GNU bug report logs - #70064
Error when loading r-sf and other spatial packages (gdal related)

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Package: guix; Reported by: Javier Vaquero Martínez <javier_vm@HIDDEN>; dated Fri, 29 Mar 2024 04:08:04 UTC; Maintainer for guix is bug-guix@HIDDEN.

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Subject: Error when loading r-sf and other spatial packages (gdal related)
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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
Information forwarded to bug-guix@HIDDEN:
bug#70064; Package guix. Full text available.

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Subject: Error when loading r-sf and other spatial packages (gdal related)
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--------------x2KYxPXsLxTQW2syl6DowcUC
Content-Type: text/plain; charset=UTF-8; format=flowed
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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 |

​
--------------x2KYxPXsLxTQW2syl6DowcUC
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!DOCTYPE html><html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    <div class="markdown-here-wrapper" data-md-url="" style="">
      <p style="margin: 0px 0px 1.2em !important;">Dear guix community,</p>
      <p style="margin: 0px 0px 1.2em !important;">I am quite new to
        Guix so I apologize if I am doing something wrong.</p>
      <p style="margin: 0px 0px 1.2em !important;">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.</p>
      <p style="margin: 0px 0px 1.2em !important;">Here, at the end of
        the message I show and example with r-rgdal but same thing
        happens with r-sf or r-terra.</p>
      <p style="margin: 0px 0px 1.2em !important;">Am I doing something
        wrong? Can you reproduce the bug?</p>
      <p style="margin: 0px 0px 1.2em !important;">Regards,</p>
      <p style="margin: 0px 0px 1.2em !important;">Javier.</p>
      <pre style="font-family: Consolas, Inconsolata, Courier, monospace;font-size: 1em; line-height: 1.2em;margin: 1.2em 0px;"><code style="font-family: Consolas, Inconsolata, Courier, monospace;margin: 0px 0.15em; padding: 0px 0.3em; white-space: pre-wrap; font-weight: 550; background-color: rgba(119, 119, 119, 0.3); border-radius: 3px; display: inline;white-space: pre; overflow: auto; border-radius: 3px; border: 1px solid rgb(204, 204, 204); padding: 0.5em 0.7em; display: block;">
$ guix shell r r-rgdal -- R -e &quot;library(rgdal)&quot;

R version 4.3.3 (2024-02-29) -- &quot;Angel Food Cake&quot;
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.

&gt; 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
</code></pre>
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--------------x2KYxPXsLxTQW2syl6DowcUC--
Acknowledgement sent to Javier Vaquero Martínez <javier_vm@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#70064; Package guix. Full text available.
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