On Wed, Jul 19, 2017 at 10:49 AM, Felipe Bastos Nunes
<felipe.bast...@gmail.com> wrote:
> Hey, I have no experience on it, but maybe I'm able to help. How are you
> tryin to install it? Pip? 2 or 3? Virtualenv?
python2.7, using pip, on Redhat 6, R version 3.3.3:
Collecting rpy2
Using cached rpy2-2.8.6.tar.gz
Requirement already satisfied (use --upgrade to upgrade): six in
/usr/local/lib/python2.7/site-packages (from rpy2)
Requirement already satisfied (use --upgrade to upgrade):
singledispatch in /usr/local/lib/python2.7/site-packages (from rpy2)
Installing collected packages: rpy2
Running setup.py install for rpy2 ... error
Complete output from command /usr/local/bin/python2.7 -u -c
"import setuptools,
tokenize;__file__='/tmp/pip-build-eFwk3n/rpy2/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record /tmp/pip-w5v7yg-record/install-record.txt
--single-version-externally-managed --compile:
R version 3.3.3 (2017-03-06) -- "Another Canoe"
/usr/local/lib64/R/bin/R CMD config --ldflags
/usr/local/lib64/R/bin/R CMD config --cppflags
Compilation parameters for rpy2's C components:
include_dirs = ['/usr/local/lib64/R/include']
library_dirs = ['/usr/local/lib64/R/lib']
libraries = ['Rblas', 'gfortran', 'm', 'readline',
'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm']
extra_link_args = ['-Wl,--export-dynamic', '-fopenmp',
'-Wl,--whole-archive', '/usr/local/lib64/R/lib/libR.a',
'-Wl,--no-whole-archive']
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/rpy2
copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
creating build/temp.linux-x86_64-2.7/rpy
creating build/temp.linux-x86_64-2.7/rpy/rinterface
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface
-I/usr/local/lib64/R/include -c ./rpy/rinterface/r_utils.c -o
build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
In file included from /usr/local/lib64/R/include/Rdefines.h:36,
from ./rpy/rinterface/r_utils.c:23:
/usr/local/lib64/R/include/R_ext/Memory.h:51: warning: function
declaration isn’t a prototype
In file included from /usr/local/lib64/R/include/Rdefines.h:40,
from ./rpy/rinterface/r_utils.c:23:
/usr/local/lib64/R/include/Rinternals.h:886: warning: function
declaration isn’t a prototype
ar rc build/temp.linux-x86_64-2.7/libr_utils.a
build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
running build_ext
R version 3.3.3 (2017-03-06) -- "Another Canoe"
building 'rpy2.rinterface._rinterface' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC -DR_INTERFACE_PTRS=1
-DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1
-DHAS_READLINE=1 -I./rpy/rinterface -I/usr/local/lib64/R/include
-I/usr/local/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o
build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
In file included from /usr/local/include/python2.7/Python.h:8,
from ./rpy/rinterface/_rinterface.c:49:
/usr/local/include/python2.7/pyconfig.h:1188:1: warning:
"_POSIX_C_SOURCE" redefined
In file included from /usr/include/signal.h:29,
from ./rpy/rinterface/_rinterface.c:45:
/usr/include/features.h:213:1: warning: this is the location of
the previous definition
In file included from /usr/local/lib64/R/include/R.h:80,
from ./rpy/rinterface/_rinterface.h:8,
from ./rpy/rinterface/_rinterface.c:52:
/usr/local/lib64/R/include/R_ext/Memory.h:51: warning: function
declaration isn’t a prototype
In file included from ./rpy/rinterface/_rinterface.h:9,
from ./rpy/rinterface/_rinterface.c:52:
/usr/local/lib64/R/include/Rinternals.h:886: warning: function
declaration isn’t a prototype
In file included from ./rpy/rinterface/_rinterface.c:64:
/usr/local/lib64/R/include/Rinterface.h:149: warning: function
declaration isn’t a prototype
In file included from ./rpy/rinterface/_rinterface.c:73:
/usr/local/lib64/R/include/R_ext/Rdynload.h:36: warning: function
declaration isn’t a prototype
In file included from ./rpy/rinterface/_rinterface.c:116:
