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

[William McCoy]

On 08/28/2010 01:15 PM, Roger Bivand wrote:
> 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
>

Yes, I had already tried gisBase = "/usr/local/grass-6.4.0svn" without 
the terminating "/".  In fact, that's what I had used when I did the 
debugging on initGRASS().  So that doesn't seem to help.

I think ldconfig is always run on startup, but I ran it again just now 
and it made no difference.  And setting and exporting LD_LIBRARY_PATH 
doesn't help either.

I should also mention that I had tried to use my grass63 installation 
for gisBase a couple of times and that gave me the same results.

In case I didn't mention it, this is all being done on Fedora 13.  The 
last time that I used spgrass6 successfully was on Fedora 12 on the same 
computer.

Any other ideas?


Thanks, Bill


>>
>>
>> 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