Rbash

Shell script to make it easy to launch R scripts from the command line.

What is it useful for?

R can read the command line arguments. But what if you want to be able to run exactly the same scripts from an IDE and from the command line, and to override some settings in a given context. Rbash tries to offer a simple way to achieve this.

Usage

Rbash does accept a few arguments:

• -f file.R let you specify a R file to source. You can use the -f argument several times to source multiple files.
• -o variableName=someValue let you set a variable name and its value that will be stored in the Options collector in R. You can use the -o argument several times to set multiple options.
• -c Automatically delete the outputs and logs upon completion,
• -q Doe snot print the R console in the terminal (you can still access it in the log file, unless you use the -c argument)

Some files will be created:

• a .R file combining the files to source and options definitions.
• a .log file with the output (ie the R console)
• a .err file might be created, if any error occurred. If you're only interested by the side effect of your script you can also use the -c (clean) argument to automatically delete these files.

Examples

The most basic use is simply executing an R script Rbash.sh -f commands.R

But it becomes interesting when you start combining multiple files and options.

The sample commands.R script available in this repo does source another file and set different values with some defaults :

# commands.R
print("sourcing 'commands.R'")

source("defaultTestValue.R")
testVal <- getOption("test",  default = "defaultTestInCommands")
print(paste0("test value is ", testVal))

testVal2 <- getOption("test2", default = "defaultTest2InCommands")
print(paste0("test2 value is ", testVal2))

So you can see that commands.R set defaults for test and test2. And source defaultTestValue.R.

Here's the defaultTestValue's code:

# defaultTestValue.R
print("sourcing 'defaultTestValue.R'")
options(test="defaultTestInSourcedFile")

As you can see, defaultTestValue set a value for the test variable. (Therefore the default in commands.R should never show up).

A similar script overrideTestValue.R set a default value for test2.

#overrideTestValue.R
print("sourcing 'overideTest2Value.R'")
options(test2="defaultTest2InOverrideFile")

With this content setup, you can see that the order in which you provide the code to run is taken into account: If you define the option before to source the overrideTestValue.R, it will be overriden by the R script. But if you add the option after, then your command line option will override the one from the script:

$ ./Rbash.sh -o test2=\"valueFromShell\" -f overrideTestValue.R -f commands.R
[1] "sourcing 'overideTest2Value.R'"
[1] "sourcing 'commands.R'"
[1] "sourcing 'defaultTestValue.R'"
[1] "test value is defaultTestInSourcedFile"
[1] "test2 value is defaultTest2InOverrideFile"

$ ./Rbash.sh -f overrideTestValue.R -o test2=\"valueFromShell\"  -f commands.R
[1] "sourcing 'overideTest2Value.R'"
[1] "sourcing 'commands.R'"
[1] "sourcing 'defaultTestValue.R'"
[1] "test value is defaultTestInSourcedFile"
[1] "test2 value is valueFromShell"

Pre-requisites

Obviously R must be installed and correctly accessible from the current Path.

Do not forget to chmod +x the Rbash.sh script.