Hi Guilherme, it looks like it might be this:
https://github.com/rdkit/rdkit/issues/2013#issuecomment-553563418 This can happen if you are using pre-compiled Boost libraries that were compiled with a different compiler from the one you are using for RDKit. To check if that's the case, compare the symbols for one of those undefined references between your RDKit binary and your Boost library, e.g.: $ nm /path/to/boost/lib/lib/libboost_serialization.so.1.74.0 | grep 'common_oarchive.*text_oarchive.*save.*class_name_type' 0000000000023b10 W _ZN5boost7archive6detail15common_oarchiveINS0_13text_oarchiveEE5vsaveERKNS0_15class_name_typeE $ nm ./Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o | grep 'common_oarchive.*text_oarchive.*save.*class_name_type' 0000000000000000 W _ZN5boost7archive6detail15common_oarchiveINS0_13text_oarchiveEE5vsaveERKNS0_15class_name_typeE They should be identical as in my example above. If they aren't, you might need to define the _GLIBCXX_USE_CXX11_ABI=0 macro as explained in the GitHub comment I linked above. HTH, cheers p. On Wed, Apr 28, 2021 at 6:48 PM Guilherme Duarte Ramos Matos < guilherme.duarteramosma...@stonybrook.edu> wrote: > Dear RDKit community, > > I use the RDKit C++ libraries (version 2019_09_1) in one of my projects > and I have a linking problem that I am having a hard time troubleshooting. > > When I try to compile and link using the CMake command below > > * cmake .. -DRDK_INSTALL_INTREE=OFF \ * > *-DCMAKE_INSTALL_PREFIX=path/to/rdkit-Release_2019_09_1 \ * > *-DBOOST_ROOT= path/to/boost \* > *-DBoost_USE_STATIC_LIBS=OFF \ * > *-DBOOST_LIBRARYDIR=path/to/boost/lib \ * > *-DBoost_NO_SYSTEM_PATHS=ON \ * > *-DEIGEN3_INCLUDE_DIR=/path/to/eigen-3.3.9 \ * > *-DPYTHON_EXECUTABLE=/path/to/python3 \ * > *-DRDK_BUILD_PYTHON_WRAPPERS=OFF* > > > I get the following error message: > > *[ 70%] Linking CXX executable testEnumeration* > *CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o: In function > boost::archive::detail::common_oarchive<boost::archive::text_oarchive>::vsave(boost::archive::class_name_type > const&)': > testEnumerate.cpp:(.text._ZN5boost7archive6detail15common_oarchiveINS0_13text_oarchiveEE5vsaveERKNS0_15class_name_typeE[_ZN5boost7archive6detail15common_oarchiveINS0_13text_oarchiveEE5vsaveERKNS0_15class_name_typeE]+0x32): > undefined reference > toboost::archive::text_oarchive_implboost::archive::text_oarchive::save(std::string > const&)'* > *CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o: In function > boost::archive::detail::iserializer<boost::archive::text_iarchive, > RDKit::EnumerateLibraryBase>::load_object_data(boost::archive::detail::basic_iarchive&, > void*, unsigned int) const': > testEnumerate.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_13text_iarchiveEN5RDKit20EnumerateLibraryBaseEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_13text_iarchiveEN5RDKit20EnumerateLibraryBaseEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x97): > undefined reference > toboost::archive::text_iarchive_implboost::archive::text_iarchive::load(std::string&)'* > *testEnumerate.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_13text_iarchiveEN5RDKit20EnumerateLibraryBaseEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_13text_iarchiveEN5RDKit20EnumerateLibraryBaseEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0xd9): > undefined reference to > boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::string&)' > CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o: In > functionboost::archive::detail::oserializer<boost::archive::text_oarchive, > RDKit::EnumerateLibraryBase>::save_object_data(boost::archive::detail::basic_oarchive&, > void const*) const':* > *testEnumerate.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit20EnumerateLibraryBaseEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit20EnumerateLibraryBaseEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0x56): > undefined reference to > boost::archive::text_oarchive_impl<boost::archive::text_oarchive>::save(std::string > const&)' > testEnumerate.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit20EnumerateLibraryBaseEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit20EnumerateLibraryBaseEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xa1): > undefined reference > toboost::archive::text_oarchive_implboost::archive::text_oarchive::save(std::string > const&)'* > *CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o: In function > boost::archive::detail::oserializer<boost::archive::text_oarchive, > RDKit::EnumerateLibrary>::save_object_data(boost::archive::detail::basic_oarchive&, > void const*) const': > testEnumerate.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit16EnumerateLibraryEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_13text_oarchiveEN5RDKit16EnumerateLibraryEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0x15a): > undefined reference > toboost::archive::text_oarchive_implboost::archive::text_oarchive::save(std::string > const&)'* > *CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o: In function > void > RDKit::EnumerateLibrary::load<boost::archive::text_iarchive>(boost::archive::text_iarchive&, > unsigned int)': > testEnumerate.cpp:(.text._ZN5RDKit16EnumerateLibrary4loadIN5boost7archive13text_iarchiveEEEvRT_j[_ZN5RDKit16EnumerateLibrary4loadIN5boost7archive13text_iarchiveEEEvRT_j]+0x18a): > undefined reference > toboost::archive::text_iarchive_implboost::archive::text_iarchive::load(std::string&)'* > *collect2: error: ld returned 1 exit status* > > > *make[2]: *** [Code/GraphMol/ChemReactions/testEnumeration] Error > 1make[1]: *** > [Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/all] Error > 2make: *** [all] Error 2* > > > As far as I can tell, it is an "*undefined reference to undefined > reference to > `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load(std::string&)'*". > Trying to compile and link RDKit using the cmake flag > -DRDK_USE_BOOST_SERIALIZATION=OFF works, but it is not enough for my > project; undefined references to RDKit::SmartsToMol pop up everywhere in > the linking phase. My Boost version is 1.70.0. > > My question is simple: where do you think I should look at in my Boost or > RDKit installation to track where the problem is? It seems something in > serialization is not properly done. Any advice would be very much > appreciated. > > Thanks so much! > > -- > ***************************************************** > Guilherme Duarte Ramos Matos > Ph.D. in Chemistry, UC Irvine (2018) > Postdoctoral Associate, Rizzo Lab > > ***************************************************** > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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