Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
Just to give this closure on the list -- the problem was that I had static libraries for boost (.a files). Once I rebuilt boost as shared libraries (.so) everything worked fine. Thanks to Greg and Paolo for their help. On 21 June 2017 at 11:02, Greg Landrum wrote: > Let's move this off the list for a bit until we get it resolved. > > Can you please do: "VERBOSE=1 make testReaction" and send the output just > to me? > > Thanks, > -greg > > > On Wed, Jun 21, 2017 at 10:24 AM, JP wrote: > >> Looks like it is finding the correct version of boost (and it is finding >> boost serialize). >> >> /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D >> RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D >> Boost_NO_SYSTEM_PATHS=ON .. >> -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY >> INCHI_INCLUDE_DIR) >> CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API >> -- Found InChI software locally >> -- Boost version: 1.61.0 >> -- Found the following Boost libraries: >> -- python >> -- Boost version: 1.61.0 >> -- Found the following Boost libraries: >> -- thread >> -- system >> -- chrono >> -- date_time >> -- atomic >> -- Boost version: 1.61.0 >> -- Found the following Boost libraries: >> -- serialization >> == Using strict rotor definition >> == Updating Filters.cpp from pains file >> == Done updating pains files >> -- Boost version: 1.61.0 >> -- Found the following Boost libraries: >> -- regex >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_ >> 03_2/build >> >> But the error prevails. >> >> If I set up rdkit to use just the system wide boost (1.58), not my >> specific install (1.61), rdkit builds successfully. I do this by clearing >> BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags. >> So this is certainly an issue with wrong libraries being picked up. >> >> >> >> >> On 21 June 2017 at 07:29, Greg Landrum wrote: >> >>> did you build boost serialize? >>> >>> On Mon, Jun 19, 2017 at 12:03 PM, JP >>> wrote: >>> Hi Greg ! Unfortunately that didn't help (I delete everything in my build directory, then): cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ -DBoost_NO_SYSTEM_PATHS=ON .. and make as usual. [ 62%] Linking CXX executable testReaction ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::text_iarchive_impl>>> chive>::load_override(boost::archive::class_name_type&)' ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)' collect2: error: ld returned 1 exit status Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed make[1]: *** [Code/GraphMol/ChemReactions/C MakeFiles/testReaction.dir/all] Error 2 Makefile:160: recipe for target 'all' failed make: *** [all] Error 2 Perhaps this isn't related to the system vs user-install, boost after all? On 19 June 2017 at 10:38, Greg Landrum wrote: > If you have a system boost install that you do not want to use, you > should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake > arguments. > This will (well, should) disable any usage of the system boost. > > -greg > > > On Mon, Jun 19, 2017 at 9:39 AM, JP > wrote: > >> HI Paul, >> >> Funny you should mention that. I have boost 1.61 (installed manually >> in /opt) and system boost I installed via sudo apt-get install >> >> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | >> grep 'Version' >> Version: 1.58.0.1ubuntu1 >> >> However I pass the BOOST path to cmake via: >> >> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ >> .. >> >> (I also have the $BOOST_ROOT env variable set, so I think that is >> redundant. Whatever). cmake output clearly shows it is finding/using >> boost 1.61 >> >> Using make VERBOSE=1 I get: >> >> [ 62%] Linking CXX executable testReaction >> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions >> && /usr/bin/cmake -E cmake_link_script >> CMakeFiles/testReaction.dir/link.txt >> --verbose=1 >> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function >> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG >> CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction >> -rdynamic ../../../lib/libRDKitChemReactions.so.1.201
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
Let's move this off the list for a bit until we get it resolved. Can you please do: "VERBOSE=1 make testReaction" and send the output just to me? Thanks, -greg On Wed, Jun 21, 2017 at 10:24 AM, JP wrote: > Looks like it is finding the correct version of boost (and it is finding > boost serialize). > > /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D > RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D > Boost_NO_SYSTEM_PATHS=ON .. > -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY > INCHI_INCLUDE_DIR) > CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API > -- Found InChI software locally > -- Boost version: 1.61.0 > -- Found the following Boost libraries: > -- python > -- Boost version: 1.61.0 > -- Found the following Boost libraries: > -- thread > -- system > -- chrono > -- date_time > -- atomic > -- Boost version: 1.61.0 > -- Found the following Boost libraries: > -- serialization > == Using strict rotor definition > == Updating Filters.cpp from pains file > == Done updating pains files > -- Boost version: 1.61.0 > -- Found the following Boost libraries: > -- regex > -- Configuring done > -- Generating