X-Loop: help-debbugs@HIDDEN Subject: bug#70064: Error when loading r-sf and other spatial packages (gdal related) Resent-From: Javier Vaquero =?UTF-8?Q?Mart=C3=ADnez?= <javier_vm@HIDDEN> Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> Resent-CC: bug-guix@HIDDEN Resent-Date: Fri, 29 Mar 2024 04:08:04 +0000 Resent-Message-ID: <handler.70064.B.17116852781019 <at> debbugs.gnu.org> Resent-Sender: help-debbugs@HIDDEN X-GNU-PR-Message: report 70064 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 70064 <at> debbugs.gnu.org X-Debbugs-Original-To: bug-guix@HIDDEN Received: via spool by submit <at> debbugs.gnu.org id=B.17116852781019 (code B ref -1); Fri, 29 Mar 2024 04:08:04 +0000 Received: (at submit) by debbugs.gnu.org; 29 Mar 2024 04:07:58 +0000 Received: from localhost ([127.0.0.1]:41395 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rq3X3-0000GL-PH for submit <at> debbugs.gnu.org; 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charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit 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 "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 </code></pre> <div title="MDH:PHA+RGVhciBndWl4IGNvbW11bml0eSw8L3A+PHA+SSBhbSBxdWl0ZSBuZXcgdG8gR3VpeCBzbyBJ IGFwb2xvZ2l6ZSBpZiBJIGFtIGRvaW5nIHNvbWV0aGluZyB3cm9uZy48L3A+PHA+SSBhZGRlZCBj aGFubmVsIGd1aXgtY3JhbiB0byBnZXQgUiBwYWNrYWdlcy4gSSBpbnN0YWxsZWQgci1zZiByLXRl cnJhLCBhbmQgb3RoZXIgcGFja2FnZXMuIEhvd2V2ZXIsIEkgY2Fubm90IGxvYWQgdGhlbSBpbiBS LjwvcD48cD5IZXJlLCBhdCB0aGUgZW5kIG9mIHRoZSBtZXNzYWdlIEkgc2hvdyBhbmQgZXhhbXBs ZSB3aXRoIHItcmdkYWwgYnV0IHNhbWUgdGhpbmcgaGFwcGVucyB3aXRoIHItc2Ygb3Igci10ZXJy YS48L3A+PHA+QW0gSSBkb2luZyBzb21ldGhpbmcgd3Jvbmc/IENhbiB5b3UgcmVwcm9kdWNlIHRo ZSBidWc/PC9wPjxwPlJlZ2FyZHMsPC9wPjxwPkphdmllci48YnI+PC9wPjxwPmBgYDxicj48L3A+ PHA+JCBndWl4IHNoZWxsIHIgci1yZ2RhbCAtLSBSIC1lICJsaWJyYXJ5KHJnZGFsKSI8YnI+PGJy PlIgdmVyc2lvbiA0LjMuMyAoMjAyNC0wMi0yOSkgLS0gIkFuZ2VsIEZvb2QgQ2FrZSI8YnI+Q29w eXJpZ2h0IChDKSAyMDI0IFRoZSBSIEZvdW5kYXRpb24gZm9yIFN0YXRpc3RpY2FsIENvbXB1dGlu Zzxicj5QbGF0Zm9ybTogeDg2XzY0LXVua25vd24tbGludXgtZ251ICg2NC1iaXQpPGJyPjxicj5S IGVzIHVuIHNvZnR3YXJlIGxpYnJlIHkgdmllbmUgc2luIEdBUkFOVElBIEFMR1VOQS48YnI+VXN0 ZWQgcHVlZGUgcmVkaXN0cmlidWlybG8gYmFqbyBjaWVydGFzIGNpcmN1bnN0YW5jaWFzLjxicj5F c2NyaWJhICdsaWNlbnNlKCknIG8gJ2xpY2VuY2UoKScgcGFyYSBkZXRhbGxlcyBkZSBkaXN0cmli dWNpb24uPGJyPjxicj5SIGVzIHVuIHByb3llY3RvIGNvbGFib3JhdGl2byBjb24gbXVjaG9zIGNv bnRyaWJ1eWVudGVzLjxicj5Fc2NyaWJhICdjb250cmlidXRvcnMoKScgcGFyYSBvYnRlbmVyIG3D oXMgaW5mb3JtYWNpw7NuIHk8YnI+J2NpdGF0aW9uKCknIHBhcmEgc2FiZXIgY8OzbW8gY2l0YXIg UiBvIHBhcXVldGVzIGRlIFIgZW4gcHVibGljYWNpb25lcy48YnI+PGJyPkVzY3JpYmEgJ2RlbW8o KScgcGFyYSBkZW1vc3RyYWNpb25lcywgJ2hlbHAoKScgcGFyYSBlbCBzaXN0ZW1hIG9uLWxpbmUg ZGUgYXl1ZGEsPGJyPm8gJ2hlbHAuc3RhcnQoKScgcGFyYSBhYnJpciBlbCBzaXN0ZW1hIGRlIGF5 dWRhIEhUTUwgY29uIHN1IG5hdmVnYWRvci48YnI+RXNjcmliYSAncSgpJyBwYXJhIHNhbGlyIGRl IFIuPGJyPjxicj4mZ3Q7IGxpYnJhcnkocmdkYWwpPGJyPkxvYWRpbmcgcmVxdWlyZWQgcGFja2Fn ZTogc3A8YnI+RXJyb3I6IHBhY2thZ2Ugb3IgbmFtZXNwYWNlIGxvYWQgZmFpbGVkIGZvciDigJhy Z2RhbOKAmSBpbiBkeW4ubG9hZChmaWxlLCBETExwYXRoID0gRExMcGF0aCwgLi4uKTo8YnI+Jm5i c3A7dW5hYmxlIHRvIGxvYWQgc2hhcmVkIG9iamVjdCAnL2dudS9zdG9yZS94anMyNmdkeHdqMjE0 OXJ6eG1xMXJmaWtibHkyaTF5ci1yLXJnZGFsLTEuNi03L3NpdGUtbGlicmFyeS9yZ2RhbC9saWJz L3JnZGFsLnNvJzo8YnI+Jm5ic3A7IC9nbnUvc3RvcmUvNzFrZ3F5cGlkZzJrc3Z3bTg0Y2Nxand5 emFpOWF5MWktZ2RhbC0zLjYuMS9saWIvbGliZ2RhbC5zby4zMjogdW5kZWZpbmVkIHN5bWJvbDog R0VPU0NvbmNhdmVIdWxsX3I8YnI+YGBgPGJyPjwvcD4=" aria-hidden="true" style="height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0;padding:0;margin:0;"></div> </div> </body> </html> --------------x2KYxPXsLxTQW2syl6DowcUC--
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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
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