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

[Manuel Spínola]

Thank you very much Roger.

I can read shapefile without any problem with st_read.

I think it works for both versions, but definitely is working with the
binary version.

How can I work around the problem with libsqlite3?

How can I install the GDAL, PROJ and GEOS without being from source?

Best,

Manuel


El mié, 31 mar 2021 a las 13:07, Roger Bivand (<Roger.Bivand using nhh.no>)
escribió:

> 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



-- 
*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/>

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