[GRASS-user] Rscript error when using v.class.mlR
Jamille Haarloo
j.r.haarloo at gmail.com
Mon Jul 17 06:56:28 PDT 2023
Thank you Micha,
This was the msg following "C:\Users\haarlooj\Documents> sessionInfo()":
'sessionInfo' is not recognized as an internal or external command,
operable program or batch file.
I looked for the location and found this as location of R:
C:\Program Files\R\R-4.3.0\bin\x64
Location for Rstudio:
C:\Program Files\RStudio
Is it correct that I need to change the paths? What is the best method?
Best,
Jamille
On Sat, Jul 15, 2023 at 9:17 AM Micha Silver <tsvibar at gmail.com> wrote:
> Hi Jamille
>
>
> On 15/07/2023 2:04, Jamille Haarloo wrote:
> > Dear all,
> >
> > What was the solution to this error? I recently got a similar error
> > from the same module v.class.mlR. I am using GRASS GIS 8.2.1 on
> > Windows 10.
> >
>
> The previous post was in reference to MacOS. Can you check on your
> system that the Rscript executable is available from the GRASS command
> window? i.e.
>
> - start grass (even without the GUI)
>
> - go to the command shell
>
> - run Rscript -e "sessionInfo()"
>
>
> This will identify if the problem is due to missing PATH in the env
> variables.
>
>
>
> > Best,
> > Jamille
> >
> > ----
> > Running R now. Following output is R output.
> > Traceback (most recent call last):
> > File "C:\Users\haarlooj\AppData\Roaming\GRASS8\addons\scri
> > pts\v.class.mlR.py <http://v.class.mlR.py>", line 977, in <module>
> > main()
> > File "C:\Users\haarlooj\AppData\Roaming\GRASS8\addons\scri
> > pts\v.class.mlR.py <http://v.class.mlR.py>", line 908, in main
> > subprocess.check_call(
> > File "C:\OSGeo4W\apps\Python39\lib\subprocess.py", line
> > 368, in check_call
> > retcode = call(*popenargs, **kwargs)
> > File "C:\OSGeo4W\apps\Python39\lib\subprocess.py", line
> > 349, in call
> > with Popen(*popenargs, **kwargs) as p:
> > File "C:\OSGeo4W\apps\Python39\lib\subprocess.py", line
> > 951, in __init__
> > self._execute_child(args, executable, preexec_fn,
> > close_fds,
> > File "C:\OSGeo4W\apps\Python39\lib\subprocess.py", line
> > 1420, in _execute_child
> > hp, ht, pid, tid = _winapi.CreateProcess(executable,
> > args,
> > FileNotFoundError: [WinError 2] The system cannot find the
> > file specified
> >
> >
> > On Sun, Feb 20, 2022 at 8:24 AM Nicklas Larsson via grass-user
> > <grass-user at lists.osgeo.org> wrote:
> >
> > 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 <http://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 <http://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/ <http://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/ <http://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/ <http://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/ <http://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
> > _______________________________________________
> > grass-user mailing list
> > grass-user at lists.osgeo.org
> > https://lists.osgeo.org/mailman/listinfo/grass-user
> >
> >
> > _______________________________________________
> > 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.osgeo.org/pipermail/grass-user/attachments/20230717/ea5db222/attachment-0001.htm>
More information about the grass-user
mailing list