[R-sig-Geo] can't initiate Grass with initGRASS()

[William McCoy]

Roger,

I think your suspicions are correct.  Here is the output from debug 
after the PATH setting if():

Browse[2]> Sys.getenv("PATH")
 
 
 
                                        PATH
"/usr/local/texlive/2009/bin/i386-linux:/usr/lib/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/wdmccoy/bin:/usr/local/grass-6.4.0svn/bin:/usr/local/grass-6.4.0svn/scripts" 

Browse[2]> list.files(Sys.getenv("PATH"))
character(0)
Browse[2]> Sys.getenv("LD_LIBRARY_PATH")
 
 
                                 LD_LIBRARY_PATH
"/usr/lib/R/lib:/usr/local/lib:/usr/lib/jvm/jre/lib/i386/server:/usr/lib/jvm/jre/lib/i386:/usr/lib/jvm/java/lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib:/usr/local/grass-6.4.0svn/lib" 

Browse[2]> list.files(Sys.getenv("LD_LIBRARY_PATH"))
character(0)


Since I last used spgrass6 many months ago, I have installed grass64svn 
along with grass63, which was long ago installed as a fedora rpm.  So my 
PATH looks like this:


[wdmccoy at boreas ~]$ echo $PATH
/usr/local/texlive/2009/bin/i386-linux:/usr/lib/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/wdmccoy/bin


But my LD_LIBRARY_PATH looks like this:

[wdmccoy at boreas ~]$ echo $LD_LIBRARY_PATH


I.e., there is nothing in LD_LIBRARY_PATH.  The reason grass64 works by 
itself (outside of R) is because I have a grass64.conf file in 
/etc/ld.so.conf.d and that .conf file contains:

/usr/local/grass-6.4.0svn/lib


What do you recommend?


Thanks, Bill


On 08/28/2010 05:41 AM, Roger Bivand wrote:
> On Fri, 27 Aug 2010, William McCoy wrote:
>
>> I am using spgrass6, but I can't seem to initiate a grass session. I
>> managed to do this correctly months ago, but can't seem to now. Here
>> is my code and sessionInfo:
>
> Something has happened to your GRASS installation and/or the
> LD_LIBRARY_PATH environment variable. The GRASS binary modules are being
> found, but the libraries (shared objects) they call are not. Try to set
> debug(initGRASS), then step through looking at what is in environment
> variables, etc. After the if () for conditionally setting the PATH, look
> at:
>
> Sys.getenv("PATH")
> list.files(Sys.getenv("PATH"))
>
> and similarly for LD_LIBRARY_PATH:
>
> Sys.getenv("LD_LIBRARY_PATH")
> list.files(Sys.getenv("LD_LIBRARY_PATH"))
>
> I suspect that the test:
>
> eLDPATH <- Sys.getenv("LD_LIBRARY_PATH")
> grep(basename(Sys.getenv("GISBASE")), eLDPATH)
>
> is not empty, so the LD_LIBRARY_PATH does not get edited to include the
> actual locations of the *.so files.
>
> Have you changed the definitions of these environment variables in a
> .bashrc or similar between this working and no longer working? Before
> starting R, say:
>
> echo $PATH
> echo $LD_LIBRARY_PATH
>
> to see if that sheds any light on things.
>
> Hope this helps,
>
> Roger
>
>
>>
>>> library(spgrass6)
>> Loading required package: sp
>> Loading required package: rgdal
>> Geospatial Data Abstraction Library extensions to R successfully loaded
>> Loaded GDAL runtime: GDAL 1.7.2, released 2010/04/23
>> Path to GDAL shared files: /usr/local/share/gdal
>> Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
>> Path to PROJ.4 shared files: (autodetected)
>> Loading required package: XML
>> GRASS GIS interface loaded with GRASS version: (GRASS not running)
>>> loc <- initGRASS(gisBase = "/usr/local/grass-6.4.0svn/", home =
>>> tempdir())
>> g.gisenv: symbol lookup error: g.gisenv: undefined symbol: G__no_gisinit
>> g.gisenv: symbol lookup error: g.gisenv: undefined symbol: G__no_gisinit
>> g.gisenv: symbol lookup error: g.gisenv: undefined symbol: G__no_gisinit
>> g.gisenv: symbol lookup error: g.gisenv: undefined symbol: G__no_gisinit
>> g.gisenv: symbol lookup error: g.gisenv: undefined symbol: G__no_gisinit
>> g.region: symbol lookup error: g.region: undefined symbol: G__gisinit
>> Error in if (file.exists(file) == FALSE) if (!missing(asText) &&
>> asText == :
>> argument is of length zero
>> Error in parseGRASS(cmd) : g.region not parsed
>>
>>> sessionInfo()
>> R version 2.11.1 (2010-05-31)
>> i386-redhat-linux-gnu
>>
>> 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=C 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] spgrass6_0.6-19 XML_3.1-1 rgdal_0.6-28 sp_0.9-66
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.11.1 lattice_0.18-8 tools_2.11.1
>>
>>
>> Any ideas about what I am doing wrong?
>>
>> Thanks, Bill
>>
>>
>


-- 
William D. McCoy
Geosciences
University of Massachusetts
Amherst, MA 01003