Running
a <- scalaInterpreter("pathtomyjar.jar")
in R is similar to
scala -classpath pathtomyjar.jar
and that's the way to go.
To add several jars, use a vector in R :
a <- scalaInterpreter(c("pathtomyjar1.jar","pathtomyjar2.jar"))
is similar to
scala -classpath pathtomyjar1.jar:pathtomyjar2.jar