spgrass causes segfault

-----Urspr?ngliche 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 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(). 

  require(spgrass6)

  sessionInfo()

  tmp <- readRAST6("geology", plugin=FALSE)

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_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>

-- 
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