Re: [Rdkit-discuss] Friday evening problem... Centos RDKit -- again

[JP <jea...@in...>]

It seems someone got it to work with python 2.4 on Centos
(at least according to http://code.google.com/p/rdkit/wiki/WorkingBuilds).
 But even this is god knows how many permutations (gcc / boost / mpfr / gmp
/ bison / flex etc) away from mine...

I'd be interested in Greg's take on supported platforms.

What a start to the weekend!


On 10 June 2011 20:04, Robert DeLisle <rkd...@gm...> wrote:

> I can't blame you there.  "One ring to bind them" would be preferred.
>
> Have you searched the RDKit discussion list archives regarding Python
> version compatibility?  I vaguely remember something about older versions of
> Python in general, but I don't know if it applies to this case.
>
>
>
>
>
>
> On Fri, Jun 10, 2011 at 1:00 PM, JP <jea...@in...> wrote:
>
>>
>> Hi there Kirk,
>>
>> Your suggestion was interesting to tinker with -- but it doesn't help my
>> specific case.
>>
>> If I set the environment to work with python 2.7 (and RDKit), I break
>> ROCKs functionality which I need from time to time.
>> I do not want to stay switching between p2.4 and p2.7 in the same
>> session...
>>
>>
>>
>>
>> On 10 June 2011 19:20, Robert DeLisle <rkd...@gm...> wrote:
>>
>>> 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 <jea...@in...>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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>>>>
>>>
>>
>