[Rcpp-devel] Fwd: Rcpp and rpy2
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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|
| --
| 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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