Segmentation fault

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Segmentation fault

Eduardo Diez
Hi everyone.
I'm having problems running spatial processes in a domino machine. I
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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Re: Segmentation fault

Roger Bivand
Administrator
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
> [hidden email]
> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Segmentation fault

Eduardo Diez
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?

Thanks,
Best

El mar., 29 oct. 2019 05:54, Roger Bivand <[hidden email]> 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
> > [hidden email]
> > 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: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>

        [[alternative HTML version deleted]]

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Re: Segmentation fault

Roger Bivand
Administrator
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 <[hidden email]> 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
>>> [hidden email]
>>> 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: [hidden email]
>> 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
> [hidden email]
> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Segmentation fault

Eduardo Diez
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 <[hidden email]> 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 <[hidden email]>
> 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
> >>> [hidden email]
> >>> 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: [hidden email]
> >> 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
> > [hidden email]
> > 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: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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Re: Segmentation fault

Roger Bivand
Administrator
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 <[hidden email]> 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 <[hidden email]>
>> 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
>>>>> [hidden email]
>>>>> 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: [hidden email]
>>>> 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
>>> [hidden email]
>>> 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: [hidden email]
>> 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
> [hidden email]
> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway