Cleaning up manually the previous installs in python-libs may also help
L. On Mon, 2008-11-17 at 08:23 -0500, laurent oget wrote: > 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 > > 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 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