That way it works:
[...]
###########
set(COMPILE_OPTIONS_VALA ${COMPILE_OPTIONS_VALA} -D USE_APPINDICATOR)
set(PACKAGES_VALA ${PACKAGES_VALA} "appindicator3-0.1")
###########
include(ValaPrecompile)
vala_precompile(VALA_C
src/Calm.vala
src/CalmApp.vala
src/CalmWindow.vala
PACKAGES
gtk+-3.0
gstreamer-0.10
gstreamer-audio-0.10
appindicator3-0.1
CUSTOM_VAPIS
vapi/config.vapi
OPTIONS
--thread
)
[...]