Hi, I'm wondering if anyone has experience of installing rpy on 64 bit
ubuntu gutsty?
I've built R version 2.6.2 from source and am running python version 2.5.1.
I'm fairly certain i've followed all instructions correctly (R as
shlib, configuring path to R library etc.), but when i go to install
Rpy, I get the following:
RHOMES= []
DEBUG= True
Setting RHOMES to ['/usr/local/lib64/R']
### Using R verion 2.6.2 installed at /usr/local/lib64/R ###
RHOME= /usr/local/lib64/R
copying src/rpymodule.c -> src/rpymodule2062.c
copying src/R_eval.c -> src/R_eval2062.c
copying src/io.c -> src/io2062.c
running install
running build
running build_py
running build_ext
building '_rpy2062' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
-Wstrict-prototypes -fPIC -DWITH_NUMERIC=1 -DRPY_SHNAME=_rpy2062
-DINIT_RPY=init_rpy2062 -UPRE_2_2 -I/usr/local/lib64/R/include -Isrc
-I/usr/share/R/include -I/usr/include/python2.5 -c src/rpymodule2062.c
-o build/temp.linux-x86_64-2.5/src/rpymodule2062.o -shared
In file included from /usr/local/lib64/R/include/R.h:48,
from src/RPy.h:51,
from src/rpymodule2062.c:43:
/usr/local/lib64/R/include/R_ext/Random.h:58: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/R_ext/Random.h:60: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/R_ext/Random.h:61: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/R_ext/Random.h:63: warning: function
declaration isn't a prototype
In file included from src/rpymodule2062.c:43:
src/RPy.h:56:20: error: Python.h: No such file or directory
In file included from src/RPy.h:57,
from src/rpymodule2062.c:43:
/usr/local/lib64/R/include/R_ext/Rdynload.h:25: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/R_ext/Rdynload.h:100: warning: function
declaration isn't a prototype
In file included from src/RPy.h:73,
from src/rpymodule2062.c:43:
/usr/local/lib64/R/include/Rinterface.h:52: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/Rinterface.h:63: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/Rinterface.h:68: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/Rinterface.h:69: warning: function
declaration isn't a prototype
/usr/local/lib64/R/include/Rinterface.h:70: warning: function
declaration isn't a prototype
In file included from src/RPy.h:96,
from src/rpymodule2062.c:43:
/usr/include/python2.5/Numeric/arrayobject.h:23: error: expected '=',
',', ';', 'asm' or '__attribute__' before '*' token
/usr/include/python2.5/Numeric/arrayobject.h:24: error: expected ')'
before '*' token
/usr/include/python2.5/Numeric/arrayobject.h:29: error: expected
specifier-qualifier-list before 'PyArray_GetItemFunc'
/usr/include/python2.5/Numeric/arrayobject.h:49: error: expected
specifier-qualifier-list before 'PyObject_HEAD'
/usr/include/python2.5/Numeric/arrayobject.h:71: error: expected
specifier-qualifier-list before 'Py_intptr_t'
In file included from src/RPy.h:108,
from src/rpymodule2062.c:43:
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:57: warning: function declaration isn't a prototype
src/robjobject.h: In function 'DL_IMPORT':
src/robjobject.h:57: error: expected declaration specifiers before 'Robj_Type'
In file included from src/rpymodule2062.c:43:
src/RPy.h:115: error: expected ')' before '*' token
src/RPy.h:116: error: expected declaration specifiers before 'PyObject'
src/RPy.h:117: error: expected declaration specifiers before 'PyObject'
src/RPy.h:118: error: expected declaration specifiers before 'PyObject'
src/RPy.h:134: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:135: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:136: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:141: error: storage class specified for parameter 'Rf_initEmbeddedR'
src/RPy.h:142: error: storage class specified for parameter 'init_io_routines'
src/RPy.h:148: error: storage class specified for parameter 'R_Outputfile'
src/RPy.h:156: error: storage class specified for parameter 'ptr_R_WriteConsole'
src/RPy.h:157: error: storage class specified for parameter 'ptr_R_ReadConsole'
src/RPy.h:158: error: storage class specified for parameter 'ptr_R_ShowFiles'
src/RPy.h:175: error: expected declaration specifiers before 'PyObject'
src/RPy.h:176: error: expected declaration specifiers before 'PyObject'
src/RPy.h:177: error: expected declaration specifiers before 'PyObject'
src/RPy.h:178: error: expected declaration specifiers before 'PyObject'
src/RPy.h:179: error: expected declaration specifiers before 'PyObject'
src/RPy.h:180: error: expected declaration specifiers before 'PyObject'
src/RPy.h:186: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'python_sigint'
src/RPy.h:189: error: storage class specified for parameter 'jump_now'
src/RPy.h:192: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:195: error: storage class specified for parameter 'R_interact'
