If you have a system boost install that you do not want to use, you should
be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This
will (well, should) disable any usage of the system boost.

-greg


On Mon, Jun 19, 2017 at 9:39 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:

> 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_iar
>>> chive>::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.
>>
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>>
>
>
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