Hi there all,
I have searched previous posts, nothing since 2010. I have a local install
(production config - postgres, etc - on CENTOS 6.5).
Does anyone have RPY working? I install via toolshed and the folder is empty,
and shows missing dependencies.
>From Galaxy User:
Dataset generation errors
Dataset 81: Build base quality distribution on data 9
Tool execution generated the following error message:
Traceback (most recent call last):
File
"/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py", line
12, in <module>
from rpy import *
ImportError: No module named rpy
I have attempted to download/install the scripts but they fail with multiple
errors (most posts out there have a bad URL) -
http://getgalaxyp.org/install.html says use: curl
http://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz
if you view that it redirects you to another URL.
Via shell: R is installed: R version 2.13.0 (2011-04-13)
Can someone provide me some help please to get it working via Galaxy? I
understand it works in Central.
>From Toolshed:
Name
Version
Type
Installation status
rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_repository_tool_dependencies?tool_dependency_ids=fb85969571388350>
1.0.3
package
Error
Toolshed Error:
In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: Python.h:
No such file or directory In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68,
from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:89, from src/rpymodule2110.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2:
error: #error Must use Python with unicode enabled. <truncated>
Thanks,
Curt
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[root@seachlinux rpy]# python setup.py install
RHOMES= []
DEBUG= False
Setting RHOMES to ['/usr/lib64/R']
### Using R verion 2.13.0 installed at /usr/lib64/R ###
RHOME= /usr/lib64/R
copying src/rpymodule.c -> src/rpymodule2130.c
copying src/R_eval.c -> src/R_eval2130.c
copying src/io.c -> src/io2130.c
running install
running build
running build_py
running build_ext
building '_rpy2130' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-D_GNU_SOURCE -fPIC -fwrapv -fPIC -DWITH_NUMERIC=3
-DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2130 -DINIT_RPY=init_rpy2130
-UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include
-I/usr/lib64/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c src/rpymodule2130.c -o
build/temp.linux-x86_64-2.6/src/rpymodule2130.o -shared -llapack
In file included from src/rpymodule2130.c:51:
src/RPy.h:63:20: error: Python.h: No such file or directory
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68,
from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2:
error: #error Must use Python with unicode enabled.
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:227:
error: expected =, ,, ;, asm or __attribute__ before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:228:
error: expected =, ,, ;, asm or __attribute__ before npy_uintp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:330:
error: expected =, ,, ;, asm or __attribute__ before * token
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:331:
error: expected ) before * token
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:333:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:334:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:344:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:344:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:346:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:346:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:347:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:349:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:359:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:361:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:362:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:362:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:364:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:368:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:370:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:371:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:372:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:373:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:373:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:374:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:374:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:378:
error: expected specifier-qualifier-list before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:391:
error: expected specifier-qualifier-list before PyArray_GetItemFunc
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:492:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:526:
error: expected specifier-qualifier-list before PyObject
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:536:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:561:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:569:
error: expected specifier-qualifier-list before PyObject_HEAD
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:578:
error: expected declaration specifiers or ... before PyObject
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:728:
error: expected declaration specifiers or ... before npy_intp
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:731:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:883:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:937:
error: expected specifier-qualifier-list before PyObject_HEAD
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:980:
error: expected specifier-qualifier-list before PyObject_HEAD
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1036,
from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:
In function _PyArrayNeighborhoodIter_IncrCoord:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40:
