Laurent and Others,
Thanks so much for your speedy reply.
Python did indeed seem to be pointing to the wrong directory.
Unfortunately after correcting that issue, the problem persists.
I corrected the rpy path and also updated rpy2 as follows:
~/installers/rpy2-2.3.0beta1$ python setup.py build --r-home
$HOME/usr/lib64/R install
Output from this installation can be read at the bottom of this email.
Now,
ldd `python -c 'import rpy2;
print(rpy2.__path__[0])'`/rinterface/_rinterface.so | grep libR
libR.so => /usr/lib64/R/lib/libR.so (0x00002ad23820d000)
libRblas.so => /usr/lib64/R/lib/libRblas.so (0x00002ad23901c000)
Unfortunately, I still get the same error message when I test rpy2
cram@hpc-login2:~/installers/rpy2-2.3.0beta1$ python -m "rpy2.tests"
Traceback (most recent call last):
File "/home/rcf-40/cram/usr/lib/python2.7/runpy.py", line 162, in
_run_module_as_main
"__main__", fname, loader, pkg_name)
File "/home/rcf-40/cram/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/auto/rcf-proj/jac/usr/lib/python2.7/site-packages/rpy2/tests.py",
line 2, in <module>
import sys, rpy2.rinterface
File
"/home/rcf-40/cram/usr/lib/python2.7/site-packages/rpy2/rinterface/__init__.py",
line 90, in <module>
from rpy2.rinterface._rinterface import *
ImportError:
/home/rcf-40/cram/usr/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so:
undefined symbol: Rf_translateCharUTF8
I had previously installed R with as follows:
./configure --enable-R-shlib --enable-R-static-lib --enable-shared
--prefix=/$HOME/usr
make
make install
Python was installed as follows
./configure --prefix=$HOME/usr --enable-shared
make && make install && make test
Text from rpy2 instalation:
running build
running build_py
running build_ext
returned an empty string.
returned an empty string.
Configuration for R as a library:
include_dirs: ('/home/rcf-40/cram/usr/lib64/R/include',)
libraries: ('R',)
library_dirs: ('/home/rcf-40/cram/usr/lib64/R/lib',)
extra_link_args: ()
# OSX-specific (included in extra_link_args)
framework_dirs: ()
frameworks: ()
running install
running install_lib
running install_egg_info
Removing
/home/rcf-40/cram/usr/lib/python2.7/site-packages/rpy2-2.3.0beta1-py2.7.egg-info
Writing
/home/rcf-40/cram/usr/lib/python2.7/site-packages/rpy2-2.3.0beta1-py2.7.egg-info
Please let me know if you have further advice on how I can get rpy2 to run
on this system. Thank you for your help.
Sincerely,
Jacob
On Mon, Nov 12, 2012 at 12:53 PM, Laurent Gautier <lgaut...@gmail.com>wrote:
> On 2012-11-12 12:05, Jacob Cram wrote:
>
> Hello All,
> I am attempting to install rpy2 on a high performance cluster and am
> getting some strange results.
> I am running R 2.14.12 (have also tried with 2.15.12).
> Python is 2.7.3.
> Using rpy2-2.2.1
>
> Hi,
>
> I'd recommend to consider switching to 2.3.0, and if not ready to do so
> rpy2-2.2.7 is the latest in the 2.2 series.
> (more below)
>
>
> I do not have root privileges.
> Installing rpy2 doesn't seem to give me any unusual error messages.
>
>
> Do not hesitate to share how you are installing. There might be clues
> about the problem.
>
>
>
> However
> python
> >>>import rpy2
> >>>import rpy2.tests
> File "<stdin>", line 1, in <module>
> File "/home/rcf-40/mmmm/usr/lib/
> python2.7/site-packages/rpy2/tests.py", line 3, in <module>
> import rpy2.robjects.tests
> File
> "/home/rcf-40/mmmm/usr/lib/python2.7/site-packages/rpy2/robjects/__init__.py",
> line 14, in <module>
> import rpy2.rinterface as rinterface
> File
> "/home/rcf-40/mmmm/usr/lib/python2.7/site-packages/rpy2/rinterface/__init__.py",
> line 78, in <module>
> from rpy2.rinterface._rinterface import *
> ImportError:
> /home/rcf-40/mmmm/usr/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so:
> undefined symbol: Rf_translateCharUTF8
>
> I can't seem to find any other examples of someone experiencing this
> import error elsewhere. Does anybody have a suggestion about what I might
> be able to do to get rpy2 to work.
>
>
> I think that I have seen a report about a similar problem. I suspect that
> the R libraries from an older R version are picked up during the
> initialisation.
>
> Check in a shell if the following it pointing to the right Python
> libraries:
>
> ldd `python -c 'import rpy2;
> print(rpy2.__path__[0])'`/rinterface/_rinterface.so | grep libR
>
>
> L.
>
> I'd be happy to provide any additional information. Thanks for your
> help.
> -Jacob
>
>
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