[Rpy] Installing rpy on a 64 bit ubuntu server
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:18
Re: [Rpy] Installing rpy on a 64 bit ubuntu server
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
[Rpy] RPy 1.0.2 Now available
Hi All, I've uploaded RPy 1.0.2 to sourceforge. The NEWS entry for this version is below. Importantly, this should version should (re-) correct crashes due to issues with R's C stack checking code. -Greg CHANGES IN RPY 1.0.2 - 2008-04-10 - New features: - The 'Robj' type is now exported. - Add simple neural net example. Bug fixes: - Stack checking code was incorrectly disabled on all platforms, corrected so that it is properly included for R 2.3.0 and later everywhere except Win32. - Fixes for compatibility with Python 2.4 and later. - Updates to debian install files (Dirk Eddelbuettel) - Correct simple line plot example in the documentation - Minor internal changes to code and tests - Automatic build tool now uses 'tail -n 1' instead of 'tail -1' when calling 'R RHOME' to make recent versions of tail happy - Add startup options to prevent initialization of console read/write/showfiles which causes problems with R when run without a controlling console. Other changes: - Deletion of R's temporary directory now uses R's own internal function for this task for R versions after 2.4.0. - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] Installing rpy on a 64 bit ubuntu server
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
Re: [Rpy] RPy 1.0.2 Now available
On Apr 11, 2008, at 8:47 AM, Gregory. R. Warnes wrote: s > I've uploaded RPy 1.0.2 to sourceforge. The NEWS entry for this > version is below. Importantly, this should version should (re-) > correct crashes due to issues with R's C stack checking code. The problem seems to be solved -- thanks, Greg! - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
