Cant run R command from PHP. Paths issue?

Question

I am trying to run an R command from PHP using exec. I know that it would make much more sense to use RServer, or a socket connection, but those options are currently not available to me.

The code looks like this:

$cmd = '/var/www/r.sh';
exec($cmd, $out, $return_var);

r.sh contains the following

#!/bin/bash
source /home/ubuntu/.bashrc
cd /home/ubuntu
R CMD BATCH RFile.R

When I the command from the shell, it works absolutely fine. When I run the command from PHP, I get the following error:

> test( read.csv("OutData.csv",header=T,stringsAsFactors=FALSE,encoding="UTF-8"))
Error in library(randomForest) :
  there is no package called 'randomForest'
Calls: test -> library
Execution halted

My initial thought was that it might be permission related. I have given www-data read an execute permission to everything to no avail. I have also run the command from the shell as the www-data user and it works fine. Its only when invoked from PHP that it fails.

So, I am now thinking that its a paths issue. randomForest is an R library and is correctly installed on the box:

ubuntu@<removed>:/var/www$ sudo find / -name randomForest
/home/ubuntu/R/x86_64-unknown-linux-gnu-library/3.0/randomForest
/home/ubuntu/R/x86_64-unknown-linux-gnu-library/3.0/randomForest/R/randomForest

I can't find any shell environment variables which set up paths, so I don't understand why the command works from the shell, but not from PHP.

Any ideas?

from within R, try ss <- Sys.getenv(); ss[grep("^R_",names(ss))], or ss[grep("^R_LIB",names(ss))] — Ben Bolker
– Ben Bolker, Commented Nov 11, 2013 at 1:52
What should I be seeing here? Looks like ss is populated with all the env data from the shell. Unfortunately my experience with R is very very limited so I am not sure what I should be looking for. — mrwooster
– mrwooster, Commented Nov 11, 2013 at 1:54
R_LIBS, R_LIBS_USER. (The "R Installation and Administration Manual", e.g. cran.stat.sfu.ca/doc/manuals/R-admin.html , is the reference for this stuff.) — Ben Bolker
– Ben Bolker, Commented Nov 11, 2013 at 2:22
Thanks, this is exactly what I needed. If you will put the above in an answer, I can accept it :) — mrwooster
– mrwooster, Commented Nov 11, 2013 at 18:51

Ben Bolker · Accepted Answer · 2013-11-11 20:05:47Z

2

The relevant environment variables are R_LIBS and R_LIBS_USER; the R Installation and Administration Manual is the relevant reference. If you want to see how these variables are set from within an R session, try

ss <- Sys.getenv()
ss[grep("^R_LIB",names(ss))]

answered Nov 11, 2013 at 20:05

Ben Bolker

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