Hi. To follow this one up-- switching to Continuum's Anaconda python distribution (and then a clean pip install rpy2) resolved the problem. It's still unclear what the actual issue was, however.
Thanks Nik On Feb 18, 2014, at 5:55 PM, Laurent Gautier wrote: > > > On 02/18/2014 08:37 PM, Nik Krumm wrote: >> Hi all, >> >> After attempting to upgrade R, I now for the life of me cannot get rpy2 to >> interface. Installation of R and rpy2 do proceed (though some warnings on >> compile there, see below), but then this happens when importing `robjects`: >> >> 05:19:21 ~$ python -c "import rpy2.robjects" >> Traceback (most recent call last): >> File "<string>", line 1, in <module> >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/robjects/__init__.py", >> line 15, in <module> >> import rpy2.rinterface as rinterface >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/rinterface/__init__.py", >> line 101, in <module> >> from rpy2.rinterface._rinterface import * >> ImportError: >> dlopen(/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so, >> 2): Symbol not found: _R_BaseEnv >> Referenced from: >> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so >> Expected in: flat namespace >> in >> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so >> >> I am running the following versions: >> - R 3.02 (Platform: x86_64-apple-darwin10.8.0 (64-bit)) downloaded from >> CRAN, though I have tried various compile-from-source options. >> - Python 2.7.3 (Enthought) >> - Mac OS X 10.6.8 with gcc 4.2.1 > > There are sporadic reports of problem with Enthought's Python + OS X (for > example > http://stackoverflow.com/questions/16220465/importing-rpy2-modules-in-enthought-canopy-python > ). > No explanation for the problem though. IIRC the resolution is to compile > Python on the machine (homebrew makes the process relatively painless). > >> >> I've tried a couple different releases of rpy2, all have the same effect. >> >> I've also tried the hint in the docs: >> env ARCHFLAGS="-arch i386 -arch x86_64" python setup.py build install >> ... but this has no different effects. >> >> However, I can get a different error I specify "-arch x86_64" ONLY: >> >> 05:30:13 ~$ python -c "import rpy2.robjects" >> Traceback (most recent call last): >> File "<string>", line 1, in <module> >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/robjects/__init__.py", >> line 15, in <module> >> import rpy2.rinterface as rinterface >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/rpy2/rinterface/__init__.py", >> line 101, in <module> >> from rpy2.rinterface._rinterface import * >> ImportError: dynamic module does not define init function (init_rinterface) >> >> >> >From the installation_log.txt (attached), a snippet containing warnings >> >potentially interesting: >> >> /Library/Frameworks/Python.framework/Versions/7.3/include/python2.7/pymacconfig.h:56:1: >> warning: this is the location of the previous definition >> ld: warning: in /Library/Frameworks/R.framework/Resources/lib/libR.dylib, >> file was built for unsupported file format which is not the architecture >> being linked (i386) >> /Library/Frameworks/Python.framework/Versions/7.3/include/python2.7/pymacconfig.h:56:1: >> warning: this is the location of the previous definition >> ld: warning: in /Library/Frameworks/R.framework/Resources/lib/libR.dylib, >> file was built for unsupported file format which is not the architecture >> being linked (i386) >> >> Thank you VERY much for any help, >> Nik >> ------------------------------------------------------------------------------ >> Managing the Performance of Cloud-Based Applications >> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. >> Read the Whitepaper. >> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk >> _______________________________________________ >> rpy-list mailing list >> rpy-list@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rpy-list > ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk _______________________________________________ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
