so you have the right python, but somehow your rpy is looking for symbols that are not there. i suspect part of your rpy was leftover from the initial built against the old python. one thing you can do is hide your rpy folder, extract the .tar.gz again and do the python setup.py install from scratch.
good luck Laurent 2008/11/17 Paul Geeleher <[EMAIL PROTECTED]>: > Hi, > > I'm importing into version 2.5.2. Thats the version that I compiled from > source and that now starts by default when I type "python" at the command > prompt. > > -Paul. > > On Mon, Nov 17, 2008 at 3:53 AM, laurent oget <[EMAIL PROTECTED]> wrote: >> >> One question i forgot to ask: >> -which python are you importing into? >> >> Laurent >> >> 2008/11/16 Paul Geeleher <[EMAIL PROTECTED]>: >> > Hi again. >> > >> > I did a "find / -name "*libpython*"" which should find any libpython >> > files >> > (I think). It outputted the following. >> > >> > /usr/lib/libpython2.4.so.1.0 >> > /usr/lib64/libpython2.5.so >> > /usr/lib64/libpython2.5.so.1.0 >> > /usr/lib64/gnome-vfs-2.0/modules/libpythonmethod.so >> > /usr/lib64/python2.5/config/libpython2.5.a >> > /usr/local/lib/python2.5/config/libpython2.5.a >> > /root/Python-2.5.2/Doc/lib/libpython.tex >> > /root/Python-2.5.2/libpython2.5.a >> > >> > >> > I tried renaming (to pylib.bak) both "/usr/lib/libpython2.4.so.1.0" and >> > "/usr/lib64/libpython2.5.so" and reinstalling and running rpy after each >> > time, but to no avail. >> > >> > I wonder is there any way to manually specify the libpython, if that is >> > in >> > fact definately the problem? >> > >> > >> > >> > If this is any help, this is the output when Rpy installs: >> > >> > >> > hcux321:~/rpy-1.0.3 # python setup.py install >> > 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 >> > running install_lib >> > running install_egg_info >> > Removing /usr/local/lib/python2.5/site-packages/rpy-1.0.3-py2.5.egg-info >> > Writing /usr/local/lib/python2.5/site-packages/rpy-1.0.3-py2.5.egg-info >> > >> > >> > >> > -Paul >> > >> > >> > On Sun, Nov 16, 2008 at 5:30 PM, laurent oget <[EMAIL PROTECTED]> wrote: >> >> >> >> Is the libpython in /usr/lib being picked up instead of the new one at >> >> runtime? can you put this aside and try again? >> >> >> >> 2008/11/15 Paul Geeleher <[EMAIL PROTECTED]>: >> >> > Hi again, >> >> > >> >> > Building version 2.5.2 of Python from source (overwriting version >> >> > 2.5.1) seems to have solved that problem alright. Rpy now seems to >> >> > install, >> >> > but when I go to import it I'm faced witht he following error: >> >> > >> >> > >> >> > >> >> >>>> from rpy import * >> >> > Traceback (most recent call last): >> >> > File "<stdin>", line 1, in <module> >> >> > File "/usr/local/lib/python2.5/site-packages/rpy.py", line 134, in >> >> > <module> >> >> > """ % RVERSION) >> >> > RuntimeError: /usr/local/lib/python2.5/site-packages/_rpy2062.so: >> >> > undefined >> >> > symbol: PyUnicodeUCS4_AsASCIIString >> >> > >> >> > RPy module can not be imported. Please check if your rpy >> >> > installation supports R 2.6.2. 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 * >> >> > >> >> > >> >> > >> >> > Any ideas here would be greatly appreciated. >> >> > >> >> > Thanks, >> >> > >> >> > -Paul. >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > On 11/14/08, Paul Geeleher <[EMAIL PROTECTED]> wrote: >> >> >> >> >> >> Thanks for the response Laurent. I'll give it a go and let you know >> >> >> how >> >> >> it >> >> >> works out. >> >> >> >> >> >> -Paul. >> >> >> >> >> >> On Fri, Nov 14, 2008 at 7:18 PM, laurent oget <[EMAIL PROTECTED]> >> >> >> wrote: >> >> >>> >> >> >>> This definitely looks weird. I have built rpy and rpy2 on 64-bit >> >> >>> linux, but this was always using a python i built before, since the >> >> >>> machine i am using come with an antiquated python in the >> >> >>> distribution. >> >> >>> I just looked at one of those machine and I noticed my hand-built >> >> >>> python does not have a libpython.so but only a libpython.a . >> >> >>> >> >> >>> Now that i think about it i am not sure you can use a stripped >> >> >>> library >> >> >>> to link against. how would the linker know the address of those >> >> >>> symbols in this library? >> >> >>> >> >> >>> In any case building your own python might be a workaround... >> >> >>> >> >> >>> Laurent >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> 2008/11/14 Paul Geeleher <[EMAIL PROTECTED]>: >> >> >>> > Hi >> >> >>> > >> >> >>> > I posted this message about 10 days ago and I didn't get a reply, >> >> >>> > so >> >> >>> > I'm >> >> >>> > going to chance re-posting, hopefully somebody can help me out >> >> >>> > because >> >> >>> > I >> >> >>> > still haven't managed to fix it... >> >> >>> > >> >> >>> > _______________ >> >> >>> > >> >> >>> > >> >> >>> > Hi all, >> >> >>> > >> >> >>> > I'm trying to install Rpy on a 64 bit Suse Enterprise Edition >> >> >>> > Server. >> >> >>> > I'm >> >> >>> > running R version 2.6.2 and python version 2.5.1 and Rpy 1.0.3. >> >> >>> > I've >> >> >>> > set up >> >> >>> > the path >> >> >>> > to the R library by creating a link to libR.so and running >> >> >>> > ldconfig. >> >> >>> > I've got the python-devel package installed. I'm getting the >> >> >>> > following >> >> >>> > error when I run "python setup.py install" >> >> >>> > >> >> >>> > >> >> >>> > 