Hi Thomas,
Thanks for reporting this. I’ll provide a fix ASAP.
Cheers,
p.
> On 16 Jul 2021, at 16:22, Veith, Thomas 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, std::allocator 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
> 30d0 T
> _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
>
> The symbol is in the DLL
> bin/libRDKitDepictor.dll
> 6f204470 T
> _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
>
> The symbol in in the tree in libRDKitDepictor_static.a
> nm libRDKitDepictor_static.a | grep compute2DC
> 30d0 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
>
>
>
>
>
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