done > -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_ > 03_2/build > > But the error prevails. > > If I set up rdkit to use just the system wide boost (1.58), not my > specific install (1.61), rdkit builds successfully. I do this by clearing > BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags. > So this is certainly an issue with wrong libraries being picked up. > > > > > On 21 June 2017 at 07:29, Greg Landrum wrote: > >> did you build boost serialize? >> >> On Mon, Jun 19, 2017 at 12:03 PM, JP wrote: >> >>> Hi Greg ! >>> >>> Unfortunately that didn't help (I delete everything in my build >>> directory, then): >>> >>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ >>> -DBoost_NO_SYSTEM_PATHS=ON .. >>> >>> and make as usual. >>> >>> [ 62%] Linking CXX executable testReaction >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >>> to `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)' >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >>> to >>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception >>> const&)' >>> collect2: error: ld returned 1 exit status >>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed >>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >>> CMakeFiles/Makefile2:4157: recipe for target >>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >>> make[1]: *** [Code/GraphMol/ChemReactions/C >>> MakeFiles/testReaction.dir/all] Error 2 >>> Makefile:160: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> >>> Perhaps this isn't related to the system vs user-install, boost after >>> all? >>> >>> >>> On 19 June 2017 at 10:38, Greg Landrum wrote: >>> If you have a system boost install that you do not want to use, you should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This will (well, should) disable any usage of the system boost. -greg On Mon, Jun 19, 2017 at 9:39 AM, JP wrote: > HI Paul, > > Funny you should mention that. I have boost 1.61 (installed manually > in /opt) and system boost I installed via sudo apt-get install > > /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep > 'Version' > Version: 1.58.0.1ubuntu1 > > However I pass the BOOST path to cmake via: > > cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. > > (I also have the $BOOST_ROOT env variable set, so I think that is > redundant. Whatever). cmake output clearly shows it is finding/using > boost 1.61 > > Using make VERBOSE=1 I get: > > [ 62%] Linking CXX executable testReaction > cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions > && /usr/bin/cmake -E cmake_link_script > CMakeFiles/testReaction.dir/link.txt > --verbose=1 > /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function > -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG > CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction > -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2 > ../../../lib/libRDKitChemTransforms.so.1.2017.03.2 > ../../../lib/libRDKitDescriptors.so.1.2017.03.2 > ../../../lib/libRDKitFingerprints.so.1.2017.03.2 > ../../../lib/libRDKitDepictor.so.1.2017.03.2 > ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization > ../../../lib/libRDKitPartialCharges.so.1.2017.03.2 > ../../../lib/libRDKitMolTransforms.so.1.2017.03.2 > ../../../
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
Looks like it is finding the correct version of boost (and it is finding boost serialize). /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D Boost_NO_SYSTEM_PATHS=ON .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API -- Found InChI software locally -- Boost version: 1.61.0 -- Found the following Boost libraries: -- python -- Boost version: 1.61.0 -- Found the following Boost libraries: -- thread -- system -- chrono -- date_time -- atomic -- Boost version: 1.61.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition == Updating Filters.cpp from pains file == Done updating pains files -- Boost version: 1.61.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_ 03_2/build But the error prevails. If I set up rdkit to use just the system wide boost (1.58), not my specific install (1.61), rdkit builds successfully. I do this by clearing BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags. So this is certainly an issue with wrong libraries being picked up. On 21 June 2017 at 07:29, Greg Landrum wrote: > did you build boost serialize? > > On Mon, Jun 19, 2017 at 12:03 PM, JP wrote: > >> Hi Greg ! >> >> Unfortunately that didn't help (I delete everything in my build >> directory, then): >> >> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ >> -DBoost_NO_SYSTEM_PATHS=ON .. >> >> and make as usual. >> >> [ 62%] Linking CXX executable testReaction >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >> to `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)' >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >> to >> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception >> const&)' >> collect2: error: ld returned 1 exit status >> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed >> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >> CMakeFiles/Makefile2:4157: recipe for target >> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] >> Error 2 >> Makefile:160: recipe for target 'all' failed >> make: *** [all] Error 2 >> >> Perhaps this isn't