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 -shared >> >> >>> > build/temp.linux-x86_64-2.5/src/rpymodule2062.o >> >> >>> > build/temp.linux-x86_64-2.5/src/R_eval2062.o >> >> >>> > build/temp.linux-x86_64-2.5/src/io2062.o >> >> >>> > build/temp.linux-x86_64-2.5/src/setenv.o -L/usr/local/lib64/R/bin >> >> >>> > -L/usr/local/lib64/R/lib -L/usr/lib64 >> >> >>> > -Wl,-R/usr/local/lib64/R/bin >> >> >>> > -Wl,-R/usr/local/lib64/R/lib -lR -lRlapack -lpython2.5 -o >> >> >>> > build/lib.linux-x86_64-2.5/_rpy2062.so >> >> >>> > /usr/lib64/libpython2.5.so: file not recognized: File format not >> >> >>> > recognized >> >> >>> > collect2: ld returned 1 exit status >> >> >>> > error: command 'gcc' failed with exit status 1 >> >> >>> > >> >> >>> > ------------------------------------ >> >> >>> > >> >> >>> > So the file libpython2.5.so seems to be throwing up some kind of >> >> >>> > a >> >> >>> > problem. >> >> >>> > >> >> >>> > The output of 'file libpython2.5.so' is: >> >> >>> > "libpython2.5.so: symbolic link to `libpython2.5.so.1.0'" >> >> >>> > >> >> >>> > So its a link and the output of 'file libpython2.5.so.1.0' is: >> >> >>> > "libpython2.5.so.1.0: ELF 64-bit LSB shared object, AMD x86-64, >> >> >>> > version >> >> >>> > 1 >> >> >>> > (SYSV), stripped" >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > Any ideas here guys? (please!) >> >> >>> > >> >> >>> > -Paul. >> >> >>> > >> >> >>> >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > ------------------------------------------------------------------------- >> >> >>> > This SF.Net email is sponsored by the Moblin Your Move >> >> >>> > Developer's >> >> >>> > challenge >> >> >>> > Build the coolest Linux based applications with Moblin SDK & win >> >> >>> > great >> >> >>> > prizes >> >> >>> > Grand prize is a trip for two to an Open Source event anywhere in >> >> >>> > the >> >> >>> > world >> >> >>> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >>> > _______________________________________________ >> >> >>> > rpy-list mailing list >> >> >>> > rpy-list@lists.sourceforge.net >> >> >>> > https://lists.sourceforge.net/lists/listinfo/rpy-list >> >> >>> > >> >> >>> > >> >> >>> >> >> >>> >> >> >>> >> >> >>> ------------------------------------------------------------------------- >> >> >>> This SF.Net email is sponsored by the Moblin Your Move Developer's >> >> >>> challenge >> >> >>> Build the coolest Linux based applications with Moblin SDK & win >> >> >>> great >> >> >>> prizes >> >> >>> Grand prize is a trip for two to an Open Source event anywhere in >> >> >>> the >> >> >>> world >> >> >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >>> _______________________________________________ >> >> >>> rpy-list mailing list >> >> >>> rpy-list@lists.sourceforge.net >> >> >>> https://lists.sourceforge.net/lists/listinfo/rpy-list >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Paul Geeleher >> >> >> Department of Mathematics >> >> >> National University of Ireland >> >> >> Galway >> >> >> Ireland >> >> >> >> >> > >> >> > >> >> > >> >> > -- >> >> > Paul Geeleher >> >> > Department of Mathematics >> >> > National University of Ireland >> >> > Galway >> >> > Ireland >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------- >> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >> >> > challenge >> >> > Build the coolest Linux based applications with Moblin SDK & win >> >> > great >> >> > prizes >> >> > Grand prize is a trip for two to an Open Source event anywhere in the >> >> > world >> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> > _______________________________________________ >> >> > rpy-list mailing list >> >> > rpy-list@lists.sourceforge.net >> >> > https://lists.sourceforge.net/lists/listinfo/rpy-list >> >> > >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> >> challenge >> >> Build the coolest Linux based applications with Moblin SDK & win great >> >> prizes >> >> Grand prize is a trip for two to an Open Source event anywhere in the >> >> world >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> _______________________________________________ >> >> rpy-list mailing list >> >> rpy-list@lists.sourceforge.net >> >> https://lists.sourceforge.net/lists/listinfo/rpy-list >> > >> > >> > >> > -- >> > Paul Geeleher >> > Department of Mathematics >> > National University of Ireland >> > Galway >> > Ireland >> > >> > >> > >> > ------------------------------------------------------------------------- >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >> > challenge >> > Build the coolest Linux based applications with Moblin SDK & win great >> > prizes >> > Grand prize is a trip for two to an Open Source event anywhere in the >> > world >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > _______________________________________________ >> > rpy-list mailing list >> > rpy-list@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rpy-list >> > >> > >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> rpy-list mailing list >> rpy-list@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rpy-list > > > > -- > Paul Geeleher > Department of Mathematics > National University of Ireland > Galway > Ireland > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > rpy-list mailing list > 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