I'm glad to hear that the build worked!
On Saturday, January 26, 2013, Taka Seri wrote:
> 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] <javascript:_e({}, 'cvml',
> '[email protected]');>>
>
>> Dear Takayuki,
>>
>> On Sat, Jan 26, 2013 at 5:37 AM, Taka Seri
>> <[email protected]<javascript:_e({}, 'cvml', '[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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