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

[Micha Silver]

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
>
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-- 
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918