science/afni: Use BUILD_DEPENDS/RUN_DEPENDS instead of LIB_DEPENDS for
math/R, because R may be configured without libR.

While here, fix some stage-qa warnings about indirect dependencies.

Reviewed by: AMDmi3
Approved by: bacon4000@gmail.com (maintainer) swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8649