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.
T 650.243.6375 | M 808.221.7566 | F 650.243.6301 |
ja...@veracyte.com<mailto:ja...@veracyte.com>
7000 Shoreline Court, Suite 250 | South San Francisco, CA 94080 |
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