related to the system vs user-install, boost after all? >> >> >> On 19 June 2017 at 10:38, Greg Landrum wrote: >> >>> If you have a system boost install that you do not want to use, you >>> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. >>> This will (well, should) disable any usage of the system boost. >>> >>> -greg >>> >>> >>> On Mon, Jun 19, 2017 at 9:39 AM, JP wrote: >>> HI Paul, Funny you should mention that. I have boost 1.61 (installed manually in /opt) and system boost I installed via sudo apt-get install /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep 'Version' Version: 1.58.0.1ubuntu1 However I pass the BOOST path to cmake via: cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. (I also have the $BOOST_ROOT env variable set, so I think that is redundant. Whatever). cmake output clearly shows it is finding/using boost 1.61 Using make VERBOSE=1 I get: [ 62%] Linking CXX executable testReaction cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2 ../../../lib/libRDKitChemTransforms.so.1.2017.03.2 ../../../lib/libRDKitDescriptors.so.1.2017.03.2 ../../../lib/libRDKitFingerprints.so.1.2017.03.2 ../../../lib/libRDKitDepictor.so.1.2017.03.2 ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2017.03.2 ../../../lib/libRDKitMolTransforms.so.1.2017.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2 ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2 ../../../lib/libRDKitSubgraphs.so.1.2017.03.2 ../../../lib/libRDKitSmilesParse.so.1.2017.03.2 ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2 ../../../lib/libRDKitGraphMol.so.1.2017.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 ../../../lib/libRDKitData
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
did you build boost serialize? On Mon, Jun 19, 2017 at 12:03 PM, JP wrote: > Hi Greg ! > > Unfortunately that didn't help (I delete everything in my build directory, > then): > > cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ > -DBoost_NO_SYSTEM_PATHS=ON .. > > and make as usual. > > [ 62%] Linking CXX executable testReaction > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)' > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::archive_exception::archive_exception( > boost::archive::archive_exception const&)' > collect2: error: ld returned 1 exit status > Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: > recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed > make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 > CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/ > CMakeFiles/testReaction.dir/all' failed > make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] > Error 2 > Makefile:160: recipe for target 'all' failed > make: *** [all] Error 2 > > Perhaps this isn't related to the system vs user-install, boost after all? > > > On 19 June 2017 at 10:38, Greg Landrum wrote: > >> If you have a system boost install that you do not want to use, you >> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. >> This will (well, should) disable any usage of the system boost. >> >> -greg >> >> >> On Mon, Jun 19, 2017 at 9:39 AM, JP wrote: >> >>> HI Paul, >>> >>> Funny you should mention that. I have boost 1.61 (installed manually in >>> /opt) and system boost I installed via sudo apt-get install >>> >>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep >>> 'Version' >>> Version: 1.58.0.1ubuntu1 >>> >>> However I pass the BOOST path to cmake via: >>> >>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. >>> >>> (I also have the $BOOST_ROOT env variable set, so I think that is >>> redundant. Whatever). cmake output clearly shows it is finding/using >>> boost 1.61 >>> >>> Using make VERBOSE=1 I get: >>> >>> [ 62%] Linking CXX executable testReaction >>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions >>> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt >>> --verbose=1 >>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function >>> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG >>> CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction >>> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2 >>> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2 >>> ../../../lib/libRDKitDescriptors.so.1.2017.03.2 >>> ../../../lib/libRDKitFingerprints.so.1.2017.03.2 >>> ../../../lib/libRDKitDepictor.so.1.2017.03.2 >>> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization >>> ../../../lib/libRDKitPartialCharges.so.1.2017.03.2 >>> ../../../lib/libRDKitMolTransforms.so.1.2017.03.2 >>> ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2 >>> ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2 >>> ../../../lib/libRDKitSubgraphs.so.1.2017.03.2 >>> ../../../lib/libRDKitSmilesParse.so.1.2017.03.2 >>> ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2 >>> ../../../lib/libRDKitGraphMol.so.1.2017.03.2 >>> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 >>> ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization >>> ../../../lib/libRDKitCatalogs.so.1.2017.03.2 >>> ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread >>> -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Re >>> lease_2017_03_2/build/lib >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >>> to `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)' >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >>> to >>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception >>> const&)' >>> collect2: error: ld returned 1 exit status >>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed >>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >>> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' >>> CMakeFiles/Makefile2:4157: recipe for target >>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >>> make[1]: *** [Code/GraphMol/ChemReactions/C >>> MakeFiles/testReaction.dir/all] Error 2 >>> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' >>> Makefile:160: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> >>> /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH. >>> >>> Thanks for your help and time. I really appreciate it. >>> >>>
