I am trying to compile a test program by linking statically against
RDKit. I am able to do dynamic linking and the program works fine. But
static linking results in errors (pls see below)
Here is the test program test.cpp:
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/MolWriters.h>
using namespace std;
int main(int argc,char **argv)
{
string fName = argv[1];
RDKit::ROMol *m = RDKit::Mol2FileToMol(fName,true,false);
cout<<m->getNumAtoms()<<endl;
string outfile="out.mol2";
RDKit::SDWriter *writer = new RDKit::SDWriter(outfile);
writer->write(*m);
writer->close();
delete writer;
}
RDBASE=rdkit-Release_2014_09_2 (This is the version I compiled)
Here is what I do to compile with dynamic linking (with success):
g++ -g test.cpp -I${RDBASE}/Code -L/${RDBASE}/lib -lFileParsers
-lRDGeneral -lSmilesParse -lDepictor -lRDGeometryLib -lDataStructs
-lGraphMol
Here is what I do to compile with static linking (with failure)
g++ -g test.cpp -I${RDBASE}/Code \
${RDBASE}/lib/libFileParsers_static.a \
${RDBASE}/lib/libRDGeneral_static.a \
${RDBASE}/lib/libSmilesParse_static.a \
${RDBASE}/lib/libDepictor_static.a \
${RDBASE}/lib/libRDGeometryLib_static.a \
${RDBASE}/lib/libDataStructs_static.a \
${RDBASE}/lib/libGraphMol_static.a
I get errors like this:
${RDBASE}/lib/libGraphMol_static.a(QueryOps.cpp.o): In function
`RDKit::queryAtomBondProduct(RDKit::Atom const*)':
QueryOps.cpp:(.text+0x4e2): undefined reference to
`RDKit::firstThousandPrimes'
${RDBASE}/lib/libGraphMol_static.a(QueryOps.cpp.o): In function
`RDKit::queryAtomAllBondProduct(RDKit::Atom const*)':
QueryOps.cpp:(.text+0x5e4): undefined reference to
`RDKit::firstThousandPrimes'
QueryOps.cpp:(.text+0x6a3): undefined reference to
`RDKit::firstThousandPrimes'
${RDBASE}/lib/libGraphMol_static.a(AddHs.cpp.o): In function
`RDKit::(anonymous namespace)::setHydrogenCoords(RDKit::ROMol*, unsigned
int, unsigned int)':
AddHs.cpp:(.text+0x3291): undefined reference to
`RDGeom::Transform3D::SetRotation(double, RDGeom::Point3D const&)'
AddHs.cpp:(.text+0x32a6): undefined reference to
`operator*(RDGeom::Transform3D const&, RDGeom::Point3D const&)'
AddHs.cpp:(.text+0x34a5): undefined reference to
`RDGeom::Transform3D::SetRotation(double, RDGeom::Point3D const&)'
AddHs.cpp:(.text+0x34ba): undefined reference to
`operator*(RDGeom::Transform3D const&, RDGeom::Point3D const&)'
AddHs.cpp:(.text+0x3b29): undefined reference to
`RDGeom::Transform3D::SetRotation(double, RDGeom::Point3D const&)'
AddHs.cpp:(.text+0x3b3c): undefined reference to
`operator*(RDGeom::Transform3D const&, RDGeom::Point3D const&)'
If I change the order of libraries while statically linking, I get
different errors. A similar issue seems to have been visited previously:
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03832.html
So I was wondering if there exists a recommended order of libraries by
which we should link against RDKit while compiling statically.
Thank you.
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