"/bin/bash: R: command not found" when trying to run R from MATLAB (mac)

I'm trying to call R from MATLAB (R2016b/R2017a prerelease) on macOS (10.12 Siera).

I've installed R and on Terminal.app, command "R" results in loanching R software successfully.

In my understanding, something like this in MATLAB command window should do the job.

> system('R CMD BATCH "script1.R"');

However, simply "system('R')" in MATLAB returns an error message as below (let alone more complicated "system('R CMD BATCH "script1.R"')"):

>> system('R')
/bin/bash: R: command not found

ans =

 127

I'm a little puzzled because the same "R" command works in Terminal and I thought "system('R')" or "unix('R')" in MATLAB is equivalent.

Can anybody suggest a solution?

For Windows, I have found a solution here. You need to properly change Environment Variables. But what about macOS?

Answer 1

[Walter Roberson]

In OS-X, because applications launched from the dock do not go through a login shell, the full shell initialization files are not used, so the PATH environment variable will probably not be the same.

You can either use the full path to R or you can setenv('PATH') to include the path to R, or you can alter the OS-X environment variables.

You might be able to modify /etc/paths but I am not sure that works in newer versions.

In newer versions it appears you should use launchctl -- see http://apple.stackexchange.com/questions/51677/how-to-set-path-for-finder-launched-applications

[Kouichi C. Nakamura]

Thanks a lot.

I thought editing `.bash_profile` as below might work, but it didn't. I can't really understand how launchctl works.

export PATH=/usr/local/bin/R:$PATH
launchctl setenv PATH $PATH

Nevertheless, the following worked. Cheers!

> system('/usr/bin/local/R CMD BATCH "script1.R"');

[Walter Roberson]

Do not include the executable name in the path, just the directory

[Kouichi C. Nakamura]

Thanks. This (below) does not work either. In fact, "/usr/local/bin" is already found in $PATH, so I don't quite see why simply "system('R')" doesn't work.

export PATH=/usr/local/bin:$PATH
launchctl setenv PATH $PATH

[Walter Roberson]

On OS-X El Capitan, /usr/local/bin is not part of the default path given to apps.