[R-sig-Geo] Segmentation fault

Tue Oct 29 17:35:55 CET 2019

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.
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

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