[R-sig-Geo] R crashes when reading geopackage files with st_read (sf package) in macOS

[Roger Bivand]

On Wed, 31 Mar 2021, Manuel Spínola wrote:

> Thank you very much Roger.
>
> I reinstalled the sf and rgdal packages from binaries and the problem
> persisted.

This must be either because you did not remove all of the traces of the 
previous attempts. If sf failed, then 
https://cran.r-project.org/web/checks/check_results_sf.html
would show errors for MacOS.

>
> To install GDAL, PROJ and GEOS i followed the instructions in the sf github
> site.

Please avoid installing the source package unless there is functionality 
not provided by the CRAN binary.

>
> Yes, the problem is with several geopackages files.  I see the problem also
> with st_write when working trying to save a file in geopackage format.
>

Which other drivers are affected - if only GPKG, then libsqlite3 is the 
most likely culprit. However, unless you must have facilities only 
available by source install, avoid source installs.

> I can read the files without problem with readOGR.
>

Installed as the CRAN binary or source?

Roger

> Manuel
>
> El mié, 31 mar 2021 a las 10:26, Roger Bivand (<Roger.Bivand using nhh.no>)
> escribió:
>
>> Please refer to the associated sf issue on github:
>> https://github.com/r-spatial/sf/issues/1606 for completeness. Please
>> confirm that you are not using the MacOS sf CRAN binary package, but have
>> installed GDAL, PROJ and GEOS yourself. Please also confirm that you see
>> the same error with every GPKG file.
>>
>> --
>> Roger Bivand
>> Norwegian School of Economics
>> Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
>> Roger.Bivand using nhh.no
>>
>>
>> ________________________________________
>> Fra: R-sig-Geo <r-sig-geo-bounces using r-project.org> på vegne av Manuel
>> Spínola <mspinola10 using gmail.com>
>> Sendt: onsdag 31. mars 2021 17.55
>> Til: r-sig-geo
>> Emne: [R-sig-Geo] R crashes when reading geopackage files with st_read (sf
>> package) in macOS
>>
>> Dear list members,
>>
>> When reading geopackages files with st_read (sf package) RStudio crashes (R
>> session aborted) in macOS.  Any suggestions to fix this problem?
>>
>> Should I ask this question to the macOS group (r-sig-mac)?
>>
>> library(sf)
>> Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
>>
>>
>> library(spData)
>>
>>
>> world = st_read(system.file("shapes/world.gpkg", package = "spData"))
>>
>>
>>
>>
>> --
>> *Manuel Spínola, Ph.D.*
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> mspinola using una.cr <mspinola using una.ac.cr>
>> mspinola10 using gmail.com
>> Teléfono: (506) 8706 - 4662
>> Personal website: Lobito de río <
>> https://sites.google.com/site/lobitoderio/>
>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway.
e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en