QGIS » QGIS Application

Hi, can you share the script you tried to run and the values with which you run it? Have tried with a previous version of R (R < 3.0.0)?

(You filled this ticket on the "wrong" bugtracker. But soon one of the moderators wil change it to the Sextante bugtracker: https://issues.qgis.org/projects/sextante/issues)

Hi Filipe,
Thanks for the quick reply. I have not tried it with a previous version of R (which by the way, I am using in Linux); I should do that and report back to you.
In the meantime, here is the script:

##layer=vector
##sst=field layer
##z=field layer
##clor=field layer
##[GAM scripts]=group

cor(layerz, layersst)
cor(layerclor, layerz)
cor(layersst, layerclor)

It is very simple: it takes a vector layer (e.g. a Shapefile), and three fields; then, it calculates the correlation between the fields and it should output it in the results viewer (as you can see in the log, it is calculating correctly the correlations)

In Qgis Master, Sextante 1.10 and R 2.15.3 it works as expected. Please try in Linux with R < 3.0.0. and report back.

The problem can be from Sextante 1.9 (if you have the chance try it the script with Qgis Master, that ships with Sextante 1.10 by default, and R 3.0.0) or it can be R related. I don't think R 3.0.0 has been tested with Sextante.

My report does not relate to Linux, but only to Windows (Linux works fine).
I tested it now with R 2.15 and the same problem comes up (no error, but empty console output). Here is the log:

R execution console output

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

options("repos"="http://cran.us.r-project.org")
tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", lib="C:/Documents and Settings/joana/.qgis//sextante/rlibs"))
[1] "C:/Programas/R/R-2.15.1/library/rgdal"
library("rgdal")
Loading required package: sp
rgdal: version: 0.8-6, (SVN revision Unversioned directory)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.9.2, released 2012/10/08
Path to GDAL shared files: C:/Programas/R/R-2.15.1/library/rgdal/gdal
GDAL does not use iconv for recoding strings.
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: C:/Programas/R/R-2.15.1/library/rgdal/proj
Warning messages:
1: package 'rgdal' was built under R version 2.15.3
2: package 'sp' was built under R version 2.15.3
layer = readOGR("//VBOXSVR/tmp/35_sextante_R",layer="updated_table_no_nulls")
OGR data source with driver: ESRI Shapefile
Source: "//VBOXSVR/tmp/35_sextante_R", layer: "updated_table_no_nulls"
with 684 features and 36 fields
Feature type: wkbPoint with 2 dimensions
sst="sst"
z="z"
clor="clor"
cor(layerz, layersst)
[1] 0.3850661
cor(layerclor, layerz)
[1] 0.7935047
cor(layersst, layerclor)
[1] 0.3175419

proc.time()
user system elapsed
1.45 5.39 25.37

Looks like Windows-specific bug of Sextante 1.9. Can you test in QGIS Master/Sextante 1.10 on Windows? If still get the same problem, then file a bug report here in Sextante bugtracker.

I installed now qgis-dev for Windows, using the osgeo4w installer. These are the specifications:

Versão do QGIS 1.9.0-Master Revisão do código do QGIS 404d89f
Compilado contra Qt 4.7.1 Em execução contra Qt 4.7.1
Compilado contra GDAL/OGR 1.9.2 Em execução contra GDAL/OGR 1.9.2
Versão GEOS 3.3.8 Versão de cliente PostgreSQL 8.3.10
Versão SpatiaLite 3.0.1 Versão QWT 5.2.1
Versão PROJ.4 480 QScintilla2 Version 2.6.2

I tried both R 3.00 and R 2.15, but R does not appear in the SEXTANTE toolbox (after I activate it and ammended the R path to point to the correct folder; also R is on the Windows path)...

Therefore I cannot test the bug.

Btw, I am using Wxp and SEXTANTE 1.09.

Thanks!

Thanks for that! I was now able to see the R section.

Now it seems that my Rscript (and all other Rscripts) are falling into a python error:

AttributeError: 'QgsVectorDataProvider' object has no attribute 'select'

For instance, when running one of the example scripts (quadrat analysis):

sextante.runalg("r:quadratanalysis","//VBOXSVR/tmp/35_sextante_R/updated_table_no_nulls.shp",None,None)

I get this:

Uncaught error while executing algorithm
Traceback (most recent call last):
Traceback (most recent call last):
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\core\\GeoAlgorithm.py", line 145, in execute
self.processAlgorithm(progress)
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\
\\RAlgorithm.py", line 204, in processAlgorithm
loglines += self.getFullSetOfRCommands()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\
\\RAlgorithm.py", line 222, in getFullSetOfRCommands
commands += self.getImportCommands()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\
\\RAlgorithm.py", line 269, in getImportCommands
value = param.getSafeExportedLayer()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\parameters\\ParameterVector.py", line 82, in getSafeExportedLayer
self.exported = LayerExporter.exportVectorLayer(layer)
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\core\\LayerExporter.py", line 53, in exportVectorLayer
provider.select( allAttrs )
AttributeError: 'QgsVectorDataProvider' object has no attribute 'select'

I get many "flavours" of this error by running different scripts; it always complains about some attribute that it cannot find in the API. I saw a similar bug report here:

#7106

Btw, I am using the python that came with the osgeo4w distribution:

Versão do Python:
2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]

you must remove sextante installed as python plugin before testing the (updated) version that is shipped with qgis master,

so delete first

C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante

Joana Simoes wrote:

Thanks for that! I was now able to see the R section.

