Re: [Rdkit-discuss] order of libraries in static linking

[Greg L. <gre...@gm...>]

Hi,

A good place to check for things like this is the link order for the tests
in the RDKit source tree.
For examples, here's the order for the ChemTransforms tests (
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/ChemTransforms/CMakeLists.txt#L14
):

rdkit_test(testChemTransforms testChemTransforms.cpp
LINK_LIBRARIES ChemTransforms FileParsers SmilesParse SubstructMatch
GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS})

-greg

On Fri, Jan 16, 2015 at 7:37 PM, E. Prabhu Raman <
pr...@ou...> wrote:

> 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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