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

[William McCoy]

Since this issue was first brought up on this list and then continued on 
grass-stats and grass-dev, I think I should summarize what has been 
found out so far regarding this issue.

As mentioned below, I have grass63 installed on this computer along with 
the grass64svn that I was trying to access via initGRASS() in spgrass6. 
  Apparently, the grass63 libraries were being accessed before the 
grass64svn libraries were found and, hence, the symbol lookup error.

I have found that if I modify initGRASS() to prepend the grass64svn 
directories, rather than append them, to PATH and LD_LIBRARY_PATH, the 
error does not occur.  I don't know if this is the best solution, but it 
works temporarily and at least we know the source of the problem.  See 
here for more details on the source of the problem and the temporary "fix":

http://lists.osgeo.org/pipermail/grass-stats/2010-August/001268.html

Thanks to Roger Bivand, Markus Neteler, and Glynn Clements (in 
chronological order) for sorting this out.


Bill


On 08/28/2010 02:09 PM, William McCoy wrote:
> On 08/28/2010 01:57 PM, Roger Bivand wrote:
>> On Sat, 28 Aug 2010, William McCoy wrote:
>>
>>> 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?
>>
>> Trying ldd on GRASS modules when running GRASS outside R to work out
>> which shared object library they are using. I run Fedora 13 (among
>> others) so I doubt that it is the system, rather some changes in your
>> installed software that occurred at around the same time. Using ldd may
>> help. When I type:
>>
>>> ldd /home/rsb/topics/grass/g64_rc6/grass-6.4.0RC6/bin/g.region
>>
>> I see an extra directory level before the /bin, /lib, etc., both in the
>> input and the output, but your mileage may vary.
>>
>> Roger
>>
>> PS: Could I suggest moving this thread to statsgrass, which is
>> specifically for the R/GRASS interface? Could you summarise there to
>> attract attention from GRASS people (who are not too busy with FOSS4G in
>> Barcelona)?
>>
>
> I will try summarizing this issue in a message to statsgrass this
> afternoon.
>
> With regard to ldd, I don't see the extra directory level:
>
> [wdmccoy at boreas ~]$ ldd /usr/local/grass-6.4.0svn/bin/g.region
> linux-gate.so.1 => (0x0036c000)
> libgrass_vect.so => /usr/local/grass-6.4.0svn/lib/libgrass_vect.so
> (0x00110000)
> libgrass_dbmibase.so =>
> /usr/local/grass-6.4.0svn/lib/libgrass_dbmibase.so (0x00f52000)
> ...
>
>
> Thanks, Bill
>
>
>>>
>>>
>>> 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