error: npy_intp undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40:
error: (Each undeclared identifier is reported only once
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40:
error: for each function it appears in.)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:40:
error: expected ; before i
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:42:
error: i undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:42:
error: PyArrayNeighborhoodIterObject has no member named nd
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: wb undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:43:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:
In function _PyArrayNeighborhoodIter_IncrCoord2D:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:55:
error: npy_intp undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:55:
error: expected ; before wb
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: wb undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:57:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:58:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:
In function PyArrayNeighborhoodIter_Next:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71:
error: PyArrayNeighborhoodIterObject has no member named dataptr
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71:
error: PyArrayNeighborhoodIterObject has no member named translate
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:71:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:
In function PyArrayNeighborhoodIter_Reset:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:82:
error: npy_intp undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:82:
error: expected ; before i
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:84:
error: i undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:84:
error: PyArrayNeighborhoodIterObject has no member named nd
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:85:
error: PyArrayNeighborhoodIterObject has no member named coordinates
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:85:
error: PyArrayNeighborhoodIterObject has no member named bounds
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87:
error: PyArrayNeighborhoodIterObject has no member named dataptr
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87:
error: PyArrayNeighborhoodIterObject has no member named translate
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h:87:
error: PyArrayNeighborhoodIterObject has no member named coordinates
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h: At
top level:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1223:
error: expected specifier-qualifier-list before npy_intp
In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1238,
from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:99,
from src/rpymodule2130.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:
In function _import_array:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190:
error: PyObject undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190:
error: numpy undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1190:
warning: implicit declaration of function PyImport_ImportModule
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1191:
error: c_api undeclared (first use in this function)
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1193:
warning: implicit declaration of function PyObject_GetAttrString
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1194:
warning: implicit declaration of function Py_DECREF
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1195:
warning: implicit declaration of function PyCObject_Check
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1196:
warning: implicit declaration of function PyCObject_AsVoidPtr
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1203:
warning: implicit declaration of function PyErr_Format
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1203:
error: PyExc_RuntimeError undeclared (first use in this function)
In file included from src/rpymodule2130.c:51:
src/RPy.h: At top level:
src/RPy.h:101: error: expected =, ,, ;, asm or __attribute__ before
n_intp
In file included from src/RPy.h:115,
from src/rpymodule2130.c:51:
src/robjobject.h:46: error: expected specifier-qualifier-list before
PyObject_HEAD
src/robjobject.h:57: warning: return type defaults to int
src/robjobject.h: In function DL_IMPORT:
src/robjobject.h:57: error: expected declaration specifiers before Robj_Type
In file included from src/rpymodule2130.c:51:
src/RPy.h:122: error: expected ) before * token
src/RPy.h:123: error: expected declaration specifiers before PyObject
src/RPy.h:124: error: expected declaration specifiers before PyObject
src/RPy.h:125: error: expected declaration specifiers before PyObject
src/RPy.h:141: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:142: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:143: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:148: error: storage class specified for parameter Rf_initEmbeddedR
src/RPy.h:149: error: storage class specified for parameter init_io_routines
src/RPy.h:155: error: storage class specified for parameter R_Outputfile
src/RPy.h:163: error: storage class specified for parameter ptr_R_WriteConsole
src/RPy.h:164: error: storage class specified for parameter ptr_R_ReadConsole
src/RPy.h:165: error: storage class specified for parameter ptr_R_ShowFiles
src/RPy.h:182: error: expected declaration specifiers before PyObject
src/RPy.h:183: error: expected declaration specifiers before PyObject
src/RPy.h:184: error: expected declaration specifiers before PyObject
src/RPy.h:185: error: expected declaration specifiers before PyObject
src/RPy.h:186: error: expected declaration specifiers before PyObject
