HI Paul,
Funny you should mention that. I have boost 1.61 (installed manually in
/opt) and system boost I installed via sudo apt-get install
/opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
'Version'
Version: 1.58.0.1ubuntu1
However I pass the BOOST path to cmake via:
cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ ..
(I also have the $BOOST_ROOT env variable set, so I think that is
redundant. Whatever). cmake output clearly shows it is finding/using
boost 1.61
Using make VERBOSE=1 I get:
[ 62%] Linking CXX executable testReaction
cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions &&
/usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
--verbose=1
/usr/bin/c++ -mpopcnt -Wno-deprecated -Wno-unused-function
-fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction -rdynamic
../../../lib/libRDKitChemReactions.so.1.2017.03.2
../../../lib/libRDKitChemTransforms.so.1.2017.03.2
../../../lib/libRDKitDescriptors.so.1.2017.03.2
../../../lib/libRDKitFingerprints.so.1.2017.03.2
../../../lib/libRDKitDepictor.so.1.2017.03.2
../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
../../../lib/libRDKitPartialCharges.so.1.2017.03.2
../../../lib/libRDKitMolTransforms.so.1.2017.03.2
../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
../../../lib/libRDKitSubgraphs.so.1.2017.03.2
../../../lib/libRDKitSmilesParse.so.1.2017.03.2
../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
../../../lib/libRDKitGraphMol.so.1.2017.03.2
../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2
../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
../../../lib/libRDKitCatalogs.so.1.2017.03.2
../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread -lboost_system
-lpthread -Wl,-rpath,/opt/rdkit/rdkit-Release_2017_03_2/build/lib
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load_override(boost::archive::class_name_type&)'
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
const&)'
collect2: error: ld returned 1 exit status
Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
CMakeFiles/Makefile2:4157: recipe for target
'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
Error 2
make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
/opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH.
Thanks for your help and time. I really appreciate it.
Cheers
On 16 June 2017 at 14:12, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 16/06/2017 12:08, JP wrote:
>
>> Hi Folks,
>>
>> Must have been eons ago last time I posted to this mailing list. The
>> italians have a saying "chi non muore si rivede".
>>
>> I am trying to install the RDKit (release 2017_03_2) from source, without
>> conda, and I thought this will be a breeze. But I am getting an error. I
>> am pretty sure this is because of the boost version I am using (1.61).
>>
>> The error is:
>>
>> [ 62%] Linking CXX executable testReaction
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>> reference to
>> `boost::archive::text_iarchive_impl<boost::archive::text_
>> iarchive>::load_override(boost::archive::class_name_type&)'
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>> reference to
>> `boost::archive::archive_exception::archive_exception(boost:
>> :archive::archive_exception
>> const&)'
>> collect2: error: ld returned 1 exit status
>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>> recipe for
>> target 'Code/GraphMol/ChemReactions/testReaction' failed
>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>> CMakeFiles/Makefile2:4157: recipe for target
>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>> make[1]: *** [Code/GraphMol/ChemReactions/C
>> MakeFiles/testReaction.dir/all] Error 2
>> Makefile:160: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>
> If you are using an outdated version of boost, this is not the most
> elegant way for RDKit to tell you so.
>
> But I don't think that that's the case. I think that you are not linking
> with the correct boost libraries. Hard to say at the moment.
>
> $ make VERBOSE=1
>
>>
>> As I side note, but this is just a deprecation warning, I do get a ton of
>> these,
>> /opt/boost_1_61_0/include/boost/type_traits/detail/template_arity_spec.hpp:13:84:
>> note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp)
>> is deprecated
>> # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is
>> deprecated")
>>
>
> I see such things also - I comment out the pragmas in the header.
>
>
> Paul.
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
