Thanks for the replies - I did actually get it to build by using Dirk's changes
in SVN along with commenting out the rpy_tools call for the lapack lib location
(in setup.py) and specifying the library manually instead:
# extra_compile_args += [ rpy_tools.get_R_LAPACK_LIB_FLAGS( RHOME ) ]
libraries=['R','Rlapack']
Thanks,
-j
-----Original Message-----
From: Dirk Eddelbuettel [mailto:[email protected]]
Sent: Tuesday, June 04, 2013 1:29 PM
To: RPy help, support and design discussion list
Cc: James Diggans
Subject: Re: [Rpy] Compiling against R 3.0.1 - error?
On 30 May 2013 at 19:27, Laurent Gautier wrote:
| Not a direct answer to your question, but as the long list of
| deprecation warnings occurring during the installation suggest it,
| investing the (presumably little) effort required to help Galaxy move
| to rpy2 might be a better idea.
|
| The direct answer is: an include file from R has moved, or
| disappeared. Dirk Eddelbuettel has been maintaining the rpy package on
| debian. Check if there is .deb for rpy/R-3.0. If yes, the SVN source
| for rpy should build. If not, you are probably on your own.
Yes, something had come up as R Core tends to tighten the APU over time. The
changelog below was from my build against R 3.0.0 a few weeks ago (and I took
this as reminder to update things for R 3.0.1 just now):
rpy (1.0.3-25) unstable; urgency=low
* src/RPy.h: Comment-out (Rf_)PrintWarnings() which is no longer
available under R 3.0.0; change committed to upstream SVN too
* src/rpymodule.c: Idem (Closes: #705847)
-- Dirk Eddelbuettel <[email protected]> Mon, 22 Apr 2013 19:22:49 -0500
The last few commits to the rpy SVN were in all mine as I kept the Debian
package going -- mostly to continuity. I generally second Laurent's
recommendation: you probably really want to use RPy2.
Hth, Dirk
--
Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com
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