Hi,
I've installed my own R on the server, but there are also some other Rs
installed elsewhere.
I managed to install the rpy2, but I can't get it work.
In [1]: import rpy2.robjects
Error in .Internal(getLoadedDLLs()) :
no internal function "getLoadedDLLs"
In addition:
Warning message:
In local({ : bytecode version mismatch; using eval
Error in identical(env, as.environment(i)) :
7 arguments passed to .Internal(identical) which requires 5
---------------------------------------------------------------------------
LookupError Traceback (most recent call last)
<ipython-input-1-bd461266c9bc> in <module>()
----> 1 import rpy2.robjects
/TL/stat_learn/work/ajalali/opt/lib/python3.3/site-packages/rpy2/robjects/__init__.py
in <module>()
16 import rpy2.rlike.container as rlc
17
---> 18 from rpy2.robjects.robject import RObjectMixin, RObject
19 from rpy2.robjects.vectors import *
20 from rpy2.robjects.functions import Function,
SignatureTranslatedFunction
/TL/stat_learn/work/ajalali/opt/lib/python3.3/site-packages/rpy2/robjects/robject.py
in <module>()
7 from . import conversion
8
----> 9 class RObjectMixin(object):
10 """ Class to provide methods common to all RObject instances """
11 __rname__ = None
/TL/stat_learn/work/ajalali/opt/lib/python3.3/site-packages/rpy2/robjects/robject.py
in RObjectMixin(__locals__)
20 __rclass = rpy2.rinterface.baseenv.get("class")
21 __rclass_set = rpy2.rinterface.baseenv.get("class<-")
---> 22 __show = rpy2.rinterface.baseenv.get("show")
23
24 def __str__(self):
LookupError: 'show' not found
In [2]: import rpy2.rinterface
In [3]: rpy2.rinterface.R_VERSION_BUILD
Out[3]: ('3', '0.2', '', 63987)
In [4]: rpy2.rinterface.initr()
Out[4]: 0
This is the installation log:
$ pip install rpy2
Downloading/unpacking rpy2
Downloading rpy2-2.3.8.tar.gz (185kB): 185kB downloaded
Running setup.py egg_info for package rpy2
warning: no previously-included files matching '*patch*' found anywhere
in distribution
warning: no previously-included files matching '*diff*' found anywhere
in distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
no previously-included directories found matching 'dist'
Using 2to3 to translate Python2-only idioms into Python3 code. Please
wait...
done.
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config --ldflags
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config --cppflags
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config LAPACK_LIBS
returned an empty string.
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config BLAS_LIBS
returned an empty string.
Configuration for R as a library:
include_dirs: ('/TL/stat_learn/work/ajalali/opt/lib64/R/include',)
libraries: ('R',)
library_dirs: ('/TL/stat_learn/work/ajalali/opt/lib64/R/lib',)
extra_link_args: ()
# OSX-specific (included in extra_link_args)
framework_dirs: ()
frameworks: ()
warning: no previously-included files matching '*patch*' found anywhere
in distribution
warning: no previously-included files matching '*diff*' found anywhere
in distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
no previously-included directories found matching 'dist'
Installing collected packages: rpy2
Running setup.py install for rpy2
warning: no previously-included files matching '*patch*' found anywhere
in distribution
warning: no previously-included files matching '*diff*' found anywhere
in distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
no previously-included directories found matching 'dist'
Using 2to3 to translate Python2-only idioms into Python3 code. Please
wait...
done.
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config --ldflags
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config --cppflags
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config LAPACK_LIBS
returned an empty string.
"/TL/stat_learn/work/ajalali/opt/lib64/R/bin/R" CMD config BLAS_LIBS
returned an empty string.
