How to send R variable to bash and again being read by another R process?

Question

I am trying to create a process mainly using R, where a R variable will be sent to bash and then another Rscript file will read that value from bash, do some calculation based on that.

My primary R code looks like below -

library(parallel) 
mclapply(letters, 
                    function(Let) 
                        return(system("/usr/lib/R/bin/Rscript '/opt/R/Try.R' $Let")), mc.cores = 6)

So, basically in above code, the individual letters are being sent to bash through variable Let, and then the 2nd R process 'Try.R' will read that value and print it.

My 'Try.R' looks like below -

GetValue = commandArgs(TRUE)

print(GetValue); flush.console()

quit(save = "no")

With above implementation, it doesnt look like the value of 'Let' variable is getting passed to bash. Can someone please help me with right approach. The codes above I put just for explanation purpose to describe what I am trying to do, and hence can be executed directly in R without passing to bash, however my actual process is quite complex so needs this kind of implementation.

Any pointer will be highly appreciated.

I am using Ubuntu 18 machine with latest R.

How are you declaring `Let`? R env won't survive a session, e.g. via `R` then `Sys.setenv(Let = 4); q('no')`. Check `env | grep Let` and you'll see `Let` hasn't survived — MichaelChirico, Dec 26 '19 at 12:43
You might benefit from: https://stackoverflow.com/q/49738564/3576984 — MichaelChirico, Dec 26 '19 at 12:44

StupidWolf · Accepted Answer · 2019-12-26T13:33:56.853

If you are only going to execute the bash file (and not read in the output), then the below will work:

First I write the R script:

BASH = c("GetValue = commandArgs(TRUE)",
"print(GetValue); flush.console()","quit(save='no')")

writeLines(BASH,"./Try.R")

And I execute the system call like you did, except to have the command line as a character that includes the variable, and run that:

library(parallel) 
mclapply(letters,function(Let){
CMD = paste("Rscript ./Try.R",Let)
return(system(CMD))}, 
mc.cores = 6)

How to send R variable to bash and again being read by another R process?

1 Answers1