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
Hi Greg ! Unfortunately that didn't help (I delete everything in my build directory, then): cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ -DBoost_NO_SYSTEM_PATHS=ON .. and make as usual. [ 62%] Linking CXX executable testReaction ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)' ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)' collect2: error: ld returned 1 exit status Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] Error 2 Makefile:160: recipe for target 'all' failed make: *** [all] Error 2 Perhaps this isn't related to the system vs user-install, boost after all? On 19 June 2017 at 10:38, Greg Landrum wrote: > If you have a system boost install that you do not want to use, you should > be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This > will (well, should) disable any usage of the system boost. > > -greg > > > On Mon, Jun 19, 2017 at 9:39 AM, JP wrote: > >> HI Paul, >> >> Funny you should mention that. I have boost 1.61 (installed manually in >> /opt) and system boost I installed via sudo apt-get install >> >> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep >> 'Version' >> Version: 1.58.0.1ubuntu1 >> >> However I pass the BOOST path to cmake via: >> >> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. >> >> (I also have the $BOOST_ROOT env variable set, so I think that is >> redundant. Whatever). cmake output clearly shows it is finding/using >> boost 1.61 >> >> Using make VERBOSE=1 I get: >> >> [ 62%] Linking CXX executable testReaction >> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions >> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt >> --verbose=1 >> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function >> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG >> CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction >> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2 >> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2 >> ../../../lib/libRDKitDescriptors.so.1.2017.03.2 >> ../../../lib/libRDKitFingerprints.so.1.2017.03.2 >> ../../../lib/libRDKitDepictor.so.1.2017.03.2 >> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization >> ../../../lib/libRDKitPartialCharges.so.1.2017.03.2 >> ../../../lib/libRDKitMolTransforms.so.1.2017.03.2 >> ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2 >> ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2 >> ../../../lib/libRDKitSubgraphs.so.1.2017.03.2 >> ../../../lib/libRDKitSmilesParse.so.1.2017.03.2 >> ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2 >> ../../../lib/libRDKitGraphMol.so.1.2017.03.2 >> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 >> ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization >> ../../../lib/libRDKitCatalogs.so.1.2017.03.2 >> ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread >> -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Re >> lease_2017_03_2/build/lib >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >> to `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)' >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference >> to >> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception >> const&)' >> collect2: error: ld returned 1 exit status >> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed >> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' >> CMakeFiles/Makefile2:4157: recipe for target >> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] >> Error 2 >> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' >> Makefile:160: recipe for target 'all' failed >> make: *** [all] Error 2 >> >> /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH. >> >> Thanks for your help and time. I really appreciate it. >> >> Cheers >> >> On 16 June 2017 at 14:12, Paul Emsley wrote: >> >>> On 16/06/2017 12:08, JP wrote: >>> Hi Folks, Must have been eons ago last time I posted to this mailing list. The italians have a saying "chi
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
