Greetings!
Neither of the two suggestions from the January thread (listed below) provide
relief for "my" undefined symbol - R_alloc.
The symbol R_alloc is defined in libR.so, and Python is showing the correct
LD_LIBRARY_PATH
>>> print(os.environ.get('LD_LIBRARY_PATH'))
/usr/local/lib64/R/lib:/usr/local/lib64:/usr/local/lib64/R/lib::/usr/lib64/gcj-4.1.2:/usr/local/lib64/R/bin:/usr/local/lib64/R/lib:/usr/local/lib64/R/library/sp/libs:/usr/local/lib64/R/library/gbm/libs:/usr/local/lib/vtk-5.4:/opt/fontconfig-2.8.0/lib:
>>> print(os.environ.get('R_HOME'))
/usr/local/lib64/R
>>> import rpy2.rinterface as rinterface
>>> print(rinterface.get_initoptions())
('rpy2', '--quiet', '--vanilla', '--no-save')
>>> rinterface.set_initoptions(('rpy2', '--quiet', '--no-save'))
>>> import rpy2.robjects as robjects
>>> robjects.r(['require(sp)\n'])
Loading required package: sp
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/local/lib64/R/library/sp/libs/sp.so':
/usr/local/lib64/R/library/sp/libs/sp.so: undefined symbol: R_alloc
Any suggestions?
Thank you.
KFW
> - $RHOME/etc/ldpaths is ignored when an embedded R is started with
> the option "--vanilla" (and this is what rpy2 has by default - may
> be not such a good thing). Try if the following helps:
>
> #do this *before* your import anything from rpy2
> import rpy2.rinterface as ri
> ri.set_initoptions(('--quiet', '--no-save'))
> # now import whatever from rpy2 as usual
>
> Documentation for that at:
>
> http://rpy.sourceforge.net/rpy2/doc-2.1/html/rinterface.html#initialization
>
> - $RHOME/etc/ldpaths is only used by the R console (and rpy/rpy2
> have use an embedded R that can't know about it). In that case, you
> should define your LD_LIBRARY_PATH *before* starting python.
> For example:
> source $RHOME/etc/ldpaths
> python
>
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