Re: [Rdkit-devel] problem building rdkit
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Re: [Rdkit-devel] problem building rdkit
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From: TJ O'D. <tj...@ac...> - 2018-03-19 02:31:40
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Thanks for the quick reply, Greg. I just did a git pull and it merged in lots of files. I may try a clone to a "fresh" folder and see how that goes. Anyway, here's the output from VERBOSE=1 make FilterCatalog tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 FilterCatalog make[1]: Entering directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles 9 make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all make[2]: Entering directory `/home/tj/RDKit/rdkit/build' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDGeneral.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 64 [ 11%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/DataStructs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 7 [ 22%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 66 [ 33%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 35 36 37 38 [ 77%] Built target GraphMol make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 77%] Built target Subgraphs make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Catalogs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 77%] Built target Catalogs make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 71 [ 88%] Built target SmilesParse make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 88%] Built target SubstructMatch make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: /usr/bin/ld: cannot find -lBoost::serialization collect2: error: ld returned 1 exit status make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make[2]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] Error 2 make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/rule] Error 2 make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' make: *** [FilterCatalog] Error 2 On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> wrote: > Hi TJ, > > Hrm, that's ugly. Just to confirm: Are you building the master branch from > github? > It looks like there's no fundamental problem with master; at least the > travis builds pass: https://travis-ci.org/rdkit/rdkit > > To help track this down, can you please send the results of doing: > VERBOSE=1 make FilterCatalog > > Best, > -greg > > > On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: > >> I'm trying to build rdkit from the latest git source. >> Linux Mint 17 >> >> I get this error >> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >> /usr/bin/ld: cannot find -lBoost::serialization >> collect2: error: ld returned 1 exit status >> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >> make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] >> Error 2 >> make: *** [all] Error 2 >> >> but cmake seemed to find this lib OK >> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >> -- The C compiler identification is GNU 4.8.4 >> -- The CXX compiler identification is GNU 4.8.4 >> .... >> -- Found Threads: TRUE >> -- Boost version: 1.54.0 >> -- Found the following Boost libraries: >> -- thread >> -- system >> -- Boost version: 1.54.0 >> -- Found the following Boost libraries: >> -- serialization >> == Using strict rotor definition >> == Updating Filters.cpp from pains file >> >> Can you help me figure out how to get past this? >> >> Thanks, >> TJ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Rdkit-devel mailing list >> Rdk...@li... >> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >> >> > |
