did you build boost serialize?

On Mon, Jun 19, 2017 at 12:03 PM, JP <jeanpaul.ebe...@inhibox.com> wrote:

> Hi Greg !
>
> Unfortunately that didn't help (I delete everything in my build directory,
> then):
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
> -DBoost_NO_SYSTEM_PATHS=ON ..
>
> and make as usual.
>
> [ 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/CMakeFiles/testReaction.dir/all]
> Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> Perhaps this isn't related to the system vs user-install, boost after all?
>
>
> On 19 June 2017 at 10:38, Greg Landrum <greg.land...@gmail.com> wrote:
>
>> 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-Re
>>> lease_2017_03_2/build/lib
>>> ../../../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
>>> 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/C
>>> MakeFiles/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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>>>
>>
>
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