Now it seems that my Rscript (and all other Rscripts) are falling into a python error:

AttributeError: 'QgsVectorDataProvider' object has no attribute 'select'

For instance, when running one of the example scripts (quadrat analysis):

sextante.runalg("r:quadratanalysis","//VBOXSVR/tmp/35_sextante_R/updated_table_no_nulls.shp",None,None)

I get this:

_Uncaught error while executing algorithm
Traceback (most recent call last):
Traceback (most recent call last):
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\core\\GeoAlgorithm.py", line 145, in execute
self.processAlgorithm(progress)
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\

\\RAlgorithm.py", line 204, in processAlgorithm

loglines += self.getFullSetOfRCommands()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\

\\RAlgorithm.py", line 222, in getFullSetOfRCommands

commands += self.getImportCommands()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\

\\RAlgorithm.py", line 269, in getImportCommands

value = param.getSafeExportedLayer()
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\parameters\\ParameterVector.py", line 82, in getSafeExportedLayer
self.exported = LayerExporter.exportVectorLayer(layer)
File "C:\\Documents and Settings\\joana/.qgis2/python/plugins\\sextante\\core\\LayerExporter.py", line 53, in exportVectorLayer
provider.select( allAttrs )
AttributeError: 'QgsVectorDataProvider' object has no attribute 'select'
_

I get many "flavours" of this error by running different scripts; it always complains about some attribute that it cannot find in the API. I saw a similar bug report here:

#7106

Btw, I am using the python that came with the osgeo4w distribution:

Versão do Python:
2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]

Just tested it in here, with the latest version and Win 7, and output is not empty.

Please remove the old version as Giovanni mentioned and try the latest master version of SEXTANTE and QGIS. It should work fine.

Thanks for your help!

Joana Simoes wrote:

I just removed the previous installation of QGIS, directories ~/.qgis, ~/.qgis2 and some temporary folders on the home directory that contained reference to Sextante.
Then I installed the latest version of QGIS for Windows (qgis-dev, using the OSGeo4W):

Versão do QGIS 1.9.0-Master Revisão do código do QGIS db762dd
Compilado contra Qt 4.7.1 Em execução contra Qt 4.7.1
Compilado contra GDAL/OGR 1.9.2 Em execução contra GDAL/OGR 1.9.2
Versão GEOS 3.3.8 Versão de cliente PostgreSQL 8.3.10
Versão SpatiaLite 3.0.1 Versão QWT 5.2.1
Versão PROJ.4 480 QScintilla2 Version 2.6.2
Esta cópia do QGIS escreve a depuração de saída

It is a mistery to me why, but when I run the plugin fetcher, it stated "SEXTANTE" as installed, and it did not give me the option of uninstalling it, but to install it again. I reinstalled SEXTANTE (latest version: 1.09) and restarted QGIS. The version of R is also the latest: 3.0.0.
Now I am unable to run any R, algorithms as it complaineds about some property that is not in the API (screenshots in attachment)

Thanks in advance for your help.

Hi Joana,

forget about what you see in "fetch python plugins", sextante is now a core plugin, but still a python plugin, so it shows in that menu but it is not removable. If you choose to install it you will actually install the obsolete version. This confusion will go away soon when qgis2 will be ready.

To test the latest code just be sure you don't have any "sextante" folder inside .qgis2/python/plugins

then just activate sextante inside "manage plugins" and you are good to go.

cheers.

Thanks for that! Now I was able to run SEXTANTE (version 1.1).
Unfortunately, the same problem I had in other versions, reproduced here: empty console output (see image in attachment). This is the log that I get:

Algorithm correlation started
R execution commands
options("repos"="http://cran.at.r-project.org/")
deflibloc
.libPaths(c("C:/Documents and Settings/joana/.qgis2//sextante/rlibs",deflibloc))
tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", dependencies=TRUE, lib="C:/Documents and Settings/joana/.qgis2//sextante/rlibs"))
library("rgdal")
tryCatch(find.package("raster"), error=function(e) install.packages("raster", dependencies=TRUE, lib="C:/Documents and Settings/joana/.qgis2//sextante/rlibs"))
library("raster")
layer = readOGR("//VBOXSVR/tmp/35_sextante_R",layer="updated_table_no_nulls")
sst="AUTO"
z="AUTO"
clor="AUTO"
cor(layerz, layersst)
cor(layerclor, layerz)
cor(layersst, layerclor)
R execution console output

