Integrating R in QGIS with Mac OS El Captain: missing dependencies

Question

I have a Mac OS (El Captain) and I'm trying to run R scripts within QGIS 2.14. When I open a script (like one from the online list) I receive the error message:

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

Please note that:

1. R is correctly installed
2. I followed instructions from http://osgeo-org.1560.x6.nabble.com/R-in-QGIS-on-OSX-using-Kyngchaos-build-td5254567.html
3. It is not possible to set the R folder, as I did in Windows (see the figure here below), but only the R script folder.

Answer 1

I just solved the problem following these steps:

• open the Terminal, digit touch ~/.bash_profile; open ~/.bash_profile and add two rows:

  export R_HOME=“/Library/Frameworks/R.framework/Versions/3.3/Resources” export PYTHONPATH="/Applications/QGIS.app/Contents/Resources/python"

  save the file and close the Terminal

• open a new Terminal digit sudo nano /etc/paths

  enter your password when prompted

  Go to the bottom of the file, and enter the path you wish to add (in my case was /Library/Frameworks/R.framework/Versions/3.3/Resources).

  Hit control-x to quit.

  Enter “Y” to save the modified buffer.

• copying the two link files (R and Rscripts) that are in "/usr/local/bin" folder and pasting to "/usr/bin".

• Restart your MAC

;)

Answer 2

OSX 10.13, R 3.4.3, QGIS 2.18.2, GDAL 2.1.2 Python 2.7 I just solved the problem like above:

1. open the Terminal, type

   nano ~/.bash_profile

2. add two rows:

   export R_HOME=/Library/Frameworks/R.framework/Versions/3.4/Resources 
   export PYTHONPATH=/Applications/QGIS.app/Contents/Resources/python
   

3. save the file and close the Terminal

4. open a new Terminal digit

   sudo nano /etc/paths

   enter your password when prompted Go to the bottom of the file, and enter

   /Library/Frameworks/R.framework/Versions/3.4/Resources

   Hit control-x to quit. Enter “Y” to save the modified buffer.

5. copying the two link files (R and Rscript) that are in "/usr/local/bin" folder and pasting to "/usr/bin". Pay attention to the version of the R.Framework. Open a terminal window and type

   sudo cp /usr/local/bin/R /Library/Frameworks/R.framework/Versions/3.4/Resources/bin

   cp /usr/local/bin/Rscript /Library/Frameworks/R.framework/Versions/3.4/Resources/bin

6. Restart OSX

Answer 3

Either one of these solutions posted above work, but there is a critical missing bit of information. You need to disable the System Integrity Protection feature in El Capitan as per this link. Once you disable the SIP, you can copy the R and Rscript link files from "/usr/local/bin" folder to "/usr/bin". It worked for me after about 24 hours of frustration and now I can run R scripts in QGIS.

Answer 4

Mac Os X is an Unix system and the processing Python module search for an R executable because it uses the subprocess module to execute the script directly with R.

The Python script involved is /Applications/QGIS.app/Contents/Resources/python/plugins/processing/algs/r/RUtils.py

1) it search for the R executable
2) it creates a R script with the command that should be executed (/.../.qgis2/processing/processing_script.r)
3) it executes R processing_script.r with the subprocess module

Therefore, if you can launch R from the terminal (Terminal.app), no problem, you have nothing to do.

If not, try in the Terminal.app

which R 

• In Yosemite the result is /usr/bin/R with an R executable witch is a symbolic link of /Library/Frameworks/R.framework/Versions/3.x/Resources/bin/R
• In El Capitan the result is /usr/local/bin/R because of the System Integrity Protection (SIP), About System Integrity Protection on your Mac (you cannot use /usr/bin/, amongst other things, only Apple is allowed to install software under /usr/bin . /usr/local/bin is for the others)

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

Simply add PATH="/usr/local/bin:/usr/bin:$PATH" in your .bash_profile file (search in /usr/local/bin/ before /usr/bin/)