[GRASS-user] Rscript error when using v.class.mlR

[Nicklas Larsson]

Daniel,

I assume you use the official GRASS app bundle for mac. If you are not using the final 8.0.0 version, but one of the release candidates, I'd suggest you download the latest. There are changes in the startup script in the final version that relate to PATH issues like this.



Best,
Nicklas







On Sunday, 20 February 2022, 01:55:28 CET, Daniel Kozar via grass-user <grass-user at lists.osgeo.org> wrote: 





Hi Micha, 

Thanks for the reply. I ran the script lines you sent both in the terminal as well as a GRASS session. Rscript is recognized in the terminal command but not in the GRASS 8.0 command. Since GRASS 8.0 did not recognize Rscript I tried making a symbolic link for "Rscript" to the full path: /usr/local/bin/Rscript. This still doesn't recognize the command and I'm unsure how else to work around it. 

Any Mac aficionados reading this - do you have an idea to resolve this? 

Thanks
Daniel

On Sat, Feb 19, 2022 at 1:46 AM Micha Silver <tsvibar at gmail.com> wrote:
> Hi
> 
> 
> On 19/02/2022 04:27, Daniel Kozar via grass-user wrote:
>> Hi everyone,
>>
>> When using the extension "v.class.mlR" I get an error [Message 1] (see 
>> below) that "Rscript" cannot be located. I traced this back to the 
>> script for "v.class.mlR" and edited line 908 to read the direct path 
>> to Rscript - '/usr/local/bin/Rscript' rather than 'Rscript' alone. 
>> However, when I re-open GRASS 8.0 I get an error [Message 2] that the 
>> extension failed when loading and that the operation isn't permitted. 
>> I allowed for the application to have administrative rights but it 
>> still doesn't work. Does anyone know how to work around this or solve 
>> the issue finding "Rscript"?
>>
>> I have R running and have installed necessary packages. I'm 
>> running GRASS on MacOS Monterey.
> 
> 
> This looks like a Mac problem (which I know nothing about).
> 
> To test, can you run, first from a terminal:
> 
> micha at RMS:~$ Rscript -e "sessionInfo()"
> 
> Now run the same from within a GRASS session:
> 
> (here's what I get)
> 
> micha at RMS:QGIS$ g.version
> GRASS 8.1.dev (2022)
> 
> micha at RMS:QGIS$ Rscript -e "sessionInfo()"
> R version 4.1.2 (2021-11-01)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 11 (bullseye)
> 
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/ openblas-pthread/libblas.so.3
> LAPACK: /usr/lib/x86_64-linux-gnu/ openblas-pthread/libopenblasp- r0.3.13.so
> 
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.1.2
> 
> If the Rscript executable is not found, then v.class.mlR cannot be run.
> 
> 
>>
>> Any help would be appreciated.
>> - Daniel
>> ------------------------------ ------------------------------ -----------------
>> *[Message 1]*
>>
>> Running R now. Following output is R output.
>>
>> Traceback (most recent call last):
>>
>> File "/Users/dankozar/Library/ GRASS/8.0/Addons/scripts/v. class.mlR", 
>> line 977, in <module>
>>
>> main()
>>
>> File "/Users/dankozar/Library/ GRASS/8.0/Addons/scripts/v. class.mlR", 
>> line 908, in main
>>
>> subprocess.check_call(
>>
>> File 
>> "/Applications/GRASS-8.0.app/ Contents/Resources/lib/ python3.9/subprocess.py", 
>> line 368, in check_call
>>
>> retcode = call(*popenargs, **kwargs)
>>
>> File 
>> "/Applications/GRASS-8.0.app/ Contents/Resources/lib/ python3.9/subprocess.py", 
>> line 349, in call
>>
>> with Popen(*popenargs, **kwargs) as p:
>>
>> File 
>> "/Applications/GRASS-8.0.app/ Contents/Resources/lib/ python3.9/subprocess.py", 
>> line 951, in __init__
>>
>> self._execute_child(args, executable, preexec_fn, close_fds,
>>
>> File 
>> "/Applications/GRASS-8.0.app/ Contents/Resources/lib/ python3.9/subprocess.py", 
>> line 1821, in _execute_child
>>
>> raise child_exception_type(errno_ num, err_msg, err_filename)
>>
>> FileNotFoundError: [Errno 2] No such file or directory: 'Rscript'
>>
>>
>> *[Message 2]*
>>
>> Details: <[Errno 1] Operation not permitted: 'v.class.mlR'>
>>
>> WARNING: Some addons failed when loading. Please consider to update 
>> your addons by running 'g.extension.all -f'.
>>
>>
>> -- 
>> Thank you,
>>
>> Daniel Kozar
>> PhD Candidate
>> UC Davis - Hydrologic Sciences
>> djkozar at ucdavis.edu
>> (814) 380-6900
>>
>> ______________________________ _________________
>> grass-user mailing list
>> grass-user at lists.osgeo.org
>> https://lists.osgeo.org/ mailman/listinfo/grass-user
> 
> -- 
> Micha Silver
> Ben Gurion Univ.
> Sde Boker, Remote Sensing Lab
> cell: +972-523-665918
> 
> 


-- 
Thank you, 

Daniel Kozar
Graduate Student
UC Davis - Hydrologic Sciences
djkozar at ucdavis.edu
(814) 380-6900


-- 
Thank you, 

Daniel Kozar
Graduate Student
UC Davis - Hydrologic Sciences
djkozar at ucdavis.edu
(814) 380-6900


_______________________________________________
grass-user mailing list
grass-user at lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-user