[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 can read shapefile without any problem with st_read.
>
> I think it works for both versions, but definitely is working with the
> binary version.

I really feel that you should remove all traces of your source installs of 
PROJ, GDAL and GEOS and anything they installed, and should rely only on 
CRAN binary packages. Do not accept any suggestions to install R packages 
from source. However, if other software that you use regularly needs PROJ, 
GDAL, GEOS, they may be present and may interfere with R packages. CRAN 
binary packages are built static, so do not need other dylibs, but have 
files under share/ in their own space that may conflict.

>
> How can I work around the problem with libsqlite3?

How was the version of libsqlite3 that GDAL links to installed? How would 
one

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

What do you need them for - if only for R packages, just don't install 
them.

A further alternative - consider installing from

https://r-spatial.r-universe.dev/ui#builds

These track the development versions of packages, but should be OK.

Please report back whether any of these can read (and write) GPKG.

Roger

> 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
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>>>>
>>>
>>>
>>>
>>
>> --
>> 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
>
>
>
>

-- 
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