R crashes when reading geopackage files with st_read (sf package) in macOS

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 at nhh.no


________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Manuel Sp?nola <mspinola10 at 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 Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>


_______________________________________________
R-sig-Geo mailing list
R-sig-Geo at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Further, with R 4.0.4 on Rosetta but with CRAN binary packages, there is no problem. It is most likely that the problem is caused by user-installed upstream software components, and sf or rgdal installed from source, possibly with libsqlite3 also installed from source. Please report back if any other drivers fail - RSQLite does not use local binaries, but bundles the software library itself.

--
Roger Bivand
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
Roger.Bivand at nhh.no


________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Roger Bivand <Roger.Bivand at nhh.no>
Sendt: onsdag 31. mars 2021 18.25
Til: Manuel Sp?nola; r-sig-geo
Emne: Re: [R-sig-Geo]  R crashes when reading geopackage files with st_read (sf package) in macOS

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 at nhh.no


________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Manuel Sp?nola <mspinola10 at 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 Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>


_______________________________________________
R-sig-Geo mailing list
R-sig-Geo at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

_______________________________________________
R-sig-Geo mailing list
R-sig-Geo at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Thank you very much Roger.

I reinstalled the sf and rgdal packages from binaries and the problem
persisted.

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

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.

I can read the files without problem with readOGR.

Manuel

El mi?, 31 mar 2021 a las 10:26, Roger Bivand (<Roger.Bivand at nhh.no>)
escribi?:

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 at nhh.no

________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Manuel
Sp?nola <mspinola10 at 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 Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <
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 at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

	[[alternative HTML version deleted]]

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 mi?, 31 mar 2021 a las 10:26, Roger Bivand (<Roger.Bivand at nhh.no>)
escribi?:

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 at nhh.no

________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Manuel
Sp?nola <mspinola10 at 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 Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <
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 at 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 at nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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 mi?, 31 mar 2021 a las 13:07, Roger Bivand (<Roger.Bivand at nhh.no>)
escribi?:

On Wed, 31 Mar 2021, Manuel Sp?nola 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 mi?, 31 mar 2021 a las 10:26, Roger Bivand (<Roger.Bivand at nhh.no>)
escribi?:

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 at nhh.no

________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces at r-project.org> p? vegne av Manuel
Sp?nola <mspinola10 at 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 Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <
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 at 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 at nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

	[[alternative HTML version deleted]]