Here's the issue:
I am using R to run some statistical analysis. The results of which will eventually be sent to a an embedded swf on the user's client machine.
To do this, I have PHP execute a shell script to run the R program, and I want to retrieve the results of that program so I can parse them in PHP and respond with the appropriate data.
So, it's simply:
$output = shell_exec("R CMD BATCH /home/bitnami/r_script.R");
echo $output;
But, I receive nothing of course, because R CMD BATCH writes to a file. I've tried redirecting the output in a manner similar to this question which changes my script to
$output = shell_exec('R CMD BATCH /home/bitnami/raschPL.R /dev/tty');
echo $output;
But what I get on the console is a huge spillout of the source code, and nothing is echoed.
I've also tried this question's solution in my R script.
tl;dr; I need to retrieve the results of an R script in PHP.
Cheers!
Found it, the answer is through Rscript. Rscript should be included in the latest install of R.
Using my code as an example, I would enter this at the very top of r_script.R
#!/usr/bin/Rscript --options-you-need
This should be the path to your Rscript executable. This can be found easily by typing
which Rscript
in the terminal. Where I have --options-you-need, place the options you would normally have when doing the CMD BATCH, such as --slave to remove extraneous output.
You should now be able to run your script like so:
./r_script.R arg1 arg2
Important! If you get the error
Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
could not find function "is"
You need to include the "methods" package, like so:
require("methods");
If it writes to file perhaps you could use file_get_contents to read it?
Perhaps,a much simpler workaround, would be:
$output = shell_exec('R CMD BATCH /home/bitnami/raschPL.R > /dev/tty 2>&1');
echo $output;
Redirects both STDOUT and STDERR, since R outputs to STDERR, by default.