If you have a system boost install that you do not want to use, you should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This will (well, should) disable any usage of the system boost. -greg On Mon, Jun 19, 2017 at 9:39 AM, JP wrote: > HI Paul, > > Funny you should mention that. I have boost 1.61 (installed manually in > /opt) and system boost I installed via sudo apt-get install > > /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep > 'Version' > Version: 1.58.0.1ubuntu1 > > However I pass the BOOST path to cmake via: > > cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. > > (I also have the $BOOST_ROOT env variable set, so I think that is > redundant. Whatever). cmake output clearly shows it is finding/using > boost 1.61 > > Using make VERBOSE=1 I get: > > [ 62%] Linking CXX executable testReaction > cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions > && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt > --verbose=1 > /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function > -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG > CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction -rdynamic > ../../../lib/libRDKitChemReactions.so.1.2017.03.2 ../../../lib/ > libRDKitChemTransforms.so.1.2017.03.2 ../../../lib/ > libRDKitDescriptors.so.1.2017.03.2 > ../../../lib/libRDKitFingerprints.so.1.2017.03.2 > ../../../lib/libRDKitDepictor.so.1.2017.03.2 ../../../lib/ > libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization ../../../lib/ > libRDKitPartialCharges.so.1.2017.03.2 ../../../lib/ > libRDKitMolTransforms.so.1.2017.03.2 ../../../lib/ > libRDKitEigenSolvers.so.1.2017.03.2 ../../../lib/ > libRDKitFilterCatalog.so.1.2017.03.2 ../../../lib/ > libRDKitSubgraphs.so.1.2017.03.2 ../../../lib/ > libRDKitSmilesParse.so.1.2017.03.2 ../../../lib/ > libRDKitSubstructMatch.so.1.2017.03.2 > ../../../lib/libRDKitGraphMol.so.1.2017.03.2 > ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 ../../../lib/ > libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization > ../../../lib/libRDKitCatalogs.so.1.2017.03.2 ../../../lib/ > libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread -lboost_system -lpthread > -Wl,-rpath,/opt/rdkit/rdkit-Release_2017_03_2/build/lib > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)' > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::archive_exception::archive_exception( > boost::archive::archive_exception const&)' > collect2: error: ld returned 1 exit status > Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: > recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed > make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 > make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' > CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/ > CMakeFiles/testReaction.dir/all' failed > make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] > Error 2 > make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' > Makefile:160: recipe for target 'all' failed > make: *** [all] Error 2 > > /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH. > > Thanks for your help and time. I really appreciate it. > > Cheers > > On 16 June 2017 at 14:12, Paul Emsley wrote: > >> On 16/06/2017 12:08, JP wrote: >> >>> Hi Folks, >>> >>> Must have been eons ago last time I posted to this mailing list. The >>> italians have a saying "chi non muore si rivede". >>> >>> I am trying to install the RDKit (release 2017_03_2) from source, >>> without conda, and I thought this will be a breeze. But I am getting an >>> error. I am pretty sure this is because of the boost version I am using >>> (1.61). >>> >>> The error is: >>> >>> [ 62%] Linking CXX executable testReaction >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined >>> reference to >>> `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)' >>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined >>> reference to >>> `boost::archive::archive_exception::archive_exception(boost: >>> :archive::archive_exception >>> const&)' >>> collect2: error: ld returned 1 exit status >>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >>> recipe for >>> target 'Code/GraphMol/ChemReactions/testReaction' failed >>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >>> CMakeFiles/Makefile2:4157: recipe for target >>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >>> make[1]: *** [Code/GraphMol/ChemReactions/C >>> MakeFiles/testReaction.dir/all] Error 2 >>> Makefile:160: recipe for target 'all' failed >>> ma
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
HI Paul, Funny you should mention that. I have boost 1.61 (installed manually in /opt) and system boost I installed via sudo apt-get install /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep 'Version' Version: 1.58.0.1ubuntu1 However I pass the BOOST path to cmake via: cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ .. (I also have the $BOOST_ROOT env variable set, so I think that is redundant. Whatever). cmake output clearly shows it is finding/using boost 1.61 Using make VERBOSE=1 I get: [ 62%] Linking CXX executable testReaction cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2 ../../../lib/libRDKitChemTransforms.so.1.2017.03.2 ../../../lib/libRDKitDescriptors.so.1.2017.03.2 ../../../lib/libRDKitFingerprints.so.1.2017.03.2 ../../../lib/libRDKitDepictor.so.1.2017.03.2 ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2017.03.2 ../../../lib/libRDKitMolTransforms.so.1.2017.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2 ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2 ../../../lib/libRDKitSubgraphs.so.1.2017.03.2 ../../../lib/libRDKitSmilesParse.so.1.2017.03.2 ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2 ../../../lib/libRDKitGraphMol.so.1.2017.