Dear Greg, thanks for your answer. This morning I have freshly compiled the whole package (rdkit + cartridge) and now it works! I can not say what has caused the error in the first place, please excuse me for bothering all of you. Thanks a lot for all your help and this great package! I could literally not do my work without it!
For other Arch Linux users I would like to mention that I have downgraded bison from version 3.0 to 2.7 (bison27 from AUR) and also have downgraded postgresql and postgresql-libs from 9.3.1-3 to 9.2.4-2, since the rdkit cartridge of RDKit_2013_06_1.tgz won't compile against Postgresql 9.3.x because of the removal of the typedef for int4 in Postgresql 9.3.x (http://www.postgresql.org/docs/9.3/static/release-9-3.html). Kind regards, Axel Gesendet: Dienstag, 22. Oktober 2013 um 02:03 Uhr Von: "Greg Landrum" <greg.land...@gmail.com> An: chemis...@gmx.de Cc: "RDKit Discuss" <rdkit-discuss@lists.sourceforge.net> Betreff: Re: [Rdkit-discuss] (no subject) Hi Axel, On Mon, Oct 21, 2013 at 4:58 PM, <chemis...@gmx.de> 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 ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