R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

options("repos"="http://cran.at.r-project.org/")
deflibloc
.libPaths(c("C:/Documents and Settings/joana/.qgis2//sextante/rlibs",deflibloc))
tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", dependencies=TRUE, lib="C:/Documents and Settings/joana/.qgis2//sextante/rlibs"))
[1] "C:/Programas/R/R-3.0.0/library/rgdal"
library("rgdal")
Loading required package: sp
rgdal: version: 0.8-6, (SVN revision Unversioned directory)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.9.2, released 2012/10/08
Path to GDAL shared files: C:/Programas/R/R-3.0.0/library/rgdal/gdal
GDAL does not use iconv for recoding strings.
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: C:/Programas/R/R-3.0.0/library/rgdal/proj
tryCatch(find.package("raster"), error=function(e) install.packages("raster", dependencies=TRUE, lib="C:/Documents and Settings/joana/.qgis2//sextante/rlibs"))
[1] "C:/Documents and Settings/joana/.qgis2/sextante/rlibs/raster"
library("raster")
layer = readOGR("//VBOXSVR/tmp/35_sextante_R",layer="updated_table_no_nulls")
OGR data source with driver: ESRI Shapefile
Source: "//VBOXSVR/tmp/35_sextante_R", layer: "updated_table_no_nulls"
with 684 features and 36 fields
Feature type: wkbPoint with 2 dimensions
sst="AUTO"
z="AUTO"
clor="AUTO"
cor(layerz, layersst)
[1] 1
cor(layerclor, layerz)
[1] 1
cor(layersst, layerclor)
[1] 1

proc.time()
user system elapsed
2.64 5.00 24.10
Converting outputs
Loading resulting layers
Algorithm correlation finished
HTML output has been generated by this algorithm.
Open the SEXTANTE results dialog to check it.

And my original script is here:

##layer=vector
##sst=field layer
##z=field layer
##clor=field layer
##[GAM scripts]=group

cor(layerz, layersst)
cor(layerclor, layerz)
cor(layersst, layerclor)

The command, that should trigger the output is this one ">".
Note that I have the same problem, running the example scripts (e.g.: "Field Summary Statistics")

All the other outputs from R (images), are looking ok on the results viewer.

Joana

I am having no problems with that, so let's see if R is correctly working on your machine and producing the text. Please, do the following.

- Run the algorithm that produces no output
- FInd this file in your system C:/Documents and Settings/joana/.qgis2/sextante/sextante_script.r.Rout.

If it is not there, that is the problem, because the resulta are generated from this file
If it is there, send it here, so I can see why SEXTNATE is not processing it correctly

Hopefully this will help us solve this issue

Thanks for your help!

See also #8012

Is this still valid with the current Qgis Master?

Alexander Bruy wrote:

Closed for lack of feedback. Please reopen if necessary

so I tested both R 2.15.x and 3.x on both Windows and Linux, and the script work, but on Windows the results dialog is empty.

Is this still happening? Were you able to determine the cause?

Hello everyone,

It seems the R has a package R2HTML that convert the R objects to HTML.

http://cran.r-project.org/web/packages/R2HTML/index.html

Small tutorial: http://statmath.wu.ac.at/courses/data-analysis/lectures/RandHTML.pdf (quick search in the internet)

Perhaps is more easy put R doing the job of converting to html and processing toolbox shows the output of the results?

I hope this helps.

Regards
Joao

Hello,

I'm having the open described problems with R-processing in QGIS. And I didn't find any solution in the Internet. It's the same situation as described in bug #9203. Everything works good only the "R Console Output" gave me an blanc Window back. As suggested in bug #9203 I know use the 32 bit versions of:
- R 3.1.2
- QGIS 2.4.0 Chugiak

My PC works with the operating system windows 7.

I look as Joana did in the HTML folder with her results - empty files. I installed the R2HTML package nothing changed.

My question is: Have you got any hint for me to get the R Console Output in QGIS. I'm as well interested in unconeventional solutions.

Thank you
Regards
Franziska

This bug should be fixed in QGIS 2.8. Can you please check?

Hello,

thanks a lot. I installed QGIS 2.8 via OSgeo4W and now it works. I get the "R console output". So far I can see it really works ... For your information: to play a bit safe I only used the 32-bit-version. Until now I didn't try the 64-version. If it comes to this point i will inform you.

Thanks a lot
Best regards
Franziska

Some providers are being removed from QGIS/Processing (will be available as plugin) and so are their categories in the bug tracker. To not leave them orphaned of a category they are being reassigned to processing/core.