[Rcpp-devel] Fwd: Rcpp and rpy2

Mon Aug 15 15:52:52 CEST 2011

Sorry, I don't have a small example. I could come up with one, but that
would be purely artificial.

I am using Rcpp and rpy2 so I can use OpenOpt, a python optimization
framework with interfaces to a ton of different open source and proprietary
nonlinear and linear solvers. My objective function is very expensive to
evaluate and is implemented in R using Rcpp and various other R libraries.
Using OpenOpt allows to try a lot of different solvers without having to
change my implementation.

On Mon, Aug 15, 2011 at 2:59 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> On 15 August 2011 at 10:00, Jonas Rauch wrote:
> | Just to close this up:
> | I found out that my Rcpp installation must have occured when my R was not
> built
> | with shared lib. Thus Rcpp was not linked to libR. Just reinstalling Rcpp
> from
> | source solved the problem.
>
> That makes sense, and thank you for closing the loop by reporting back.  If
> you have a small self-contained example of rpy2 and Rcpp, can you send it
> my
> way?  It may make sense to add this to the Rcpp_FAQ vignette.
>
> Dirk
>
> | Regards,
> | Jonas
> |
> | On Fri, Aug 12, 2011 at 3:16 PM, Dirk Eddelbuettel <edd at debian.org>
> wrote:
> |
> |
> |     On 12 August 2011 at 14:33, Jonas Rauch wrote:
> |     | Hi Dirk and Romain,
> |     |
> |     | Aparrently libR is not loaded by rpy2, at least not in a way such
> that
> |     Rcpp can
> |     | access it. I have solved the problem by adding -lR to the linker
> flags
> |     when
> |     | building Rcpp. Since for normal use of Rcpp from R this does not
> make a
> |     | difference, would you mind adding this to the Makevars file in a
> future
> |     version
> |     | of Rcpp? Or does this lead to problems in case R is build without
> |     libR.so?
> |
> |     I would be somewhat hesitant to do so as it may affect all users of
> Rcpp.
> |
> |     Rcpp is for getting code into R, and we can take libR as given as R
> is
> |     always
> |     around when loading Rcpp.  I think the problem is really with the
> linker
> |     and
> |     passing symbols through from one end to the other.
> |
> |     Other views, anyone?
> |
> |     Dirk
> |
> |
> |     | Best regards,
> |     | Jonas
> |     |
> |     | ---------- Forwarded message ----------
> |     | From: Jonas Rauch <jonas.rauch at googlemail.com>
> |     | Date: Fri, Aug 12, 2011 at 10:36 AM
> |     | Subject: Rcpp and rpy2
> |     | To: rcpp-devel <rcpp-devel at r-forge.wu-wien.ac.at>
> |     |
> |     |
> |     | Is Rcpp compatible with rpy2?
> |     | I would like to call a very complex R function from python. My
> function
> |     depends
> |     | on code implemented with Rcpp. When I try to load Rcpp from python
> via
> |     |
> |     | import rpy2.robjects as robjects
> |     | robjects.r('library(Rcpp)')
> |     |
> |     | I get the following:
> |     |
> |     | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |     |   unable to load shared object '/home/jonas/R/
> |     x86_64-unknown-linux-gnu-library
> |     | /2.13/Rcpp/libs/Rcpp.so':
> |     |
> /home/jonas/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/libs/Rcpp.so:
> |     | undefined symbol: R_ClassSymbol
> |     | Error: package/namespace load failed for 'Rcpp'
> |     | Traceback (most recent call last):
> |     |   File "RcppTest.py", line 2, in <module>
> |     |     robjects.r('library(Rcpp)')
> |     |   File "/usr/local/lib/python2.7/dist-packages/
> |     |
> rpy2-2.2.2dev_20110811-py2.7-linux-x86_64.egg/rpy2/robjects/__init__.py",
> |     line
> |     | 225, in __call__
> |     |     res = self.eval(p)
> |     |   File "/usr/local/lib/python2.7/dist-packages/
> |     | rpy2-2.2.2dev_20110811-py2.7-linux-x86_64.egg/rpy2/robjects/
> |     functions.py", line
> |     | 82, in __call__
> |     |     return super(SignatureTranslatedFunction, self).__call__(*args,
> |     | **kwargs)
> |     |   File "/usr/local/lib/python2.7/dist-packages/
> |     | rpy2-2.2.2dev_20110811-py2.7-linux-x86_64.egg/rpy2/robjects/
> |     functions.py", line
> |     | 34, in __call__
> |     |     res = super(Function, self).__call__(*new_args, **new_kwargs)
> |     | rpy2.rinterface.RRuntimeError: Error: package/namespace load failed
> for
> |     'Rcpp'
> |     |
> |     | From what I understand R_ClassSymbol is supplied by libR.so, which
> should
> |     by
> |     | loaded by rpy2 anyway in order to work at all, or am I totally
> wrong
> |     here?
> |     |
> |     | Running python 2.7.1, rpy2-2.2.2, R 2.13.0
> |     | I would appreciate any help.
> |     |
> |     | Regards,
> |     | Jonas
> |     |
> |     |
> |     |
> ----------------------------------------------------------------------
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> |     |
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> |
> |     --
> |     Two new Rcpp master classes for R and C++ integration scheduled for
> |     New York (Sep 24) and San Francisco (Oct 8), more details are at
> |     http://dirk.eddelbuettel.com/blog/2011/08/04#
> |     rcpp_classes_2011-09_and_2011-10
> |     http://www.revolutionanalytics.com/products/training/public/
> |     rcpp-master-class.php
> |
> |
>
> --
> Two new Rcpp master classes for R and C++ integration scheduled for
> New York (Sep 24) and San Francisco (Oct 8), more details are at
>
> http://dirk.eddelbuettel.com/blog/2011/08/04#rcpp_classes_2011-09_and_2011-10
>
> http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php
>
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