src/RPy.h:198: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:200: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
src/RPy.h:208: error: expected declaration specifiers or '...' before 'PyObject'
src/RPy.h:208: error: storage class specified for parameter 'to_Pyobj_proc'
src/RPy.h:209: error: expected declaration specifiers or '...' before 'PyObject'
src/RPy.h:209: error: storage class specified for parameter 'to_Pyobj_class'
src/RPy.h:210: error: expected declaration specifiers or '...' before 'PyObject'
src/RPy.h:210: error: storage class specified for parameter 'to_Pyobj_basic'
src/RPy.h:211: error: expected declaration specifiers or '...' before 'PyObject'
src/RPy.h:211: error: storage class specified for parameter 'to_Pyobj_vector'
src/rpymodule2062.c:55: error: storage class specified for parameter
'use_numeric'
src/rpymodule2062.c:55: error: parameter 'use_numeric' is initialized
src/rpymodule2062.c:59: error: expected declaration specifiers before
'DL_EXPORT'
src/rpymodule2062.c:60: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:62: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:69: error: storage class specified for parameter 'get_item'
src/rpymodule2062.c:70: error: storage class specified for parameter 'set_item'
src/rpymodule2062.c:71: error: storage class specified for parameter 'length'
src/rpymodule2062.c:72: error: storage class specified for parameter 'aperm'
src/rpymodule2062.c:73: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:74: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:75: error: storage class specified for parameter
'default_mode'
src/rpymodule2062.c:76: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:77: error: expected declaration specifiers before 'PyObject'
src/rpymodule2062.c:78: error: expected declaration specifiers before 'PyObject'
src/rpymodule2062.c:79: error: expected declaration specifiers before 'PyObject'
src/rpymodule2062.c:81: error: storage class specified for parameter 'RHOME'
src/rpymodule2062.c:82: error: storage class specified for parameter 'RVERSION'
src/rpymodule2062.c:83: error: storage class specified for parameter 'RVER'
src/rpymodule2062.c:84: error: storage class specified for parameter 'RUSER'
src/rpymodule2062.c:87: error: expected declaration specifiers before
'PyInterpreterState'
src/rpymodule2062.c:90: error: redefinition of parameter 'R_interact'
src/RPy.h:195: error: previous definition of 'R_interact' was here
src/rpymodule2062.c:93: error: expected declaration specifiers before 'PyObject'
src/rpymodule2062.c:94: error: expected declaration specifiers before 'PyObject'
src/rpymodule2062.c:98: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:103: error: storage class specified for parameter
'R_References'
src/rpymodule2062.c:107: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:121: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:131: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:150: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:173: error: expected ')' before '*' token
src/rpymodule2062.c:197: error: expected ')' before '*' token
src/rpymodule2062.c:282: error: expected ')' before '*' token
src/rpymodule2062.c:320: error: expected ')' before '*' token
src/rpymodule2062.c:500: error: expected ')' before '*' token
src/rpymodule2062.c:616: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:642: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:676: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:700: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:741: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:742: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:764: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:765: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:890: error: expected declaration specifiers before
'PyObject'
src/rpymodule2062.c:929: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:930: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:967: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:968: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:989: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:990: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1005: error: expected declaration specifiers
before 'PyObject'
src/rpymodule2062.c:1038: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:1039: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1057: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1082: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:1083: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1129: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1181: error: expected declaration specifiers or
