Re: [Rdkit-devel] problem building rdkit

[Greg L. <gre...@gm...>]

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/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 <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
>>>>
>>>>
>>>
>>
>