Re: [Rdkit-discuss] (no subject)

[Greg L. <gre...@gm...>]

Hi Axel,

On Mon, Oct 21, 2013 at 4:58 PM, <che...@gm...> wrote:

>
> I am a medicinal chemist and am using RDKit and the Postgresql cartridge
> with much success in a small startup project as the backbone for the
> chemical / biological database and for cheminformatics (Lipinski and such,
> substructure and similarity searches, ...).
>

Welcome. Thanks for letting us know about your use of the RDKit!


> I have just upgraded from RDKit_2013_03_2.tgz to RDKit_2013_06_1.tgz on
> Arch Linux (but using bison 2.7) and as far as I can tell, the upgrade was
> ok, rdkit is working fine in IPython.
> But in postgresql, I now get this error:
>   psql (9.2.4)
>   db=# select cpd_no, mol_to_smiles(mol) as smiles, lab_code from
> chem_cpd, chem_batch
>   where cpd_pk = 150 and cpd_pk = cpd_fk;
>   ERROR:  could not load library "/usr/lib/postgresql/rdkit.so":
> /usr/lib/postgresql/rdkit.so: undefined symbol: palloc
>   db=#
> I have rebuilt the cartridge of the new version, of course.
> Do you have any ideas what might cause this error ?
>

This is a strange one. To diagnose it I am going to need a bit more info.
Please go to the $RDBASE/Code/PgSQL/rdkit directory, remove the file
rdkit.so, and then send the output of these three commands:

  make
  make install
  make installcheck

the first will show which libraries are being linked into the extension
file, the second where the extension file is being copied to, and the third
will confirm that the extension works on its own.

If those commands complete without error, please run this to display which
extensions are connected:

  psql -c "select * from pg_available_extension_versions where name
='rdkit'" chembl_16

replace "chembl_16" with whatever your database name is, based on the above
it looks like it may be "db".

Best,
-greg