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