Jan,
It is probably the order of the libraries (static linking can introduce
that).
Try moving the depiction lib to the beginning of the libs list
-greg
On Sunday, February 23, 2014, Jan Holst Jensen <[email protected]>
wrote:
> Hi Greg,
>
> I now have a working version of mol_to_ctab() - except when I add in
> depiction generation. There is a linking issue I don't understand.
>
> In adapter.cpp I have added this function that implements the C++ part of
> mol_to_ctab():
>
> extern "C" char *
> makeCtabText(CROMol data, int *len, bool createDepictionIfMissing) {
> ROMol *mol = (ROMol*)data;
>
> try {
> if (createDepictionIfMissing && mol->getNumConformers() == 0) {
> RDDepict::compute2DCoords(*mol);
> }
> StringData = MolToMolBlock(*mol);
> } catch (...) {
> ereport(WARNING,
> (errcode(ERRCODE_WARNING),
> errmsg("makeCtabText: problems converting molecule to
> CTAB")));
> StringData="";
> }
>
> *len = StringData.size();
> return (char*)StringData.c_str();
> }
>
>
> But, postgres then won't start (I preload the 'rdkit' library) and in the
> postgres startup log I see a complaint about unresolved symbols. Those are
> caused by the RDDepict::compute2DCoords() call. If I compile without the
> RDDepict::... line, all is well, and the cartridge loads.
>
> I check the built rdkit.so (with the depiction call):
>
> [jhje@bcfregbuild rdkit]$ nm -D rdkit.so | grep " U "|grep RD
> U
> _ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_
> U _ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd
> U _ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE
> [jhje@bcfregbuild rdkit]$
>
>
> So I do a naive search for those unresolved symbols in rdkit's lib
> directory to see what libs are needed:
>
> [jhje@bcfregbuild lib]$ grep
> _ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DES3_S3_S3_ *.a
> Binary file libDepictor_static.a matches
> Binary file libRDGeometryLib_static.a matches
> [jhje@bcfregbuild lib]$ grep
> _ZN6RDGeom11Transform2D12SetTransformERKNS_7Point2DEd *.a
> Binary file libDepictor_static.a matches
> Binary file libRDGeometryLib_static.a matches
> [jhje@bcfregbuild lib]$ grep
> _ZNK6RDGeom11Transform2D14TransformPointERNS_7Point2DE *.a
> Binary file libDepictor_static.a matches
> Binary file libRDGeometryLib_static.a matches
> [jhje@bcfregbuild lib]$
>
>
> I have added Depictor to the RDKLIBS in the Makefile - RDGeometryLib was
> already there:
>
> RDKLIBS = ${INCHILIBS} [...] -lDataStructs -lRDGeometryLib
> -lRDGeneral *-lDepictor*
>
> So I would have thought that all was well. But I still have these three
> unlinked symbols after adding the Depictor lib and rebuilding. Some
> secondary dependencies ... ? I hope that I can slap my forehead and say
> "DUH" when I am told the reason why...
>
> Cheers
> -- Jan
>
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