Setting "R Folder" Path in QGIS Sextante

Question

I have installed R via the R-Project website. I have QGIS installed via OSGEO4W (currently 1.9.0 Master), and have Sextante plugin installed and working with GRASS and SAGA providers. I am now trying to get R to run, but with no luck. I initially installed R to Program Files, but found mention that perhaps the space in the file path was an issue, so I have re-installed to C:\R\R-3.0.1\

What paths do I need to enter the "R Folder" and "RScripts Folder" configuration area in Sextante? Or am I missing something?

Answer 1

EDIT: I'm going to see if this bug is related (http://hub.qgis.org/issues/8012).

UPDATE: Looks like there are some issues with R in the sextante plugin for both qgis and qgis-dev. I'll file some bug reports if they haven't been already. But the two issues with R in sextante are:

1) In qgis (stable) SEXTANTE doesn't seem to use the rlib path in the Users .qgis folder. Instead it relies on the default R library path in C:/. The plugin will still download and install the missing libraries into the qgis sextante plugin folder but won't actually use them. You have to install them from R manually - eg, install.packages("rgdal")

2) In qgis-dev (unstable) SEXTANTE doesn't launch any R scripts and gives a warning about missing dependencies and that R is not properly installed. This is the OPs problem.

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2. Install R like you have.
3. Install and open QGIS, install the SEXTANTE plugin like you've also done
4. Select the pull-down menu Analysis > SEXTANTE options and configuration
5. Expand R scripts in the Sextante options window and set the R folder to your R directory (ie, C:\Program Files\R\R-3.0.1). You don't have to worry about R Scripts folder unless you have a different place where you store your RScripts.

Now the funny part, possibly a bug...

Try to run one of the R scripts in the SEXTANTE Toolbox, like Create regular sampling grid.

This fails, with the helpful error:

options("repos"="http://cran.us.r-project.org") 
tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", lib="C:/Users/userman/.qgis//sextante/rlibs")) 
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.0/rgdal_0.8-9.zip' 
Content type 'application/zip' length 11911822 bytes (11.4 Mb) 
opened URL 
downloaded 11.4 Mb 

package 'rgdal' successfully unpacked and MD5 sums checked 

The downloaded binary packages are in 
C:\Users\userman\AppData\Local\Temp\RtmpyEEQJa\downloaded_packages 
library("rgdal") 
Error in library("rgdal") : there is no package called 'rgdal' 
Execution halted 
Converting outputs
Loading resulting layers
Algorithm Create regular sampling grid finished

The plugin is downloading and installing the libraries to it's custom rlib path, but when it goes to run the actual tool/script, it's not searching that path - but instead the default system rlib path.

The FIX - Install the needed library from the R interface (ie, launch R directly). Then go back to QGIS and launch the scripts.

Now they run! Output of random sample grid:

Answer 2

I have experienced a similar issue, and slightly differently under Ubuntu and under Windows.

On Ubuntu, Sextante found R but couldn't run any of the scripts despite the relevant libraries having been installed from the R console. It looks like Sextante wants to use a different library store to the default which happens to be in a protected system folder, so my workaround was to run QGIS as a superuser once to load each script in turn so it could install the libraries it wanted, where it wanted. Afterwards it was happy to load as a normal user until the next time I need a library it doesn't see.

On Windows, I also had an issue where it wouldn't reliably set the R folder. There was nothing wrong with my R installation, it loaded fine in any manner except from within Sextante. When I looked in the Sextante folder in .qgis, the conf file was pointing to a different location than was set in the options menu. Manually correcting this seemed to solve the problem.

I then needed to run QGIS as an admin, as with Ubuntu, to ensure it loaded the libraries it needed, where it needed - again this is only needed when you first need a new library Sextante isn't aware of.

Essentially, for whatever reason, Sextante's R set-up seems to be broken from a users perspective but at least there's a workaround.

(The same works for the "Processing" plugin nuder QGIS 2.x)

Answer 3

The issue is that R is installed under Program Files by default, which is write-protected. Install R into another folder such as C:\R\R-3.1.3 and the problem goes away when you set it as the R path in QGIS. The solution is described here: http://wiki.awf.forst.uni-goettingen.de/wiki/index.php/R_installation

This worked running QGIS 2.8.1 Wien on Windows 7 64-bit.