rdkit-devel

[Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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

Re: [Rdkit-devel] problem building rdkit

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

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/
> 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
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

Re: [Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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 <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/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
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>>
>

Re: [Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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/
> 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
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> 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=
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> 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 <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
>>>
>>>
>>
>

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
>>>>
>>>>
>>>
>>
>

Re: [Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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 <gre...@gm...>
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 <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/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 <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
>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [Rdkit-devel] problem building rdkit

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

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 <tj...@ac...> 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 <gre...@gm...>
> 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 <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/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 <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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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 <gre...@gm...>
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 <tj...@ac...> 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 <gre...@gm...>
>> 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 <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/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 <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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [Rdkit-devel] problem building rdkit

[TJ O'D. <tj...@ac...>]

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 <tj...@ac...> 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 <gre...@gm...>
> 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 <tj...@ac...> 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 <gre...@gm...>
>>> 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 <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'
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>>>>>> 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
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>>>>>> 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
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>>>>>> 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
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>>>>>> 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
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>>>>>> Code/GraphMol/CMakeFiles/GraphMol.dir/build
>>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build'
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>>>>>> 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=
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>>>>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build
>>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build'
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>>>>>> 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
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>>>>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make
>>>>>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend
>>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build'
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>>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs
>>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs
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>>>>>> 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=
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>>>>>> 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=
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>>>>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build
>>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build'
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>>>>>> 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 <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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>