run bash file in R : path in system() issue

Question

I am trying to run a bash file from inside R. So I have the following working fine:

setwd(path.expand("~/Documents/Rcode/"))

system("ls -F")
system('~/Documents/Rcode/GFR_test/run.sh')

So this works absolutely fine as I provided the whole path for the run.sh file. However, this gets tedious when working with long code and many bash files to run. So i needed to create a variable for each sh file as:

myPATH <- "~/Documents/Rcode/GFR_test/"

then to call the run.sh

 system(paste(myPATH, 'run.sh'))

Unfortunately this does not work as I get the error:

 sh: 1: ~/Documents/Rcode/GFR_test/ : Permission denied

The permission issue is strange as I know I got it right. Can you please help. Thanks

Answer 1

When you use paste , the default separator is a space. So :

paste(myPATH, 'run.sh')

would give :

~/Documents/Rcode/GFR_test/ run.sh

To suppress the extra space, you either have to add sep="" to your paste() , or, better, use paste0 which has a default empty separator (and is a bit faster) :

paste0(myPATH, 'run.sh')