[GRASS-user] Rscript error when using v.class.mlR
Jamille Haarloo
j.r.haarloo at gmail.com
Mon Jul 17 07:44:39 PDT 2023
ok, I misunderstood. I'm getting a similar response.
C:\Users\haarlooj\Documents>Rscript -e "sessionInfo()"
'Rscript' is not recognized as an internal or external command,
operable program or batch file.
On Mon, Jul 17, 2023 at 11:07 AM Micha Silver <tsvibar at gmail.com> wrote:
>
> On 17/07/2023 16:56, Jamille Haarloo wrote:
>
> 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.
>
> What you need to try is:
>
>
> Rscript -e "sessionInfo()"
>
>
> The GRASS module v.class.mlR needs to be able to "find" the Rscript
> executable in order to run.
>
>
> 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
>>
>> --
> Micha Silver
> Ben Gurion Univ.
> Sde Boker, Remote Sensing Lab
> cell: +972-523-665918
>
>
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