Dear Greg.
Thank you for your quick reply.
Your advice is helpful for me.
I tried rebuilding the .o files, then all tests were passed !
I'm very grateful to you.
takayuki
2013/1/26 Greg Landrum <[email protected]>
> Dear Takayuki,
>
> On Sat, Jan 26, 2013 at 5:37 AM, Taka Seri <[email protected]> wrote:
> > Dear all.
> >
> > I tried to build the postgresql cartridge.
> > (=>http://code.google.com/p/rdkit/wiki/BuildingTheCartridge)
> > Os X 10.7.5, RDKit ver 2012_12_1, and PostgreSQL ver 9.1.3
> > I could not build the cartridge.
> > I got following error messages.
> >
> >> cd $RDBASE/Code/PgSQL/rdkit
> > Then,
> >> make
> >
> > g++ -I/opt/local/include -02 -Wall -Wmissing-prototypes -Wpointer-arith
> > -Wdeclaration-after-statement -Wendif-labels -Wformat-security
> > -fno-strict-aliasing -fwrapv -bundle -multiply_defined suppress -o
> rdkit.so
> > rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o
> cache.o
> > adapter.o -L/usr/local/pgsql/lib -Wl,-dead_strip_dylibs
> > -L/Users/takayuki/Cheminfo/RDKit/RDKit_2012_12_1//lib
> > -Wl,-rpath,'/Users/takayuki/Cheminfo/RDKit/RDKit_2012_12_1//lib'
> > -lChemTransforms -lFileParsers -lSmilesParse -lFingerprints -lSubgraphs
> > -lSubstructMatch -lDescriptors -lPartialCharges -lGraphMol -lDataStructs
> > -lRDGeometryLib -lRDGeneral -pthread -bundle_loader
> > /usr/local/pgsql/bin/postgres
> > Undefined symbols for architecture x86_64:
> > "_DirectFunctionCall1", referenced from:
> > _bfp_in in rdkit_io.o
> > _bfp_out in rdkit_io.o
> > _sfp_in in rdkit_io.o
> > _sfp_out in rdkit_io.o
> > ld: symbol(s) not found for architecture x86_64
> > collect2: ld returned 1 exit status
> > make: *** [rdkit.so] Error 1
> >
> > Any advice or information you could provide would be greatly appreciated.
>
> I haven't seen this error before, but from what little I could find on
> the web (http://code.google.com/p/plv8js/issues/detail?id=40), it
> seems like this could be caused by using headers from one version of
> postgres and linking against another.
> I would suggest rebuilding the .o files and checking to see that the
> "-I" specs you see when you re-run make actually find the correct
> postgresql header files.
>
> -greg
>
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