I do a lot of scripting in R, and with ggplot2 and bioconductor; there is so much one can achieve. Pipelining was surely a issue, so we built a tool to do just that (http://docs.flowr.space). One starts with a bunch of system commands, wraps them into a tab-delim text file. When done flowr can submit to a local server (parallel using mclapply), and clusters like LSF, Torque, SLURM and MOAB etc...
flowr function [arguments]
status Detailed status of a flow(s).
rerun rerun a previously failed flow kill
Kill the flow, upon providing working directory
fetch_pipes Checking what modules and pipelines are available;
Please use 'flowr -h function' to obtain further information about the usage of a specific function.
Certainly biased (being a developer) but one may find it much easier to create a tsv file, than learning new syntax.
Second issue I faced was, say I have a R function which does a lot of things and now I wanted to call it from the terminal. R does not have a nice standard argument parse like python/perl. Now we have a package funr, where the first argument is the function you want to call, and rest are its arguments. One can call any R function of any installed package (or sourced script).
funr rnorm n=10
-1.244571 1.378112 0.02189023 -0.3723951 0.282709 -0.22854 -0.8476185 0.3222024 0.08937781 -0.4985827
Hope you find it useful. Would be curious if it works out.