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.
Best,
Laurent
On 05/30/2013 06:51 PM, James Diggans wrote:
When trying to compile rpy (on RHEL) against a newly compiled R 3.0.1
(with --enable-R-shlib) I get a compilation error, the source of which
is not clear. Has anyone compiled rpy (not rpy2; I need rpy for
compatibility with galaxy, a bioinformatics workflow tool) against new
versions of R? Output from compile included below; thanks.
-j
[jdiggans@simi rpy-1.0.3]$ python setup.py install
RHOMES= []
DEBUG= True
Setting RHOMES to ['/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/']
### Using R verion 3.0.1 installed at
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/ ###
RHOME= /nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/
copying src/rpymodule.c -> src/rpymodule3001.c
copying src/R_eval.c -> src/R_eval3001.c
copying src/io.c -> src/io3001.c
running install
running build
running build_py
copying rpy_options.py -> build/lib.linux-x86_64-2.7
running build_ext
building '_rpy3001' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DWITH_NUMERIC=3
-DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3001
-DINIT_RPY=init_rpy3001 -UPRE_2_2
-I/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include -Isrc
-I/usr/share/R/include
-I/home/VERACYTE/jdiggans/local/lib/python2.7/site-packages/numpy/core/include
-I/home/VERACYTE/jdiggans/local/include/python2.7 -c
src/rpymodule3001.c -o build/temp.linux-x86_64-2.7/src/rpymodule3001.o
-shared
In file included from
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include/R.h:40,
from src/RPy.h:51,
from src/rpymodule3001.c:51:
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include/R_ext/Memory.h:40:
warning: function declaration isn't a prototype
In file included from
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include/Rdefines.h:29,
from src/RPy.h:52,
from src/rpymodule3001.c:51:
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include/Rinternals.h:719:
warning: function declaration isn't a prototype
In file included from src/RPy.h:57,
from src/rpymodule3001.c:51:
/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include/R_ext/Rdynload.h:32:
warning: function declaration isn't a prototype
In file included from src/rpymodule3001.c:51:
src/RPy.h:77:51: error: Rdevices.h: No such file or directory
In file included from
/home/VERACYTE/jdiggans/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728,
from
/home/VERACYTE/jdiggans/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from
/home/VERACYTE/jdiggans/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from src/RPy.h:92,
from src/rpymodule3001.c:51:
/home/VERACYTE/jdiggans/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
warning: #warning "Using deprecated NumPy API, disable it by #defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
src/rpymodule3001.c:1565: warning: initialization from incompatible
pointer type
src/rpymodule3001.c:1568: warning: 'intargfunc' is deprecated
src/rpymodule3001.c:1568: warning: initialization from incompatible
pointer type
src/rpymodule3001.c:1569: warning: 'intintargfunc' is deprecated
src/rpymodule3001.c:1569: warning: initialization from incompatible
pointer type
src/rpymodule3001.c:1570: warning: initialization from incompatible
pointer type
src/rpymodule3001.c: In function 'r_finalize':
src/rpymodule3001.c:1782: warning: implicit declaration of function
'Rf_KillAllDevices'
src/rpymodule3001.c:1788: warning: implicit declaration of function
'R_CleanTempDir'
src/rpymodule3001.c:1776: warning: unused variable 'tmpdir'
src/rpymodule3001.c:1775: warning: unused variable 'buf'
error: command 'gcc' failed with exit status 1
______________________________
*James C. Diggans, PhD*| Bioinformatics Scientist | Veracyte, Inc.**
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