Execute R Commands in Automator

Question

I try to automate a simple workflow. Its a oneliner in Terminal, nothing really special. And also tested via Terminal - it works perfect.

During this workflow R should be started via Automator (run a shell script). But it's impossible to start R via Automator (run shell script). Interesting: It is also impossible to run "psql" via automator-shell script, but "Python" works.

Whats the secret behind that? (R & psql runs perfect via normal Terminal.)

If you don't need an interactive session, use Rscript -e 'library(myLibrary);mySuperScript'. — fxi
– fxi, Commented Jul 17, 2014 at 7:46

fxi · Accepted Answer · 2014-07-19 11:38:28Z

0

In (mac) OS X, start an automator process with Run Shell Script action.

Try with this command :

Rscript -e "system('say hello')"

It should work.

Example with shiny app :

Rscript -e "library(shiny);runExample('01_hello',launch.browser = T)"

edited Jul 19, 2014 at 11:38

answered Jul 17, 2014 at 7:54

fxi

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7 Comments

Teletubbi-OS X Over a year ago

Nearly perfect! With Rscript the browser start - and nothing happens. From Terminal, perfect. I run this command: Rscript -e "shiny::runApp(('/Users/ABC/Documents/Git/RShiny/shinyapp'),launch.browser=TRUE))" Automator uses a other shall than the "normal" $BASH. But which one?

fxi Over a year ago

I don't know what's going on with your shiny app. Try the example in my answer : does it work ? In automator shell script, is the shell set to /bin/bash ?

Teletubbi-OS X Over a year ago

"dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.2.0/4.8.3/libgfortran.3.dylib   Referenced from: /usr/local/Cellar/r/3.1.1/R.framework/Versions/3.1/Resources/lib/libR.dylib   Reason: image not found"

fxi Over a year ago

It's the output of the shiny example ?? It's look like R doesn't find gfortran libraries. If you type "which gfortran" in your terminal, do you have something ? If not, maybe you should install gfortran with homebrew : brew install gfortran. But, there maybe another problem, unrelated with your first question.

Teletubbi-OS X Over a year ago

Terminal output for "which gfortran": /usr/local/bin/gfortran

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