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

Daniel_Jeffrey_Kozar · February 19, 2022, 2:27am

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.

Any help would be appreciated.

Daniel

···

Thank you,

Daniel Kozar
PhD Candidate

UC Davis - Hydrologic Sciences
djkozar@ucdavis.edu
(814) 380-6900

Micha_Silver1 · February 19, 2022, 9:46am

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@RMS:~$ Rscript -e "sessionInfo()"

Now run the same from within a GRASS session:

(here's what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev (2022)

micha@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@ucdavis.edu
(814) 380-6900

_______________________________________________
grass-user mailing list
grass-user@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

Daniel_Jeffrey_Kozar · February 20, 2022, 12:55am

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@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@RMS:~$ Rscript -e “sessionInfo()”

Now run the same from within a GRASS session:

(here’s what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev (2022)

micha@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

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@ucdavis.edu
(814) 380-6900

grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

–

Thank you,

Daniel Kozar
Graduate Student

UC Davis - Hydrologic Sciences
djkozar@ucdavis.edu
(814) 380-6900

nila · February 20, 2022, 11:24am

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@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@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@RMS:~$ Rscript -e "sessionInfo()"

Now run the same from within a GRASS session:

(here's what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev (2022)

micha@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@ucdavis.edu
(814) 380-6900

______________________________ _________________
grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

--
Thank you,

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

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

Jamille_Haarloo · July 14, 2023, 11:04pm

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.

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
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@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@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@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@RMS:~$ Rscript -e “sessionInfo()”

Now run the same from within a GRASS session:

(here’s what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev (2022)

micha@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

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@ucdavis.edu
(814) 380-6900

grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

–
Thank you,

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

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

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

Micha_Silver1 · July 15, 2023, 12:17pm

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@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@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@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@RMS:~$ Rscript -e "sessionInfo()"
    >
    > Now run the same from within a GRASS session:
    >
    > (here's what I get)
    >
    > micha@RMS:QGIS$ g.version
    > GRASS 8.1.dev <http://8.1.dev> (2022)
    >
    > micha@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@ucdavis.edu
    >> (814) 380-6900
    >>
    >> ______________________________ _________________
    >> grass-user mailing list
    >> grass-user@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@ucdavis.edu
    (814) 380-6900

    -- Thank you,

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

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

_______________________________________________
grass-user mailing list
grass-user@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

Jamille_Haarloo · July 17, 2023, 1:56pm

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@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) <http://v.class.mlR.py>”, line 977, in
main()
File “C:\Users\haarlooj\AppData\Roaming\GRASS8\addons\scri
pts[v.class.mlR.py](http://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@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@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@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@RMS:~$ Rscript -e “sessionInfo()”

Now run the same from within a GRASS session:

(here’s what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev <http://8.1.dev> (2022)

micha@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

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@ucdavis.edu
(814) 380-6900

grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

–
Thank you,

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

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

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

grass-user mailing list
grass-user@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_Silver1 · July 17, 2023, 2:07pm

···

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@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) <http://v.class.mlR.py>”, line 977, in
main()
File “C:\Users\haarlooj\AppData\Roaming\GRASS8\addons\scri
pts[v.class.mlR.py](http://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@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@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@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@RMS:~$ Rscript -e “sessionInfo()”

Now run the same from within a GRASS session:

(here’s what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev <http://8.1.dev> (2022)

micha@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

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@ucdavis.edu
(814) 380-6900

grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

–
Thank you,

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

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

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

grass-user mailing list
grass-user@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

Jamille_Haarloo · July 17, 2023, 2:44pm

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@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@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) <http://v.class.mlR.py>”, line 977, in
main()
File “C:\Users\haarlooj\AppData\Roaming\GRASS8\addons\scri
pts[v.class.mlR.py](http://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@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@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@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@RMS:~$ Rscript -e “sessionInfo()”

Now run the same from within a GRASS session:

(here’s what I get)

micha@RMS:QGIS$ g.version
GRASS 8.1.dev <http://8.1.dev> (2022)

micha@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

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@ucdavis.edu
(814) 380-6900

grass-user mailing list
grass-user@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@ucdavis.edu
(814) 380-6900

–
Thank you,

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

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

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

grass-user mailing list
grass-user@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