Error when loading r-sf and other spatial packages (gdal related)

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2 participants
  • Javier Vaquero Martínez
  • Simon Tournier
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Javier Vaquero Martínez
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normal

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Javier Vaquero Martínez wrote 12 months ago
(address . bug-guix@gnu.org)
b3adea4f-849a-41a6-af63-4eca27863778@unex.es
Dear guix community,

I am quite new to Guix so I apologize if I am doing something wrong.

I added channel guix-cran to get R packages. I installed r-sf r-terra,
and other packages. However, I cannot load them in R.

Here, at the end of the message I show and example with r-rgdal but same
thing happens with r-sf or r-terra.

Am I doing something wrong? Can you reproduce the bug?

Regards,

Javier.

|$ guix shell r r-rgdal -- R -e "library(rgdal)" R version 4.3.3
(2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation
for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R
es un software libre y viene sin GARANTIA ALGUNA. Usted puede
redistribuirlo bajo ciertas circunstancias. Escriba 'license()' o
'licence()' para detalles de distribucion. R es un proyecto colaborativo
con muchos contribuyentes. Escriba 'contributors()' para obtener más
información y 'citation()' para saber cómo citar R o paquetes de R en
publicaciones. Escriba 'demo()' para demostraciones, 'help()' para el
sistema on-line de ayuda, o 'help.start()' para abrir el sistema de
ayuda HTML con su navegador. Escriba 'q()' para salir de R. >
library(rgdal) Loading required package: sp Error: package or namespace
load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object
'/gnu/store/xjs26gdxwj2149rzxmq1rfikbly2i1yr-r-rgdal-1.6-7/site-library/rgdal/libs/rgdal.so':
/gnu/store/71kgqypidg2ksvwm84ccqjwyzai9ay1i-gdal-3.6.1/lib/libgdal.so.32:
undefined symbol: GEOSConcaveHull_r |

​
Attachment: file
Javier Vaquero Martínez wrote 12 months ago
(address . 70064@debbugs.gnu.org)
147de374-ea73-4996-88c3-b33d341edf80@unex.es
So I managed to solve this. It turns out that some environment variables
where making this error to happen. Running in an isolated environment
with `guix shell -C r r-sf -- r` solves the problem.


Regards
Simon Tournier wrote 10 months ago
(name . Javier Vaquero Martínez)(address . javier_vm@unex.es)(address . 70064@debbugs.gnu.org)
87v82nmise.fsf@gmail.com
Hi,

On Thu, 04 Apr 2024 at 18:04, Javier Vaquero Martínez <javier_vm@unex.es> wrote:

Toggle quote (4 lines)
> So I managed to solve this. It turns out that some environment variables
> where making this error to happen. Running in an isolated environment
> with `guix shell -C r r-sf -- r` solves the problem.

Thanks for letting us know. Therefore, can we close?

Cheers,
simon
Javier Vaquero Martínez wrote 10 months ago
(name . Simon Tournier)(address . zimon.toutoune@gmail.com)(address . 70064@debbugs.gnu.org)
77a899e0-f404-4106-be65-3704b529807a@unex.es
Yes, it can be closed.

Regards.

El 5/6/24 a las 18:54, Simon Tournier escribió:
Toggle quote (13 lines)
> [No suele recibir correo electrónico de zimon.toutoune@gmail.com. Descubra por qué esto es importante en https://aka.ms/LearnAboutSenderIdentification]
>
> Hi,
>
> On Thu, 04 Apr 2024 at 18:04, Javier Vaquero Martínez <javier_vm@unex.es> wrote:
>
>> So I managed to solve this. It turns out that some environment variables
>> where making this error to happen. Running in an isolated environment
>> with `guix shell -C r r-sf -- r` solves the problem.
> Thanks for letting us know. Therefore, can we close?
>
> Cheers,
> simon
Simon Tournier wrote 10 months ago
control message for bug #70064
(address . control@debbugs.gnu.org)
87plsvmhcx.fsf@gmail.com
close 70064
quit
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