./rpy/rinterface/embeddedr.c: In function ‘SexpObject_clear’:
./rpy/rinterface/embeddedr.c:48: warning: unused variable ‘res’
In file included from ./rpy/rinterface/_rinterface.c:119:
./rpy/rinterface/sexp.c: In function ‘Sexp_init’:
./rpy/rinterface/sexp.c:742: warning: unused variable ‘copy’
./rpy/rinterface/_rinterface.c: At top level:
./rpy/rinterface/_rinterface.h:203: warning:
‘PyRinterface_IsInitialized’ declared ‘static’ but never defined
./rpy/rinterface/_rinterface.h:204: warning:
‘PyRinterface_FindFun’ declared ‘static’ but never defined
./rpy/rinterface/_rinterface.h:205: warning:
‘embeddedR_isInitialized’ defined but not used
./rpy/rinterface/sequence.c:2173: warning:
‘ComplexVectorSexp_AsSexp’ defined but not used
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’:
./rpy/rinterface/_rinterface.c:831: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ResetConsole’:
./rpy/rinterface/_rinterface.c:677: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_FlushConsole’:
./rpy/rinterface/_rinterface.c:643: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ChooseFile’:
./rpy/rinterface/_rinterface.c:727: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ReadConsole’:
./rpy/rinterface/_rinterface.c:498: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_WriteConsoleEx’:
./rpy/rinterface/_rinterface.c:339: warning: ‘consolecallback’ may
be used uninitialized in this function
./rpy/rinterface/_rinterface.c:354: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowMessage’:
./rpy/rinterface/_rinterface.c:429: warning: ‘gstate’ may be used
uninitialized in this function
./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_CleanUp’:
./rpy/rinterface/_rinterface.c:979: warning: ‘gstate’ may be used
uninitialized in this function
gcc -pthread -shared
build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
-L/usr/local/lib64/R/lib -Lbuild/temp.linux-x86_64-2.7
-Wl,-R/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lpcre
-llzma -lbz2 -lz -lrt -ldl -lm -lr_utils -o
build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so
-Wl,--export-dynamic -fopenmp -Wl,--whole-archive
/usr/local/lib64/R/lib/libR.a -Wl,--no-whole-archive
/usr/bin/ld: /usr/local/lib64/R/lib/libR.a(CommandLineArgs.o):
relocation R_X86_64_32 against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/usr/local/lib64/R/lib/libR.a(CommandLineArgs.o): could not read
symbols: Bad value
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/usr/local/bin/python2.7 -u -c "import setuptools,
tokenize;__file__='/tmp/pip-build-eFwk3n/rpy2/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record /tmp/pip-w5v7yg-record/install-record.txt
--single-version-externally-managed --compile" failed with error code
1 in /tmp/pip-build-eFwk3n/rpy2/
Also tried building from source and that failed with:
gcc -pthread -shared
build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
-L/usr/local/lib64/R/lib -Lbuild/temp.linux-x86_64-2.7
-Wl,-R/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lpcre
-llzma -lbz2 -lz -lrt -ldl -lm -lr_utils -o
build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so
-Wl,--export-dynamic -fopenmp -Wl,--whole-archive
/usr/local/lib64/R/lib/libR.a -Wl,--no-whole-archive
/usr/bin/ld: cannot find -lr_utils
But I could not find how to get libr_utils.
> Em qua, 19 de jul de 2017 10:22, Larry Martell <larry.mart...@gmail.com>
> escreveu:
>>
>> Anyone here any experience with the rpy2 package? I am having trouble
>> getting it to install, and I have posted to the rpy mailing list, put
>> a question on SO, and even emailed the author, but I have received no
>> replies. Before I post details I wanted to see if anyone here can
>> possibly help me.
>> --
>> https://mail.python.org/mailman/listinfo/python-list
--
https://mail.python.org/mailman/listinfo/python-list
