Re: [Rdkit-devel] problem building rdkit
Greg- I tried the build using the last release rdkit-Release_2017_09_3.tar.gz and everything compiled fine! So, I'm out of the woods, but don't understand why it failed for the latest git clone. I'm satisfied for now, but if you'd like to pursue this and need any input from me, let me know. Thanks, TJ On Mon, Mar 19, 2018 at 7:21 AM, TJ O'Donnell wrote: > Thanks for your attention to this. > Have a good ACS meeting and enjoy New Orleans! > > On Mon, Mar 19, 2018 at 7:04 AM, Greg Landrum > wrote: > >> hmm, I'm stumped. >> I'm going to have to try to reproduce the problem on a linux box. >> Since I'm traveling this week (at the ACS in New Orleans), this may take >> a while. >> >> -greg >> >> >> On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell wrote: >> >>> 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-l >>> inux-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-gn >>> u/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;RDGeom >>> etryLib;general;DataStructs;general;RDGeneral;general;RDBoos >>> t;general;/usr/lib/x86_64-linux-gnu/libpython2.7.so;gene >>> ral;/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;R >>> DGeometryLib;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 >>> 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 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 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/b
Re: [Rdkit-devel] problem building rdkit
Thanks for your attention to this. Have a good ACS meeting and enjoy New Orleans! On Mon, Mar 19, 2018 at 7:04 AM, Greg Landrum wrote: > hmm, I'm stumped. > I'm going to have to try to reproduce the problem on a linux box. > Since I'm traveling this week (at the ACS in New Orleans), this may take a > while. > > -greg > > > On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell wrote: > >> 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;RDGeom >> etryLib;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 >> 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 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 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 > enera
Re: [Rdkit-devel] problem building rdkit
hmm, I'm stumped. I'm going to have to try to reproduce the problem on a linux box. Since I'm traveling this week (at the ACS in New Orleans), this may take a while. -greg On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell wrote: > 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 > 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 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 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/DataStru
Re: [Rdkit-devel] problem building rdkit
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 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 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 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/Da
Re: [Rdkit-devel] problem building rdkit
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 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 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
Re: [Rdkit-devel] problem building rdkit
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 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/ > 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/Subg
Re: [Rdkit-devel] problem building rdkit
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/Subgr
Re: [Rdkit-devel] problem building rdkit
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 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/ > CMakeFiles/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 > Rdkit-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > > -- 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 Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