'...' before 'PyObject'
src/rpymodule2062.c:1182: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1266: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1332: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1359: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1382: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'Robj_methods'
src/rpymodule2062.c:1388: error: expected declaration specifiers
before ';' token
src/rpymodule2062.c:1394: error: expected ')' before '*' token
src/rpymodule2062.c:1413: error: expected ')' before '*' token
src/rpymodule2062.c:1439: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1477: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'Robj_as_sequence'
src/rpymodule2062.c:1486: error: expected declaration specifiers
before ';' token
src/rpymodule2062.c:1500: error: expected declaration specifiers
before 'PyTypeObject'
src/rpymodule2062.c:1567: error: expected declaration specifiers
before ';' token
src/rpymodule2062.c:1574: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1593: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1611: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1620: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1650: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1665: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1685: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1709: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1720: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '{' token
src/rpymodule2062.c:1736: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
src/rpymodule2062.c:1765: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'rpy_methods'
src/rpymodule2062.c:1779: error: expected declaration specifiers
before ';' token
src/rpymodule2062.c:1872: error: expected declaration specifiers
before 'DL_EXPORT'
src/rpymodule2062.c:103: error: declaration for parameter
'R_References' but no such parameter
src/rpymodule2062.c:90: error: declaration for parameter 'R_interact'
but no such parameter
src/rpymodule2062.c:84: error: declaration for parameter 'RUSER' but
no such parameter
src/rpymodule2062.c:83: error: declaration for parameter 'RVER' but no
such parameter
src/rpymodule2062.c:82: error: declaration for parameter 'RVERSION'
but no such parameter
src/rpymodule2062.c:81: error: declaration for parameter 'RHOME' but
no such parameter
src/rpymodule2062.c:75: error: declaration for parameter
'default_mode' but no such parameter
src/rpymodule2062.c:72: error: declaration for parameter 'aperm' but
no such parameter
src/rpymodule2062.c:71: error: declaration for parameter 'length' but
no such parameter
src/rpymodule2062.c:70: error: declaration for parameter 'set_item'
but no such parameter
src/rpymodule2062.c:69: error: declaration for parameter 'get_item'
but no such parameter
src/rpymodule2062.c:55: error: declaration for parameter 'use_numeric'
but no such parameter
src/RPy.h:211: error: declaration for parameter 'to_Pyobj_vector' but
no such parameter
src/RPy.h:210: error: declaration for parameter 'to_Pyobj_basic' but
no such parameter
src/RPy.h:209: error: declaration for parameter 'to_Pyobj_class' but
no such parameter
src/RPy.h:208: error: declaration for parameter 'to_Pyobj_proc' but no
such parameter
src/RPy.h:204: error: declaration for parameter 'start_events' but no
such parameter
src/RPy.h:203: error: declaration for parameter 'stop_events' but no
such parameter
src/RPy.h:195: error: declaration for parameter 'R_interact' but no
such parameter
src/RPy.h:189: error: declaration for parameter 'jump_now' but no such parameter
src/RPy.h:183: error: declaration for parameter 'interrupt_R' but no
such parameter
src/RPy.h:158: error: declaration for parameter 'ptr_R_ShowFiles' but
no such parameter
src/RPy.h:157: error: declaration for parameter 'ptr_R_ReadConsole'
but no such parameter
src/RPy.h:156: error: declaration for parameter 'ptr_R_WriteConsole'
but no such parameter
src/RPy.h:148: error: declaration for parameter 'R_Outputfile' but no
such parameter
src/RPy.h:142: error: declaration for parameter 'init_io_routines' but
no such parameter
src/RPy.h:141: error: declaration for parameter 'Rf_initEmbeddedR' but
no such parameter
src/RPy.h:138: error: declaration for parameter 'get_last_error_msg'
but no such parameter
src/RPy.h:131: error: declaration for parameter 'get_fun_from_name'
but no such parameter
src/RPy.h:130: error: declaration for parameter 'do_eval_fun' but no
such parameter
src/RPy.h:129: 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/rpymodule2062.c:1995: error: expected '{' at end of input
error: command 'gcc' failed with exit status 1
Any pointers are greatly appreciated!
-Paul
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