Running QGIS Python code from the R rPython package

Question

The following script works fine from python or ipython at the command line:

from qgis.core import *
from qgis.gui import *
import sys
sys.path.append("/usr/share/qgis/python/plugins")
from PyQt4.QtCore import *
from PyQt4.QtGui import *
app = QgsApplication([], True)
QgsApplication.initQgis()
from processing.core.Processing import Processing
Processing.initialize()
import processing

layer = QgsVectorLayer('ger.shp','ger','ogr')

Where ger.shp is a shapefile in the current folder. After this, layer.isValid() is True. No warnings or messages.

But if I try and run it from the rPython package, I get an error message and the layer is not valid:

library(rPython)

qtest <- function(){
    code = "from qgis.core import *
from qgis.gui import *
import sys
sys.path.append('/usr/share/qgis/python/plugins')
from PyQt4.QtCore import *
from PyQt4.QtGui import *
app = QgsApplication([], True)
QgsApplication.initQgis()
from processing.core.Processing import Processing
Processing.initialize()
import processing

layer = QgsVectorLayer('ger.shp','ger','ogr')
"
    rPython::python.exec(code)
}

qtest()
QObject::connect: Cannot connect (null)::raiseError( QString ) to QgsVectorLayer::raiseError( QString )

and then:

python.get("layer.isValid()")
[1] FALSE 

It is identical code and identical python version, so I think it can only be in the way the code is run - perhaps the python interpreter is initialised differently from the way embedded python is run in rPython? I'm stuck.

Answer 1

I'd assumed the prefix path was correct because I didn't need to set it in the console version. Using print app.showSettings() showed me this was a false assumption.

When running from R, it printed as:

Application state:
QGIS_PREFIX_PATH env var:       
Prefix:     /usr/lib/R/bin
Plugin Path:        /usr/lib/R/bin/lib/qgis/plugins
Package Data Path:  /usr/lib/R/bin/share/qgis

which is clearly wrong. Tweaking the script to set it correctly to /usr in my case:

app = QgsApplication([], True)
app.setPrefixPath('/usr', True)
app.initQgis()
print app.showSettings()

and now the layer loads Truely.