Since you appear to be working under Unix, how about:
##In a file called test_args.R
args <- commandArgs()
print (args)
which you can run from the shell
cat test_args.R | R --slave --args all your base
which prints
[1] "usr/lib64/R/bin/exec/R" "--slave"
[3] "--args" "all"
[5] "your" "base"
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