[R-sig-Geo] spgrass causes segfault

Dominik.Cullmann at Forst.bwl.de Dominik.Cullmann at Forst.bwl.de
Thu Jul 23 14:19:34 CEST 2009 

Dear Roger,
thanks a lot for your immedate help!
> -----Ursprüngliche Nachricht-----
> Von: Roger Bivand [mailto:Roger.Bivand at nhh.no] 
> Gesendet: Donnerstag, 23. Juli 2009 12:53
> An: Cullmann, Dominik (FORST)
> Cc: r-sig-geo at stat.math.ethz.ch
> Betreff: Re: [R-sig-Geo] spgrass causes segfault
> 
> 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 had given that information at the end of the original mail but I'll repeat it, see below.

> 
> 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(). 
This works:
>   require(spgrass6)
Loading required package: 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.UTF-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_IDENTIFICATION=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", plugin=FALSE)
/home/data/grass/spearfish60/PERMANENT/.tmp/f060/geology has GDAL driver GTiff
and has 140 rows and 190 columns


> 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.
Well, gdalinfo seems to work fine: 

101:~/$ gdalinfo /home/data/grass/spearfish60/PERMANENT/cellhd/geology
Driver: GRASS/GRASS Database Rasters (5.7+)
Files: /home/data/grass/spearfish60/PERMANENT/cellhd/geology
Size is 190, 140
Coordinate System is `'
Origin = (590000.000000000000000,4928000.000000000000000)
Pixel Size = (100.000000000000000,-100.000000000000000)
Corner Coordinates:
Upper Left  (  590000.000, 4928000.000)
Lower Left  (  590000.000, 4914000.000)
Upper Right (  609000.000, 4928000.000)
Lower Right (  609000.000, 4914000.000)
Center      (  599500.000, 4921000.000)
Band 1 Block=190x1 Type=Byte, ColorInterp=Palette
  Min=1.000 Max=9.000
  NoData Value=0
  Metadata:
    COLOR_TABLE_RULES_COUNT=0
  Color Table (RGB with 10 entries)
    0: 197,129,125,255
    1: 107,250,75,255
    2: 226,83,250,255
    3: 246,222,188,255
    4: 123,225,27,255
    5: 134,190,1,255
    6: 48,86,221,255
    7: 113,70,15,255
    8: 102,134,101,255
    9: 89,135,169,255

> 
> If this isn't the cause, I'd like an example using spearfish and with 
> complete details of your GRASS and GDAL installations.
> 
The example I gave was on the 'geology' raster from the spearfish60 data set.
I had given installation details at the end of the original mail: 

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
...
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



> 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,
Yes, it does. Thanks again,
Dominik

> 
> 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_COLLA
> TE=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_ID
> ENTIFICATI
> > 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>
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> 
> -- 
> 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
> 
> 


----------------------------------------------
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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