[STATSGRASS] Re: spgrass6 compile problem

[Roger Bivand]

On Wed, 17 Oct 2007, Thomas Adams wrote:

> Roger,
>
> Thank you very much for your suggestions. rgdal did fail to load into R. It 
> turns out that the version of g++ is 3.4.4 implying some kind of mismatch 
> between it and the shared library ../gcc_shlibs/libgcc_s.so.1, which I 
> believe is unused anyhow. So, I simply moved it to another name. Can't see 
> that that has caused any problems.
>
> Anyhow, I have re-compiled gdal, R 2.6.0, sp, and rgdal and now I am getting 
> the following message, which is even more perplexing to me:
>
>>  library(rgdal)
> Error in dyn.load(file, ...) :
> unable to load shared library 
> '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so':
> /awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so: undefined 
> symbol: OGR_G_GetY
> Error: package/namespace load failed for 'rgdal'
>
> which seems to imply (I think) that rgdal is not finding gdal when trying to 
> load; is this correct?

Well, it has found something, but it hasn't found at least one function 
inside that something. Are the ogr* utilities working from gdal directly, 
that is not using R? Does v.in.ogr in GRASS still work?

Roger

>
> Regards,
> Tom
>
>
> Roger Bivand wrote:
>>  On Tue, 16 Oct 2007, Thomas Adams wrote:
>> 
>> >  Roger,
>> > 
>> >  I am trying to compile spgrass6 on a Linux system with R 2.6.0. I have 
>> >  compiled all the dependencies without problems, but I am getting:
>> > 
>> >  xt4-tir:adams> R CMD INSTALL spgrass6_0.4-3.tar.gz
>> >  * Installing to library '/awips/rep/lx/local_apps/R.dir/lib/R/library'
>> >  * Installing *source* package 'spgrass6' ...
>> >  ** R
>> >  ** inst
>> >  ** preparing package for lazy loading
>> >  Loading required package: sp
>> >  Loading required package: maptools
>> >  Loading required package: foreign
>> >  Loading required package: rgdal
>> >  Error in dyn.load(file, ...) :
>> >  unable to load shared library 
>> >  '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so':
>> >  /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found 
>> >  (required by /usr/lib/libstdc++.so.6)
>> >  Error: package 'rgdal' could not be loaded
>> >  Execution halted
>> >  ERROR: lazy loading failed for package 'spgrass6'
>> >  ** Removing '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6'
>> >  ** Restoring previous 
>> >  '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6'
>> > 
>> >  I don't understand this:
>> > 
>> >  /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found 
>> >  (required by /usr/lib/libstdc++.so.6)
>> > 
>> >  Do you have any insights? I have previously compiled spgrass6 without 
>> >  problems. But we have had some system changes since that time. System 
>> >  requirements force me to install in a non-standard location.
>>
>>  What happens if you start R, say library(rgdal), and try to do - say -
>>  example(readGDAL)? If the same happens, then most likely rgdal was
>>  installed before the system upgrade, and you now have g++4, meaning that
>>  the dependencies of rgdal (or GDAL as a whole) are no longer met.
>>
>>  If library(rgdal) fails as I suspect, you'll need to re-install it:
>>
>>  install.packages("rgdal")
>>
>>  ought to be enough, though GDAL may also need to be re-installed (all C++
>>  programs are sensitive to build train upgrades, much more so than C
>>  programs). You may also do
>>
>>  update.packages(checkBuilt=TRUE)
>>
>>  which will freshen all the installed packages built with R < 2.6.
>>
>>  If rgdal itself works, then sorry, no idea. Maybe somebody on the list
>>  (STATGRASS, R-sig-geo) may have seen something similar. How were R and
>>  GDAL installed, from source? What does g++ -v say?
>>
>>  Roger
>> 
>> 
>> > 
>> >  Regards,
>> >  Tom
>> > 
>> > 
>> > 
>> 
>
>
>

-- 
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