Thanks alot that seemed to solve that problem alright.
Incidently I ran into another problem in that on 64-bit R seems to
store libR.so in RHOME/lib rahter than RHOME/bin, as is suggested in
the readme. So the line I ended up adding to /etc/ld.so.conf was:
"/usr/lib64/R/lib/"
Where "/usr/lib64/R" is RHOME.
-Paul.
On 4/11/08, Laurent Gautier <[EMAIL PROTECTED]> wrote:
> One line in the log tells:
> src/RPy.h:56:20: error: Python.h: No such file or directory
>
> wouldn't you have the development headers missing ?
>
>
>
> 2008/4/11, Paul Geeleher <[EMAIL PROTECTED]>:
> > 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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> > rpy-list@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rpy-list
> >
>
>
> --
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