That's not a compile error, that's just a warning and should not stop the compilation. MyPaint is really a very well-contained package, without much hassle. Make sure you apt-get all requirements mentioned in the INSTALL file (usually this means getting -dev versions, I think you also need python2.x-dev package) before running scons.
MyPaint saves files in OpenRaster format, the next open-source image format. GIMP does not support this out of the box, but there is a neat plugin (created by the MyPaint team) that allows you to import openraster in GIMP. Then you get layer support. Without it you have to export to GIMP as PNG.
I sketch, ink and paint in MyPaint all the time before moving to GIMP for tuning, so for me it works very well - but it's of course always a matter of taste.
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Griatch