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 <t...@acm.org> 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/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 <greg.land...@gmail.com>
> 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 <t...@acm.org> 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
>>> 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
