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 13:41:43
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I grep'd with a slight mod to your suggestion and got these few lines. There are many others with all lower case boost_thread and boost_serial tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_serialization.so Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_serialization.so //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_thread.so Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_thread.so //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 The case-insensitive search has lines like this and many more: tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general;RDGeometryLib;general;DataStructs;general;RDGeneral;general;RDBoost;general;/usr/lib/x86_64-linux-gnu/ libpython2.7.so ;general;/usr/lib/x86_64-linux-gnu/libboost_python.so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/usr/lib/x86_64-linux-gnu/libboost_system.so;general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64-linux-gnu/libboost_serialization.so; rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory;general;RDGeometryLib;general;RDGeneral;general;GraphMol;general;/usr/lib/x86_64-linux-gnu/ libpython2.7.so ;general;/usr/lib/x86_64-linux-gnu/libboost_python.so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/usr/lib/x86_64-linux-gnu/libboost_system.so;general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64-linux-gnu/libboost_serialization.so; On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> wrote: > Well, I don't see anything obvious there to explain why the serialization > library is being treated differently from the others. > > Could you please look at (and send) the output of; > grep boost_THREAD CMakeCache.txt > grep boost_SERIAL CMakeCache.txt > > Best, > -greg > > > > On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: > >> FYI I cloned https://github.com/rdkit/rdkit.git >> and get the same error >> >> TJ >> >> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >> >>> 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/CM >>> akeFiles/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/RDG >>> eneral.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/D >>> ataStructs.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/RDGe >>> ometryLib.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/Grap >>> hMol.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/CMakeFile >>> s/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/CMake >>> Files/Subgraphs.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 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/Cata >>> logs.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 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/CMakeFi >>> les/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/CMa >>> keFiles/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/CMakeFile >>> s/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/CMake >>> Files/SubstructMatch.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 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/CMake >>> Files/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/C >>> MakeFiles/FilterCatalog.dir/all] Error 2 >>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>> MakeFiles/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/C >>>>> MakeFiles/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 >>>>> >>>>> >>>> >>> >> > |