src/RPy.h:187: error: expected declaration specifiers before PyObject
src/RPy.h:193: error: expected =, ,, ;, asm or __attribute__ before
python_sigint
src/RPy.h:196: error: storage class specified for parameter jump_now
src/RPy.h:199: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:202: error: storage class specified for parameter R_interact
src/RPy.h:205: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:207: error: expected =, ,, ;, asm or __attribute__ before
* token
src/RPy.h:215: error: expected declaration specifiers or ... before PyObject
src/RPy.h:215: error: storage class specified for parameter to_Pyobj_proc
src/RPy.h:216: error: expected declaration specifiers or ... before PyObject
src/RPy.h:216: error: storage class specified for parameter to_Pyobj_class
src/RPy.h:217: error: expected declaration specifiers or ... before PyObject
src/RPy.h:217: error: storage class specified for parameter to_Pyobj_basic
src/RPy.h:218: error: expected declaration specifiers or ... before PyObject
src/RPy.h:218: error: storage class specified for parameter to_Pyobj_vector
src/rpymodule2130.c:63: error: storage class specified for parameter
use_numeric
src/rpymodule2130.c:63: error: parameter use_numeric is initialized
src/rpymodule2130.c:67: error: expected declaration specifiers before
DL_EXPORT
src/rpymodule2130.c:68: error: expected =, ,, ;, asm or __attribute__
before * token
src/rpymodule2130.c:70: error: expected =, ,, ;, asm or __attribute__
before * token
src/rpymodule2130.c:77: error: storage class specified for parameter get_item
src/rpymodule2130.c:78: error: storage class specified for parameter set_item
src/rpymodule2130.c:79: error: storage class specified for parameter length
src/rpymodule2130.c:80: error: storage class specified for parameter aperm
src/rpymodule2130.c:81: error: expected =, ,, ;, asm or __attribute__
before * token
src/rpymodule2130.c:82: error: expected =, ,, ;, asm or __attribute__
before * token
src/rpymodule2130.c:83: error: storage class specified for parameter
default_mode
src/rpymodule2130.c:84: error: expected =, ,, ;, asm or __attribute__
before * token
src/rpymodule2130.c:85: error: expected declaration specifiers before PyObject
src/rpymodule2130.c:86: error: expected declaration specifiers before PyObject
src/rpymodule2130.c:87: error: expected declaration specifiers before PyObject
src/rpymodule2130.c:89: error: storage class specified for parameter RHOME
src/rpymodule2130.c:90: error: storage class specified for parameter RVERSION
src/rpymodule2130.c:91: error: storage class specified for parameter RVER
src/rpymodule2130.c:92: error: storage class specified for parameter RUSER
src/rpymodule2130.c:93: error: parameter defaultargv is initialized
src/rpymodule2130.c:93: warning: initialization from incompatible pointer type
src/rpymodule2130.c:93: warning: excess elements in scalar initializer
src/rpymodule2130.c:93: warning: (near initialization for defaultargv)
src/rpymodule2130.c:93: warning: excess elements in scalar initializer
src/rpymodule2130.c:93: warning: (near initialization for defaultargv)
src/rpymodule2130.c:94: error: parameter defaultargc is initialized
src/rpymodule2130.c:97: error: expected declaration specifiers before
PyInterpreterState
src/rpymodule2130.c:100: error: redefinition of parameter R_interact
src/RPy.h:202: note: previous definition of R_interact was here
src/rpymodule2130.c:103: error: expected declaration specifiers before
PyObject
src/rpymodule2130.c:104: error: expected declaration specifiers before
PyObject
src/rpymodule2130.c:108: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:113: error: storage class specified for parameter
R_References
src/rpymodule2130.c:117: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:131: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:141: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:160: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:183: error: expected ) before * token
src/rpymodule2130.c:207: error: expected ) before * token
src/rpymodule2130.c:292: error: expected ) before * token
src/rpymodule2130.c:330: error: expected ) before * token
src/rpymodule2130.c:510: error: expected ) before * token
src/rpymodule2130.c:626: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:652: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:686: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:710: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:751: error: expected declaration specifiers or ... before
PyObject
src/rpymodule2130.c:752: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:774: error: expected declaration specifiers or ... before
PyObject
src/rpymodule2130.c:775: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:900: error: expected declaration specifiers before
PyObject
src/rpymodule2130.c:939: error: expected declaration specifiers or ... before
PyObject
src/rpymodule2130.c:940: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:977: error: expected declaration specifiers or ... before
PyObject
src/rpymodule2130.c:978: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:999: error: expected declaration specifiers or ... before
PyObject
src/rpymodule2130.c:1000: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1015: error: expected declaration specifiers before
PyObject
src/rpymodule2130.c:1048: error: expected declaration specifiers or ...
before PyObject
src/rpymodule2130.c:1049: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1067: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1092: error: expected declaration specifiers or ...
before PyObject
src/rpymodule2130.c:1093: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1139: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1191: error: expected declaration specifiers or ...
