Hi Thomas, Thanks for reporting this. I’ll provide a fix ASAP.
Cheers, p. > On 16 Jul 2021, at 16:22, Veith, Thomas <thomas.ve...@novartis.com> wrote: > > Hi *, > > When trying to build RDKit for Windows with the MINGW toolchain, the build > dies during linking: > > [ 49%] Building CXX object > Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.obj > [ 49%] Building CXX object > Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.obj > [ 49%] Linking CXX shared library ../../../bin/libRDKitFileParsers.dll > /usr/bin/x86_64-w64-mingw32-ld: > CMakeFiles/FileParsers.dir/objects.a(MolFileWriter.cpp.obj):MolFileWriter.cpp:(.text+0xe3ba): > undefined reference to `RDDepict::compute2DCoords(RDKit::ROMol&, > std::map<int, RDGeom::Point2D, std::less<int>, std::allocator<std::pair<int > const, RDGeom::Point2D> > > const*, bool, bool, unsigned int, unsigned int, > int, bool, bool)' > collect2: error: ld returned 1 exit status > make[2]: *** > [Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make:557: > bin/libRDKitFileParsers.dll] Error 1 > make[1]: *** [CMakeFiles/Makefile2:3249: > Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all] Error 2 > make: *** [Makefile:171: all] Error 2 > > I’m using the following cmake options: > > cmake -DRDK_BUILD_THREADSAFE_SSS=OFF \ > -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_INCHI_SUPPORT=ON \ > -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON > -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \ > -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON > -DRDK_USE_BOOST_STACKTRACE=OFF \ > -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \ > -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win .. > > When looking a bit into it, the symbol is in the obj file: > /src/rdkit-Release_2021_03_3/buildw# nm > Code/GraphMol/Depictor/CMakeFiles/Depictor_static.dir/RDDepictor.cpp.obj | > grep compute2DCo > 00000000000030d0 T > _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb > > The symbol is in the DLL > bin/libRDKitDepictor.dll > 000000006f204470 T > _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb > > The symbol in in the tree in libRDKitDepictor_static.a > nm libRDKitDepictor_static.a | grep compute2DC > 00000000000030d0 T > _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb > > But the symbol is missing in lib/libRDKitDepictor.dll.a > > The build works for linux and osx, so it seems to be specific to windows. > > I tried to compile all releases from 2021 and the bug is there since > 2021_03_1. > > I also tried crosscompile which has the same behavior as the native windows > build (with two different versions of the toolchain for two different Ubuntu > release) so it seems its not related to a specific gcc version/mingw version. > (cross compile cmake was cmake -DCMAKE_CROSSCOMPILING=ON > -DCMAKE_TOOLCHAIN_FILE=../win-x64.cmake > -DMSVC_RUNTIME_DLL=/work/mingw/msvcr110.dll – > DRDK_BUILD_THREADSAFE_SSS=OFF \ > -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_INCHI_SUPPORT=ON \ > -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON > -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \ > -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON > -DRDK_USE_BOOST_STACKTRACE=OFF \ > -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \ > -DBOOST_ROOT=/work/mingw/mingw64 -DRDK_INSTALL_INTREE=OFF > -DCMAKE_INSTALL_PREFIX=/image/rdk/win .. > ) > > I attach a Dockerfile where you can easily reproduce the issue. > > Best, > Thomas > > p.s.: Also there was a minimal patch required to allow compiling of some > explicit template instantiations, pls find attached > > > <fix_template.patch> > <win-x64.cmake> > <Dockerfile> > _______________________________________________ > Rdkit-devel mailing list > Rdkit-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-devel _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
