[R-sig-Geo] Segmentation fault
Roger Bivand
Roger@B|v@nd @end|ng |rom nhh@no
Tue Oct 29 19:54:47 CET 2019
On Tue, 29 Oct 2019, Eduardo Diez wrote:
> The OS was part of my initial post:
>
>> sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.3 LTS
>
>
> But nevermind, I'll stop posting here.
Please do raise the issue; it's the proper place for installation problems
like this.
Roger
> Thanks
>
> El mar., 29 oct. 2019 09:21, Roger Bivand <Roger.Bivand using nhh.no> escribió:
>
>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> 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,
>>>> 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
>>>>
>>>
>>> [[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,
>> 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
>
> [[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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