I will defer to Greg's expertise for a more accurate answer, but I would
suspect that the problem is the difference in using the system version of
Python and a version of RDKit that is built with a newer version of GCC.
You may be getting stuck in dependency confusion between the two versions.
You should be able to build and install Python 2.7 without disturbing the
system's Python 2.4.3.
-Kirk
On Fri, Jun 10, 2011 at 12:00 PM, JP <jeanpaul.ebe...@inhibox.com> wrote:
> I am installing the brand new RDKit (2011_03_2) on CentOS (lol!) on a
> Friday evening (6.54pm here in Oxford)... So I probably deserve the misery
> of the following.
>
> I have already gone through the whole RDKit on Centos installation
> procedure and pain on other machines and I now am undaunted by it. Bring it
> on.
> Still I installed everything (almost) according to the book (
> http://code.google.com/p/rdkit/wiki/BuildingOnCentOS) with the exception
> that I stuck to Python 2.4.3 (Python 2.7, doesn't play nicely with Rocks)
>
> And I get this anti-fancy error message
>
> >>> from rdkit import Chem
> Traceback (most recent call last):
> File "<stdin>", line 1, in ?
> File "/share/apps/RDKit_2011_03_2/rdkit/Chem/__init__.py", line 18, in ?
> from rdkit import rdBase
> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
> (required by /share/apps/RDKit_2011_03_2/rdkit/rdBase.so)
>
> Any ideas?
>
> [jp@xxx build]$ echo $LD_LIBRARY_PATH
>
> /share/apps/RDKit_2011_03_2/lib:/share/apps/boost_1_46_1/lib:/opt/gridengine/lib/lx26-amd64:/share/apps/openbabel/lib:/usr/local/lib:/share/apps/openbabel/lib:
>
> [jp@xxx build]$ echo $PYTHONPATH
> :/share/apps/RDKit_2011_03_2
>
> [jp@xxx build]$ echo $RDBASE
> /share/apps/RDKit_2011_03_2
>
> Any sympathy will be greatly appreciated.
>
> Cheers
> JP
>
>
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