Configuration for R as a library:
include_dirs: ('/TL/stat_learn/work/ajalali/opt/lib64/R/include',)
libraries: ('R',)
library_dirs: ('/TL/stat_learn/work/ajalali/opt/lib64/R/lib',)
extra_link_args: ()
# OSX-specific (included in extra_link_args)
framework_dirs: ()
frameworks: ()
building 'rpy2.rinterface._rinterface' extension
gcc -pthread -Wno-unused-result -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
-Ibuild/python3_rpy/rpy/rinterface
-I/TL/stat_learn/work/ajalali/opt/include/python3.3m
-I/TL/stat_learn/work/ajalali/opt/lib64/R/include -c
build/python3_rpy/rpy/rinterface/_rinterface.c -o
build/temp.linux-x86_64-3.3/build/python3_rpy/rpy/rinterface/_rinterface.o
In file included from
/TL/stat_learn/work/ajalali/opt/lib64/R/include/R.h:40:0,
from build/python3_rpy/rpy/rinterface/_rinterface.h:8,
from build/python3_rpy/rpy/rinterface/_rinterface.c:58:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/R_ext/Memory.h:40:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.h:9:0,
from build/python3_rpy/rpy/rinterface/_rinterface.c:58:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/Rinternals.h:719:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:70:0:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/Rinterface.h:129:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
extern void (*ptr_R_ProcessEvents)();
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:79:0:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/R_ext/Rdynload.h:32:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
typedef void * (*DL_FUNC)();
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:125:0:
build/python3_rpy/rpy/rinterface/sexp.c: In function 'Sexp_rclass_set':
build/python3_rpy/rpy/rinterface/sexp.c:369:5: warning: return makes
integer from pointer without a cast [enabled by default]
return NULL;
^
build/python3_rpy/rpy/rinterface/sexp.c: In function 'Sexp_init':
build/python3_rpy/rpy/rinterface/sexp.c:711:13: warning: unused
variable 'copy' [-Wunused-variable]
PyObject *copy = Py_True;
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:129:0:
build/python3_rpy/rpy/rinterface/sequence.c: In function
'VectorSexp_ass_slice':
build/python3_rpy/rpy/rinterface/sequence.c:477:11: warning: variable
'len_R' set but not used [-Wunused-but-set-variable]
R_len_t len_R;
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:104:0:
build/python3_rpy/rpy/rinterface/_rinterface.c: At top level:
build/python3_rpy/rpy/rinterface/embeddedr.h:20:20: warning:
'_Rpy_PreserveObject' declared 'static' but never defined
[-Wunused-function]
static SexpObject* _Rpy_PreserveObject(SEXP object);
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:129:0:
build/python3_rpy/rpy/rinterface/sequence.c:2190:1: warning:
'ComplexVectorSexp_AsSexp' defined but not used [-Wunused-function]
ComplexVectorSexp_AsSexp(PyObject *pyfloat) {
^
In file included from
build/python3_rpy/rpy/rinterface/_rinterface.c:58:0:
build/python3_rpy/rpy/rinterface/_rinterface.c: In function
'EmbeddedR_ShowFiles':
build/python3_rpy/rpy/rinterface/_rinterface.h:69:23: warning: 'gstate'
may be used uninitialized in this function [-Wmaybe-uninitialized]
PyGILState_Release(gstate); \
^
build/python3_rpy/rpy/rinterface/_rinterface.c:785:20: note: 'gstate'
was declared here
PyGILState_STATE gstate;
^
gcc -pthread -shared
build/temp.linux-x86_64-3.3/build/python3_rpy/rpy/rinterface/_rinterface.o
-L/TL/stat_learn/work/ajalali/opt/lib
-L/TL/stat_learn/work/ajalali/opt/lib64/R/lib
-L/TL/stat_learn/work/ajalali/opt/lib64/R/modules -lR -lpython3.3m -lR -o
build/lib.linux-x86_64-3.3/rpy2/rinterface/_rinterface.cpython-33m.so
building 'rpy2.rinterface._rpy_device' extension
gcc -pthread -Wno-unused-result -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 -Irpy/rinterface
-I/TL/stat_learn/work/ajalali/opt/include/python3.3m
-I/TL/stat_learn/work/ajalali/opt/lib64/R/include -c
build/python3_rpy/rpy/rinterface/_rpy_device.c -o
build/temp.linux-x86_64-3.3/build/python3_rpy/rpy/rinterface/_rpy_device.o
In file included from
/TL/stat_learn/work/ajalali/opt/lib64/R/include/R.h:40:0,
from build/python3_rpy/rpy/rinterface/_rpy_device.c:32:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/R_ext/Memory.h:40:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^
In file included from
build/python3_rpy/rpy/rinterface/_rpy_device.c:33:0:
/TL/stat_learn/work/ajalali/opt/lib64/R/include/Rinternals.h:719:1:
warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^
build/python3_rpy/rpy/rinterface/_rpy_device.c: In function
'PyInit__rpy_device':
build/python3_rpy/rpy/rinterface/_rpy_device.c:1410:17: warning:
variable 'd' set but not used [-Wunused-but-set-variable]
PyObject *m, *d;
^
build/python3_rpy/rpy/rinterface/_rpy_device.c: At top level:
build/python3_rpy/rpy/rinterface/_rpy_device.c:935:1: warning:
'GrDev_clear' defined but not used [-Wunused-function]
GrDev_clear(PyGrDevObject *self)
^
build/python3_rpy/rpy/rinterface/_rpy_device.c:1337:20: warning:
'rpydevice_methods' defined but not used [-Wunused-variable]
static PyMethodDef rpydevice_methods[] = {
^
gcc -pthread -shared
build/temp.linux-x86_64-3.3/build/python3_rpy/rpy/rinterface/_rpy_device.o
-L/TL/stat_learn/work/ajalali/opt/lib
-L/TL/stat_learn/work/ajalali/opt/lib64/R/lib
-L/TL/stat_learn/work/ajalali/opt/lib64/R/modules -lR -lpython3.3m -lR -o
build/lib.linux-x86_64-3.3/rpy2/rinterface/_rpy_device.cpython-33m.so
warning: no previously-included files matching '*patch*' found anywhere
in distribution
warning: no previously-included files matching '*diff*' found anywhere
in distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
no previously-included directories found matching 'dist'
Successfully installed rpy2
Cleaning up...
------------------------------------------------------------------------------
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