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/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
