[GRASS-stats] can't initiate Grass with initGRASS() in R
William McCoy
wdmccoy at geo.umass.edu
Sat Aug 28 21:00:41 EDT 2010
On 08/28/2010 07:24 PM, Markus Neteler wrote:
> On Sat, Aug 28, 2010 at 8:56 PM, William McCoy<wdmccoy at geo.umass.edu> wrote:
>> At the suggestion of Roger Bivand, I am moving this issue from r-sig-geo.
>>
>> 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:
>>
>>> 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
>
>
> I have checked the archives and found this interesting email which might
> explain what happens:
>
> On Thu, Aug 14, 2008 at 6:37 AM, Glynn Clements
> <glynn at gclements.plus.com> wrote:
>> G. Allegri wrote:
>>
>>> I understand that everything that needs GRASS has to be recompiled if
>>> this version changes so much to change its interface (QGis-GRASS
>>> plugin, GRASS-GDAL plugin, etc.). But I would like to know why the new
>>> develbrunch_6 revision needs the GDAL itself to be recompiled. I can
>>> understand it if GRASS would need a newer version of GDAL... is this
>>> the case?
>>
>> You only need to re-compile GDAL itself if GDAL was built with GRASS
>> support (--with-grass).
>>
>> In your original message, you wrote:
>>
>>> Even switching to develbrunch I receive the same error:
>>> usr/local/lib/libgdal.so: undefined reference to `G_no_gisinit'
>>
>> This indicates that your GDAL library was indeed built --with-grass. I
>> suggest building it without that option, and using the GDAL-GRASS
>> plugin instead.
>>
>> If you build GDAL -with-grass, you will need to re-compile GDAL every
>> time that GRASS is updated from now on. The problem arises from
>> r32695, which makes G_gisinit() check that libgis was built with the
>> same version of gis.h as the caller.
>>
>> The change adds G_gisinit() and G_no_gisinit() macros:
>>
>> #define GIS_H_VERSION "$Revision: 32726 $"
>>
>> #define G_gisinit(pgm) G__gisinit(GIS_H_VERSION, (pgm))
>> #define G_no_gisinit() G__no_gisinit(GIS_H_VERSION)
>>
>> The value of GIS_H_VERSION is automatically updated to the SVN
>> revision whenever gis.h is updated.
>>
>> The change also renames the functions to G__gisinit() and
>> G__no_gisinit() (which is why you get the "undefined reference" error
>> when using an old GDAL with a new libgis), and adds version checks:
>>
>> int G__gisinit(const char *version, const char *pgm)
>> {
>> ...
>> if (strcmp(version, GIS_H_VERSION) != 0)
>> G_fatal_error(_("Incompatible library version for module"));
>>
>> Any code which uses G_gisinit() or G_no_gisinit() passes the version
>> of gis.h with which it was compiled to the library functions, which
>> check that the same version of gis.h was used to compile the library.
>>
>> The rationale is to avoid having to track down subtle errors caused by
>> version incompatibilities between libgis and any code which uses it.
>> Now, if there is an incompatibility, you get a very unsubtle error
>> telling you that there's an incompatibility.
>>
>> --
>> Glynn Clements<glynn at gclements.plus.com>
>> _______________________________________________
>> grass-user mailing list
>> grass-user at lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-user
>
> In essence, you would need to check how old your GDAL installation is.
>
> Markus
Markus,
This is interesting. I had configured gdal 1.7.2 --without grass and
built it in July. I had then built grass pointing to the new
gdal-config on the same day. Lastly, I configured and installed
gdal-grass 1.4.2, again on the same day.
So I think I had done these things in the right order before I first had
the problem with initGRASS() yesterday. After, I noticed that problem,
I did 'svn up' and brought grass64svn up to date. I rebuilt and
reinstalled it, but I didn't reconfigure and rebuild gdal-grass.
So just now, I did 'make distclean' in the gdal-grass directory and then
reconfigured, rebuilt, and reinstalled gdal-grass. I then also removed
spgrass6 and rgdal from my R libraries and then rebuilt and reinstalled
both of them.
And now when I use initGRASS, I have exactly the same problem:
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> 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"
> 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"
> 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
> 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"
> 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"
Note that initGRASS() does add the grass-6.4.0svn directories to PATH
and LD_LIBRARY_PATH. But it still fails at the same point.
Any other ideas?
Thanks for your help.
Bill
--
William D. McCoy
Geosciences
University of Massachusetts
Amherst, MA 01003
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