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Empty console Output on R, under SEXTANTE #16564
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Author Name: Filipe Dias (@fsdias) 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) |
Author Name: Joana Simoes (@doublebyte1) Hi Filipe, ##layer=vector
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) |
Author Name: Joana Simoes (@doublebyte1) I send the script in attachment, as it seems the formatting came wrong in the previous email.
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Author Name: Filipe Dias (@fsdias) 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. |
Author Name: Joana Simoes (@doublebyte1) My report does not relate to Linux, but only to Windows (Linux works fine). R execution console output R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" R is free software and comes with ABSOLUTELY NO WARRANTY. R is a collaborative project with many contributors. Type 'demo()' for some demos, 'help()' for on-line help, or options("repos"="http://cran.us.r-project.org") proc.time() |
Author Name: Filipe Dias (@fsdias) 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. |
Author Name: Giovanni Manghi (@gioman)
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Author Name: Giovanni Manghi (@gioman)
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Author Name: Joana Simoes (@doublebyte1) 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 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! |
Author Name: Giovanni Manghi (@gioman) Joana Simoes wrote:
analysis -> options and configurations -> general and uncheck the "use categories to classify algorithms..." checkbox
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Author Name: Joana Simoes (@doublebyte1) 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 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: Btw, I am using the python that came with the osgeo4w distribution: Versão do Python: |
Author Name: Giovanni Manghi (@gioman) 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:
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Author Name: Victor Olaya (@volaya) 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! |
Author Name: Joana Simoes (@doublebyte1) I just removed the previous installation of QGIS, directories ~/.qgis, ~/.qgis2 and some temporary folders on the home directory that contained reference to Sextante. Versão do QGIS 1.9.0-Master Revisão do código do QGIS db762dd 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. Thanks in advance for your help.
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Author Name: Giovanni Manghi (@gioman) Joana Simoes wrote:
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. |
Author Name: Joana Simoes (@doublebyte1) Thanks for that! Now I was able to run SEXTANTE (version 1.1). Algorithm correlation started R version 3.0.0 (2013-04-03) -- "Masked Marvel" R is free software and comes with ABSOLUTELY NO WARRANTY. R is a collaborative project with many contributors. Type 'demo()' for some demos, 'help()' for on-line help, or options("repos"="http://cran.at.r-project.org/") proc.time() And my original script is here: ##layer=vector
The command, that should trigger the output is this one ">". All the other outputs from R (images), are looking ok on the results viewer. |
Author Name: Joana Simoes (@doublebyte1) Forgot to attach the screenshot
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Author Name: Victor Olaya (@volaya) 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.
If it is not there, that is the problem, because the resulta are generated from this file Hopefully this will help us solve this issue Thanks for your help! |
Author Name: Joana Simoes (@doublebyte1) Hi Filipe, R version 3.0.0 (2013-04-03) -- "Masked Marvel" R is free software and comes with ABSOLUTELY NO WARRANTY. R is a collaborative project with many contributors. Type 'demo()' for some demos, 'help()' for on-line help, or
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Author Name: Filipe Dias (@fsdias) Is this still valid with the current Qgis Master? |
Author Name: Alexander Bruy (@alexbruy) Closed for lack of feedback. Please reopen if necessary
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Author Name: Giovanni Manghi (@gioman) We confirmed this yesterday. I will send the log to Victor and/or attach it here together with few details.
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Author Name: Giovanni Manghi (@gioman) Alexander Bruy wrote:
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. |
Author Name: Filipe Dias (@fsdias) Is this still happening? Were you able to determine the cause? |
Author Name: João Gaspar (@jonnyforestGIS) 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 |
Author Name: Giovanni Manghi (@gioman)
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Author Name: Giovanni Manghi (@gioman)
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Author Name: Franziska Beau (Franziska Beau) 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 #17831. Everything works good only the "R Console Output" gave me an blanc Window back. As suggested in bug #17831 I know use the 32 bit versions of:
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 |
Author Name: Filipe Dias (@fsdias) This bug should be fixed in QGIS 2.8. Can you please check? |
Author Name: Giovanni Manghi (@gioman) Franziska Beau wrote:
the fix should be this 4549a38 you must try the latest qgis release, 2.8, and be sure that in .qgis2/pyhton/plugins you don't have any "processing" folder.
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Author Name: Franziska Beau (Franziska Beau) 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 |
Author Name: Giovanni Manghi (@gioman)
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Author Name: Giovanni Manghi (@gioman)
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Author Name: Giovanni Manghi (@gioman)
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Author Name: Giovanni Manghi (@gioman) 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. |
Author Name: Giovanni Manghi (@gioman)
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Author Name: Joana Simoes (@doublebyte1)
Original Redmine Issue: 7643
Affected QGIS version: master
Redmine category:processing/core
Assignee: Victor Olaya
Hi,
I am using SEXTANTE 1.09, with QGIS 1.08, in Windows and Linux. I noticed this bug in the Windows version only.
When writing an Rscript, I used the character ">" to redirect the console output to the results viewer. After successfully processing the script, SEXTANTE opens an empty console ouput; if I choose to export the results to an HTML file, it also comes empty (showing only the title).
If I go to the SEXTANTE logs and view the "R execution console output", I see that the operations were successfully processed and the numerical results are display (see bellow).
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.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-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
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(layer[[z]], layer[[sst]])
[1] 0.3850661
cor(layer[[clor]], layer[[z]])
[1] 0.7935047
cor(layer[[sst]], layer[[clor]])
[1] 0.3175419
proc.time()
user system elapsed
1.11 5.27 23.44
Related issue(s): #17831 (relates)
Redmine related issue(s): 9203
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