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sage: s = sin(x)
sage: f(x) = s
sage: f
x |--> sin(x)

No deprecation warning! What's going on here is that s(x) was really trying to evaluate your symbolic expression s at the point x - which happened to be a variable, but is still deprecated. If you use the transitive property, the above is just saying

sage: f(x) = sin(x)

which is what you want, as opposed to

sage: f(x) = sin(x)(x)

in your first attempt, which is perhaps ambiguous.