different-folders
> and would really appreciate if someone could give me a couple of ideas to try 
> out.
> 
> Thanks,
> Tiago
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