Specify which shell to use in R - r

Question

I have to run a shell script inside R. I've considered using R's system function.
However, my script involves source activate and other commands that are not available in /bin/sh shell. Is there a way I can use /bin/bash instead?
Thanks!

Answer 1

Invoke /bin/bash, and pass the commands via -c option in one of the following ways:
system(paste("/bin/bash -c", shQuote("Bash commands")))
system2("/bin/bash", args = c("-c", shQuote("Bash commands")))
If you only want to run a Bash file, supply it with a shebang, e.g.:
#!/bin/bash -
builtin printf %q "/tmp/a b c"
and call it by passing script's path to the system function:
system("/path/to/script.sh")
It is implied that the current user/group has sufficient permissions to execute the script.
Rationale
Previously I suggested to set the SHELL environment variable. But it probably won't work, since the implementation of the system function in R calls the C function with the same name (see src/main/sysutils.c):
int R_system(const char *command)
{
/*... */
res = system(command);
And
The system() library function uses fork(2) to create a child process that executes the shell command specified in command using execl(3) as follows:
execl("/bin/sh", "sh", "-c", command, (char *) 0);
(see man 3 system)
Thus, you should invoke /bin/bash, and pass the script body via the -c option.
Testing
Let's list the top-level directories in /tmp using the Bash-specific mapfile:
test.R
script <- '
mapfile -t dir < <(find /tmp -mindepth 1 -maxdepth 1 -type d)
for d in "${dir[#]}"
do
builtin printf "%s\n" "$d"
done > /tmp/out'
system2("/bin/bash", args = c("-c", shQuote(script)))
test.sh
Rscript test.R && cat /tmp/out
Sample Output
/tmp/RtmpjJpuzr
/tmp/fish.ruslan
...
Original Answer
Try to set the SHELL environment variable:
Sys.setenv(SHELL = "/bin/bash")
system("command")
Then the commands passed to system or system2 functions should be invoked using the specified shell.