before PyObject
src/rpymodule2130.c:1192: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1276: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1342: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1369: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1392: error: expected =, ,, ;, asm or
__attribute__ before Robj_methods
src/rpymodule2130.c:1398: error: expected declaration specifiers before ;
token
src/rpymodule2130.c:1404: error: expected ) before * token
src/rpymodule2130.c:1423: error: expected ) before * token
src/rpymodule2130.c:1449: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1490: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1564: error: expected =, ,, ;, asm or
__attribute__ before Robj_as_sequence
src/rpymodule2130.c:1575: error: expected declaration specifiers before ;
token
src/rpymodule2130.c:1589: error: expected declaration specifiers before
PyTypeObject
src/rpymodule2130.c:1656: error: expected declaration specifiers before ;
token
src/rpymodule2130.c:1663: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1682: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1700: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1709: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1739: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1754: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1774: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1809: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1820: error: expected =, ,, ;, asm or
__attribute__ before { token
src/rpymodule2130.c:1836: error: expected =, ,, ;, asm or
__attribute__ before * token
src/rpymodule2130.c:1865: error: expected =, ,, ;, asm or
__attribute__ before rpy_methods
src/rpymodule2130.c:1879: error: expected declaration specifiers before ;
token
src/rpymodule2130.c:1974: error: expected declaration specifiers before
DL_EXPORT
src/rpymodule2130.c:113: error: declaration for parameter R_References but no
such parameter
src/rpymodule2130.c:100: error: declaration for parameter R_interact but no
such parameter
src/rpymodule2130.c:94: error: declaration for parameter defaultargc but no
such parameter
src/rpymodule2130.c:93: error: declaration for parameter defaultargv but no
such parameter
src/rpymodule2130.c:92: error: declaration for parameter RUSER but no such
parameter
src/rpymodule2130.c:91: error: declaration for parameter RVER but no such
parameter
src/rpymodule2130.c:90: error: declaration for parameter RVERSION but no such
parameter
src/rpymodule2130.c:89: error: declaration for parameter RHOME but no such
parameter
src/rpymodule2130.c:83: error: declaration for parameter default_mode but no
such parameter
src/rpymodule2130.c:80: error: declaration for parameter aperm but no such
parameter
src/rpymodule2130.c:79: error: declaration for parameter length but no such
parameter
src/rpymodule2130.c:78: error: declaration for parameter set_item but no such
parameter
src/rpymodule2130.c:77: error: declaration for parameter get_item but no such
parameter
src/rpymodule2130.c:63: error: declaration for parameter use_numeric but no
such parameter
src/RPy.h:218: error: declaration for parameter to_Pyobj_vector but no such
parameter
src/RPy.h:217: error: declaration for parameter to_Pyobj_basic but no such
parameter
src/RPy.h:216: error: declaration for parameter to_Pyobj_class but no such
parameter
src/RPy.h:215: error: declaration for parameter to_Pyobj_proc but no such
parameter
src/RPy.h:211: error: declaration for parameter start_events but no such
parameter
src/RPy.h:210: error: declaration for parameter stop_events but no such
parameter
src/RPy.h:202: error: declaration for parameter R_interact but no such
parameter
src/RPy.h:196: error: declaration for parameter jump_now but no such parameter
src/RPy.h:190: error: declaration for parameter interrupt_R but no such
parameter
src/RPy.h:165: error: declaration for parameter ptr_R_ShowFiles but no such
parameter
src/RPy.h:164: error: declaration for parameter ptr_R_ReadConsole but no such
parameter
src/RPy.h:163: error: declaration for parameter ptr_R_WriteConsole but no
such parameter
src/RPy.h:155: error: declaration for parameter R_Outputfile but no such
parameter
src/RPy.h:149: error: declaration for parameter init_io_routines but no such
parameter
src/RPy.h:148: error: declaration for parameter Rf_initEmbeddedR but no such
parameter
src/RPy.h:145: error: declaration for parameter get_last_error_msg but no
such parameter
src/RPy.h:138: error: declaration for parameter get_fun_from_name but no such
parameter
src/RPy.h:137: error: declaration for parameter do_eval_fun but no such
parameter
src/RPy.h:136: error: declaration for parameter do_eval_expr but no such
parameter
src/setenv.h:46: error: declaration for parameter setenv but no such parameter
src/robjobject.h:62: error: declaration for parameter Robj_new but no such
parameter
src/rpymodule2130.c:2106: error: expected { at end of input
error: command 'gcc' failed with exit status 1
[root@seachlinux rpy]# python
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "rpy.py", line 134, in <module>
""" % RVERSION)
RuntimeError: No module named _rpy2130
RPy module can not be imported. Please check if your rpy
installation supports R 2.13.0. If you have multiple R versions
installed, you may need to set RHOME before importing rpy. For
example:
>>> from rpy_options import set_options
>>> set_options(RHOME='c:/progra~1/r/rw2011/')
>>> from rpy import *
>>> exit
Use exit() or Ctrl-D (i.e. EOF) to exit
>>> exit
Use exit() or Ctrl-D (i.e. EOF) to exit
>>> exit()
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