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I have a bash script that creates a csv file and an R file that creates graphs from that.
At the end of the bash script I call Rscript Graphs.R 10
The response I get is as follows:
Error in is.vector(X) : subscript out of bounds
Calls: print ... <Anonymous> -> lapply -> FUN -> lapply -> is.vector
Execution halted
The first few lines of my Graphs.R are:
#!/bin/Rscript
args <- commandArgs(TRUE)
CorrAns = args[1]
No idea what I am doing wrong? The advice on the net appears to me to say that this should work. Its very hard to make sense of commandArgs
810
Use Rscript to run R from bash You can run it using Rscript test. r . And even better, if you add an initial shebang line #!/usr/bin/env Rscript in the script above and make it executable with chmod +x test. r , you can directly launch your R script with ./test.
Arguments can be passed to the script when it is executed, by writing them as a space-delimited list following the script file name. Inside the script, the $1 variable references the first argument in the command line, $2 the second argument and so forth.
The most convenient way to run R scripts from the command line is to use Rscript, an alternative front-end to run R code. Rscript is capable of executing R code from different command interpreters, such as a bash script on Linux or a Task Scheduler task on Windows.
With the following in args.R
print(commandArgs(TRUE)[1])
and the following in args.sh
Rscript args.R 10
I get the following output from bash args.sh
[1] "10"
and no error. If necessary, convert to a numberic type using as.numeric(commandArgs(TRUE)[1]).
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