[R-sig-Geo] spgrass causes segfault
Roger Bivand
Roger.Bivand at nhh.no
Thu Jul 23 12:53:24 CEST 2009
On Thu, 23 Jul 2009, Dominik.Cullmann at Forst.bwl.de wrote:
> Dear all,
> when I call readRAST6 or readVECT6, it causes a segfault and gives
> Traceback Info I
> don't understand:
Thanks for the traceback information, and for including the verbatim
command that caused the problem. Next time, please include sessionInfo()
output too, and in this case, also the loading messages from rgdal and
spgrass6. Here, it would also have helped to see what gdalDrivers() said.
I suspect that you are in "dependency hell", and that your system has a
wrongly installed GDAL plugin for GRASS rasters and vectors. Please read
the manual pages for readVECT6() and readRAST6() - you will see that if
the plugin= argument is not given (NULL), the documentation says that the
presence (or not) of the plugin is autodetected (by looking at
ogrDrivers() and gdalDrivers()).
Unless you know definitely that the plugin does work (and it is the most
frequent cause of dependency problems), please try setting plugin=FALSE in
readRAST6() and readVECT6(). If that resolves the problem, please then try
to see what happens when gdalinfo used outside R tries to access the GRASS
raster using the plugin, see http://www.gdal.org/frmt_grass.html for the
incantation. If that fails, then you will know that the problem is with
the GDAL GRASS plugin.
If this isn't the cause, I'd like an example using spearfish and with
complete details of your GRASS and GDAL installations.
The stats-grass list would also have been a good place to ask - its
archives show that happy plugin users are most often those who build
everything from source, and unhappy ones those who install binary
versions. It is extremely hard to make sure that all the binary
versions of the dependent software are correctly alligned (and there is a
possible circular dependency here too in older versions of GRASS and
GDAL).
Hope this helps,
Roger
> =======
>> tmp<-readRAST6("geology")
>
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
>
> Traceback:
> 1: .Call("RGDAL_OpenDataset", as.character(filename), TRUE, PACKAGE =
> "rgdal")
> 2: .local(.Object, ...)
> 3: initialize(value, ...)
> 4: initialize(value, ...)
> 5: new("GDALReadOnlyDataset", filename)
> 6: GDAL.open(fname)
> 7: GDALinfo(fname)
> 8: readRAST6("geology")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> =======
> Can anybody 'round here give me a hint on how I might get this working?
>
> I'm using R version 2.9.1 (2009-06-26) from backports on Debian stable:
> =======
> ======= some system info
> =======
> 104:~/$ cat /etc/debian_version
> 5.0.2
> 105:~/$ uname -a
> Linux f060 2.6.26-2-686 #1 SMP Sun Jun 21 04:57:38 UTC 2009 i686
> GNU/Linux
> 106:~/$ dpkg -l |grep gdal
> ii gdal-bin 1.5.4-2 Geospatial Data
> Abstraction Library - Utility programs
> ii libgdal1-1.5.0 1.5.4-2 Geospatial Data
> Abstraction Library
> ii libgdal1-1.5.0-grass 1.5.2-1 GRASS extension for
> the Geospatial Data Abstraction Library
> ii libgdal1-dev 1.5.4-2 Geospatial Data
> Abstraction Library - Development files
> 115:~/$ dpkg -l |grep "Cartographic projection"
> ii proj 4.6.0-2 Cartographic
> projection filter and library
>
> =======
> ======= Now after I started R form within grass
> =======
>> library(spgrass6)
> Loading required package: sp
> Loading required package: rgdal
> Geospatial Data Abstraction Library extensions to R successfully loaded
> Loaded GDAL runtime: GDAL 1.5.4, released 2009/01/07
> Path to GDAL shared files: /usr/share/gdal15
> Loaded PROJ.4 runtime: Rel. 4.6.0, 21 Dec 2007
> Path to PROJ.4 shared files: (autodetected)
> Loading required package: XML
> GRASS GIS interface loaded with GRASS version: 6.4.0RC5
> and location: spearfish60
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
> ON=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] spgrass6_0.6-6 XML_2.5-3 rgdal_0.6-9 sp_0.9-43
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.1 lattice_0.17-25
>> tmp<-readRAST6("geology")
>
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
>
> Traceback:
> 1: .Call("RGDAL_OpenDataset", as.character(filename), TRUE, PACKAGE =
> "rgdal")
> 2: .local(.Object, ...)
> 3: initialize(value, ...)
> 4: initialize(value, ...)
> 5: new("GDALReadOnlyDataset", filename)
> 6: GDAL.open(fname)
> 7: GDALinfo(fname)
> 8: readRAST6("geology")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> =======
> =======
> =======
> oh, and I'm using grass version 6.4.0RC5 which I compiled after
> configuring via
> CFLAGS="-g -Wall" ./configure --with-opengl=no
> --with-tcltk-libs=/usr.lib --with-tcltk-includes='/usr/include/tcl8.4/
> /usr/include/tk/' --with-tcltk-libs='/usr/lib/tcl8.4/' --with-odbc=yes
> --with-fftw-libs='/usr/include' -with-gdal='/usr/bin/gdal-config'
> --with-postgres=yes --with-postgres-includes='/usr/include/postgresql/'
> --enable-largefile --with-lapack=yes --with-blas=yes
>
>
> Thanks and regards, Dominik
> ----------------------------------------------
> Andreas Dominik Cullmann
> Forstliche Versuchs- und Forschungsanstalt
> Wonnhalde 4
> 79100 Freiburg
> Tel. +49 761 4018 204
> Email: dominik.cullmann at forst.bwl.de
> <mailto:dominik.cullmann at forst.bwl.de>
> Homepage: www.fva-bw.de <http://www.fva-bw.de>
>
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>
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no
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