[R-sig-Geo] Segmentation fault

[Roger Bivand]

On Tue, 29 Oct 2019, Eduardo Diez wrote:

> Roger,
> Yes sorry about the confusion. Domino is a company (dominodatalab.com) that
> offers a an environment for data science. It's based on docker images. On
> one of those images I installed sf and lwgeom. What information should I
> get from the image that helps identify the source of the problem?

What OS is the docker image running; where do they get the image? Please 
do raise this as an issue, this is not the best channel for this, and 
nobody else uses this image I guess. The problem is most likely that the 
image does not have the necessary underlying external requirements set up 
correctly.

Roger

>
> Thanks,
> Best
>
> El mar., 29 oct. 2019 05:54, Roger Bivand <Roger.Bivand using nhh.no> escribió:
>
>> On Mon, 28 Oct 2019, Eduardo Diez wrote:
>>
>>> Hi everyone.
>>> I'm having problems running spatial processes in a domino machine. I
>>
>> Please raise an issue on https://github.com/r-spatial/sf/issues, giving
>> much more detail about your installation (domino is unknown to everybody
>> but yourself, duckduckgo says: "Domino Machine manufactures blow out
>> preventers, stuffing boxes, and API products"). Likely cause - failed
>> installation of lwgeom, or multiple installs of external software. Avoid
>> posting HTML.
>>
>> Roger
>>
>>> created a new environment with updated spatial packages but I'm unable to
>>> run simple tasks. Below an example and some information:
>>>
>>>> library(sf)Linking to GEOS 3.6.2, GDAL 2.4.2, PROJ 4.9.3> sessionInfo()
>>> R version 3.6.1 (2019-07-05)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 18.04.3 LTS
>>>
>>> Matrix products: default
>>> BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
>>> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] sf_0.8-0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.6.1     magrittr_1.5       class_7.3-15       tools_3.6.1
>>> [5] DBI_1.0.0          units_0.6-5        Rcpp_1.0.2
>>  KernSmooth_2.23-16
>>> [9] grid_3.6.1         e1071_1.7-2        classInt_0.4-2
>>>> sf_extSoftVersion()
>>>          GEOS           GDAL         proj.4 GDAL_with_GEOS     USE_PROJ_H
>>>       "3.6.2"        "2.4.2"        "4.9.3"         "true"        "false"
>>>> nc = st_read(system.file("shape/nc.shp", package="sf"))
>>> Reading layer `nc' from data source
>>> `/usr/local/lib/R/site-library/sf/shape/nc.shp' using driver `ESRI
>>> Shapefile'
>>> Simple feature collection with 100 features and 14 fields
>>> geometry type:  MULTIPOLYGON
>>> dimension:      XY
>>> bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax:
>> 36.58965
>>> epsg (SRID):    4267
>>> proj4string:    +proj=longlat +datum=NAD27 +no_defs
>>>> asd <- st_area(nc[1,]) # area from long/lat
>>>
>>>
>>> *** caught segfault ***
>>> address (nil), cause 'unknown'
>>> Traceback:
>>> 1: CPL_crs_parameters(x$proj4string)
>>> 2: structure(CPL_crs_parameters(x$proj4string), names =
>>> c("SemiMajor",     "SemiMinor", "InvFlattening", "units_gdal",
>>> "IsVertical",     "WktPretty", "Wkt"))
>>> 3: crs_parameters(crs) 4: st_crs.sfc(st_geometry(x), parameters = TRUE)
>>> 5: st_crs(st_geometry(x), parameters = TRUE)
>>> 6: lwgeom::st_geod_area(x)
>>> 7: st_area.sfc(st_geometry(x, ...))
>>> 8: st_area(st_geometry(x, ...))
>>> 9: st_area.sf(nc[1, ])
>>> 10: st_area(nc[1, ])
>>> An irrecoverable exception occurred. R is aborting now ...Segmentation
>>> fault (core dumped)
>>>
>>>
>>> Thanks in advance
>>>
>>> Best,
>>>
>>> Edu
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>
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-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en