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2017.03.2 ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Release_2017_03_2/build/lib ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)' ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)' collect2: error: ld returned 1 exit status Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] Error 2 make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build' Makefile:160: recipe for target 'all' failed make: *** [all] Error 2 /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH. Thanks for your help and time. I really appreciate it. Cheers On 16 June 2017 at 14:12, Paul Emsley wrote: > On 16/06/2017 12:08, JP wrote: > >> Hi Folks, >> >> Must have been eons ago last time I posted to this mailing list. The >> italians have a saying "chi non muore si rivede". >> >> I am trying to install the RDKit (release 2017_03_2) from source, without >> conda, and I thought this will be a breeze. But I am getting an error. I >> am pretty sure this is because of the boost version I am using (1.61). >> >> The error is: >> >> [ 62%] Linking CXX executable testReaction >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined >> reference to >> `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)' >> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined >> reference to >> `boost::archive::archive_exception::archive_exception(boost: >> :archive::archive_exception >> const&)' >> collect2: error: ld returned 1 exit status >> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: >> recipe for >> target 'Code/GraphMol/ChemReactions/testReaction' failed >> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 >> CMakeFiles/Makefile2:4157: recipe for target >> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed >> make[1]: *** [Code/GraphMol/ChemReactions/C >> MakeFiles/testReaction.dir/all] Error 2 >> Makefile:160: recipe for target 'all' failed >> make: *** [all] Error 2 >> > > If you are using an outdated version of boost, this is not the most > elegant way for RDKit to tell you so. > > But I don't think that that's the case. I think that you are not linking > with the correct boost libraries. Hard to say at the moment. > > $ make VERBOSE=1 > >> >> As I side note, but this is just a deprecation warning, I do get a ton of >> these, >> /opt/boost_1_61_0/include/boost/type_traits/detail/template_arit
Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
On 16/06/2017 12:08, JP wrote: Hi Folks, Must have been eons ago last time I posted to this mailing list. The italians have a saying "chi non muore si rivede". I am trying to install the RDKit (release 2017_03_2) from source, without conda, and I thought this will be a breeze. But I am getting an error. I am pretty sure this is because of the boost version I am using (1.61). The error is: [ 62%] Linking CXX executable testReaction ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)' ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)' collect2: error: ld returned 1 exit status Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] Error 2 Makefile:160: recipe for target 'all' failed make: *** [all] Error 2 If you are using an outdated version of boost, this is not the most elegant way for RDKit to tell you so. But I don't think that that's the case. I think that you are not linking with the correct boost libraries. Hard to say at the moment. $ make VERBOSE=1 As I side note, but this is just a deprecation warning, I do get a ton of these, /opt/boost_1_61_0/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") I see such things also - I comment out the pragmas in the header. Paul. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...
Hi Folks, Must have been eons ago last time I posted to this mailing list. The italians have a saying "chi non muore si rivede". I am trying to install the RDKit (release 2017_03_2) from source, without conda, and I thought this will be a breeze. But I am getting an error. I am pretty sure this is because of the boost version I am using (1.61). The error is: [ 62%] Linking CXX executable testReaction > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)' > ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to > `boost::archive::archive_exception::archive_exception( > boost::archive::archive_exception const&)' > collect2: error: ld returned 1 exit status > Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: > recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed > make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1 > CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/ > CMakeFiles/testReaction.dir/all' failed > make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] > Error 2 > Makefile:160: recipe for target 'all' failed > make: *** [all] Error 2 My setup: Ubuntu 16.04.2 (manually installed) boost v1.61 RDKit release - 2017.03.2 But I read somewhere that "Boost 1.61 and the RDKit work together.". https://sourceforge.net/p/rdkit/mailman/message/35124509/ - so my question is, is this combo expected to work or not? As I side note, but this is just a deprecation warning, I do get a ton of these, /opt/boost_1_61_0/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") I know, I know, not the most glamorous of a comeback ... Beers and Cheers, JP -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss