Running R script from php webpage

Question

I am trying to build a php file that allows users to run a R script so they don't need to open a session in the server, just to open a browser.

Usual bash from the script run fine (say echo "something", copy and move data files,...) but R script is not running. R is called with Rscript

Rscript --no-save --no-restore --verbose ./RAMS-mapa-onades-zones-manual.R > outputFile.Rout 2>&1

R output gives this error

running
  '/usr/lib/R/bin/R --slave --no-restore --no-save --no-restore'

Error in library("rgdal") : there is no package called 'rgdal'
Execution halted

Well, library(rgdal) is the first line of the R script. Rgdal is present on the R installation and the script runs fine (Rscript myscript.R) from the command line.

As starting from php, the user running R is www-data while on the terminal the user is meteo. It seems to me that some environment variable needs to be set in the php Rscript execution but I can't find the way to do it.

Any idea? Thanks in advance

I have no idea but... first thing I would check is that... however the script is running, in whatever environment with whatever user, has access to the same environment variables and is aware of the library path. (or whatever) It seems like somethings not defined in that scope, maybe. I would try running something without any libraries... like a print statement or something. — gloomy.penguin
– gloomy.penguin, Commented Feb 12, 2015 at 14:46
As a first guess - is there maybe multiple R installations on the machine? Check the lib.loc parameter on library() as well. — LauriK
– LauriK, Commented Feb 12, 2015 at 14:46
@LauriK library() reports packages in /home/meteo/R/i686-pc-linux-gnu-library/3.1, /usr/local/lib/R/site-library and /usr/lib/R/library and a warning In library() : library ‘/usr/lib/R/site-library’ contains no packages — pacomet
– pacomet, Commented Feb 12, 2015 at 14:54

LauriK · Accepted Answer · 2015-02-12 22:01:55Z

2

Seems we've found the root cause in comments. The library paths don't match, but you can make them match by the lib.loc parameter to library(). Like this:

library(rgdal, lib.loc = c("/home/meteo/R/i686-pc-linux-gnu-library/3.1", "/usr/local/lib/R/site-library", "/usr/lib/R/library"))

answered Feb 12, 2015 at 22:01

LauriK

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pacomet Over a year ago

Hi @Laurik you were right. There was a problem with lib.loc. Adding your suggestion gave another problem, error message said sp was not available when required by rgdal loading. Finally I linked all R library locations to /usr/lib/R/site-library and now the R script runs fine. Thank you very much

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