Jacob Cram | 12 Nov 21:05 2012
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[Rpy] Rf_translateCharUTF8

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
I do not have root privileges.
Installing rpy2 doesn't seem to give me any unusual error messages.  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'd be happy to provide any additional information.  Thanks for your help.
-Jacob
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Laurent Gautier | 12 Nov 21:53 2012
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Re: [Rpy] Rf_translateCharUTF8

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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Jacob Cram | 13 Nov 00:13 2012
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Re: [Rpy] Rf_translateCharUTF8

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 <at> 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 <lgautier <at> 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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web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
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Gmane