This is probably somewhat related... I tried to restart the server and
cannot get postgresql running...
/opt/postgresql-9.1.2/bin/postgres -D /opt/postgresql-9.1.2/data/
FATAL: could not load library "/opt/postgresql-9.1.2/lib/rdkit.so":
/opt/postgresql-9.1.2/lib/rdkit.so: undefined symbol:
pthread_mutexattr_settype
I've been playing with LD_LIBRARY_PATH ... to no avail...
-
Jean-Paul Ebejer
Early Stage Researcher
On 27 April 2012 17:03, Greg Landrum <[email protected]> wrote:
> On Fri, Apr 27, 2012 at 5:11 PM, JP <[email protected]> wrote:
> > Just installed RDKit 2012_03_1 on Debian 6.0.4, squeeze.
> >
> > RDKit works fine. I also built and installed the RDKit extension for
> > postgresql in the following manner:
> >
> > % cd $RDBASE/Code/PgSQL/rdkit
> > % make
> > % sudo make install
> >
> > (I also did create extension rdkit in my database)
> >
> > Which also seemed to work well, until I ran
>
> looks good so far.
>
> >
> > % make installcheck
> >
> > ============== running regression test queries ==============
> > test rdkit-91 ... FAILED
>
> <snip>
> >
> > SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1');
> > ! ERROR: function mol_from_smarts(unknown) does not exist
>
> hmmm
>
> > Which means that I do not have mol_from_smarts, which is a pain because
> that
> > is exactly the reason I installed this version :) (to make use of the
> > indices).
>
> It's definitely in the release. Check line 75 here:
>
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_03_1/Code/PgSQL/rdkit/rdkit.sql91.in?revision=2018&view=markup
>
> I guess that the extension didn't get created correctly somehow.
> Please look at wherever the extension is installed to and make sure
> that mol_from_smarts() is in rdkit--3.1.sql and that the .so you
> installed is in the right place. You might also try restarting the
> postgresql server.
>
>
> > Also, this method and its smiles counterpart is not mentioned
> > in
> http://code.google.com/p/rdkit/wiki/DatabaseCartridgeReferenceDocumentation
>
> that's an oversight... thanks for pointing it out.
>
> -greg
>
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