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

[Roger Bivand]

On Sat, 28 Aug 2010, William McCoy wrote:

> 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?

This is a bit difficult to say, but trying to set LD_LIBRARY_PATH before 
starting R to the correct value:

export LD_LIBRARY_PATH=/usr/local/grass-6.4.0svn/lib

and/or ensuring that ldconfig was run, might help.

Have you tried using gisBase = "/usr/local/grass-6.4.0svn" without the 
terminating "/"?

Hope this goes in the right direction,

Roger

>
>
> 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
>>> 
>>> 
>> 
>
>
>

-- 
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