can't initiate Grass with initGRASS() in R

[William McCoy]

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

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


Note that dropping the final "/" in my argument to gisBase in the
initGRASS() call does not change the results.

This is on a Fedora 13 system that has both the grass63 package
installed via rpm and also I have grass64svn updated (as of 27 Aug 2010)
compiled and installed.  I have the same problem whether I set gisBase
to the grass63 installation or the grass64svn installation.

Roger responded to my initial message on r-sig-geo with the following:

> 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

Here is the output from debug after the PATH-setting if() call:

> 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)
>

Here is the output from 'echo $PATH' and 'echo $LD_LIBRARY_PATH':

>
> [wdmccoy@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
>
>

>
> [wdmccoy@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 the single line:

/usr/local/grass-6.4.0svn/lib


I have checked that ldconfig is run and I have tried setting and
exporting LD_LIBRARY_PATH before running R -- all to no avail.

Does anyone have any ideas about getting this to work in R?


Thanks, Bill


--
William D. McCoy
Geosciences
University of Massachusetts
Amherst, MA 01003
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grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[Markus Neteler]

On Sat, Aug 28, 2010 at 8:56 PM, William McCoy <[hidden email]> 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
<[hidden email]> 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 <[hidden email]>
> _______________________________________________
> grass-user mailing list
> [hidden email]
> http://lists.osgeo.org/mailman/listinfo/grass-user

In essence, you would need to check how old your GDAL installation is.

Markus
_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[William McCoy]

On 08/28/2010 07:24 PM, Markus Neteler wrote:

> On Sat, Aug 28, 2010 at 8:56 PM, William McCoy<[hidden email]>  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
> <[hidden email]>  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<[hidden email]>
>> _______________________________________________
>> grass-user mailing list
>> [hidden email]
>> 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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grass-stats mailing list
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