[Qgis-user] R in QGIS on OSX using Kyngchaos build

[Agustin]

Hi,
R doesn’t work on my laptop running capitan [1]

My Rutils.py is in the machine
/Applications/QGIS.app/Contents/Resources/python/plugins/processing/algs/r/Rutils.py

R_Home is in .bash_proflle
export PYTHONPATH="/Applications/QGIS.app/Contents/Resources/python"
#R para Qgis
export R_HOME=/Library/Frameworks/R.framework/Versions/Current/Resources/
/Library/Frameworks/R.framework/Versions/Current/Resources/ #exists

R works typing R in a terminal

To get rid of the message claiming that (This happens when trying to activate R ?)
/Applications/QGIS.app/Contents/msys is not there I cheated creating it

Now I’m able to activate R and download the scripts but an error pop up

 Missing dependency. This algorithm cannot be run :-( 

This algorithm requires R to be run. Unfortunately it seems that R is not installed in your system or it is not correctly configured to be used from QGIS

Click here to know more about how to install and configure R to be used with QGIS

No problems in other machines running earlier versions of MacOS

Best
A.
 [1] System Version:	OS X 10.11.3 (15D21)  Kernel Version:	Darwin 15.3.0



El 6Mar, 2016, a las 9:55 AM, gene <martin.laloux at gmail.com> escribió:

> Processing has nothing to do with rpy2. it uses  subprocess
> <https://docs.python.org/2/library/subprocess.html>   to execute the
> original R script
> 
> The explication is in the
> /Applications/QGIS.app/Contents/Resources/python/plugins/processing/algs/r/RUtils.py
> script
> 
> 1) RUtils first create a temporary file named
> /Users/.../.qgis2/processing/processing_script.r with the desired R commands
> (def createRScriptFromRCommands(commands):, line 73)
> 
> Example of the content of a processing_script.r file 
> 
>    options("repos"="http://cran.at.r-project.org/")
>    tryCatch(find.package("rgdal"), error=function(e)
> install.packages("rgdal", dependencies=TRUE))
>    tryCatch(find.package("raster"), error=function(e)
> install.packages("raster", dependencies=TRUE))
>    library("raster")
>    library("rgdal")
>    Layer =
> readOGR("/Users/Shared/telechargement/04_01_16/valuerelation_testproject",layer="testo2")
>    Field="num"
>    Summary_statistics<-data.frame(rbind(sum(Layer[[Field]]),
>    length(Layer[[Field]]),
>    length(unique(Layer[[Field]])),
>    min(Layer[[Field]]),
>    max(Layer[[Field]]),
>    max(Layer[[Field]])-min(Layer[[Field]]),
>    mean(Layer[[Field]]),
> 
> median(Layer[[Field]]),sd(Layer[[Field]])),row.names=c("Sum:","Count:","Unique
> values:","Minimum value:","Maximum value:","Range:","Mean value:","Median
> value:","Standard deviation:"))
>    colnames(Summary_statistics)<-c(Field)
>    Summary_statistics
> 
> 2) it execute the script with subprocess (def executeRAlgorithm:, line 88). 
> 
>      command = ["R", "CMD","BATCH", "--vanilla",  
> RUtils.getRScriptFilename(),RUtils.getConsoleOutputFilename()]
>      proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
> stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True)
> 
> 3) If you want, you can also use R directly to execute the script 
> 
>     source("processing_script.r")
> 
> Conclusions
> 
> a) you need access to R in command line (Terminal.app) 
> 
>   export R_HOME=/Library/Frameworks/R.framework/Versions/Current/Resources/
> in the .bash_profile file
> 
> b) you need to install all the R packages independently of QGIS
>      install.packages('rgdal')
>      install.package('raster') 
>      .....
> 
> 
> 
> 
> --
> View this message in context: http://osgeo-org.1560.x6.nabble.com/R-in-QGIS-on-OSX-using-Kyngchaos-build-tp5254567p5254644.html
> Sent from the Quantum GIS - User mailing list archive at Nabble.com.
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