Just to give this closure on the list -- the problem was that I had static
libraries for boost (.a files). Once I rebuilt boost as shared libraries
(.so) everything worked fine.
Thanks to Greg and Paolo for their help.
On 21 June 2017 at 11:02, Greg Landrum <greg.land...@gmail.com> wrote:
> Let's move this off the list for a bit until we get it resolved.
>
> Can you please do: "VERBOSE=1 make testReaction" and send the output just
> to me?
>
> Thanks,
> -greg
>
>
> On Wed, Jun 21, 2017 at 10:24 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
>> Looks like it is finding the correct version of boost (and it is finding
>> boost serialize).
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D
>> RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D
>> Boost_NO_SYSTEM_PATHS=ON ..
>> -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY
>> INCHI_INCLUDE_DIR)
>> CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API
>> -- Found InChI software locally
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> -- python
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> -- thread
>> -- system
>> -- chrono
>> -- date_time
>> -- atomic
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> -- serialization
>> == Using strict rotor definition
>> == Updating Filters.cpp from pains file
>> == Done updating pains files
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> -- regex
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_
>> 03_2/build
>>
>> But the error prevails.
>>
>> If I set up rdkit to use just the system wide boost (1.58), not my
>> specific install (1.61), rdkit builds successfully. I do this by clearing
>> BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags.
>> So this is certainly an issue with wrong libraries being picked up.
>>
>>
>>
>>
>> On 21 June 2017 at 07:29, Greg Landrum <greg.land...@gmail.com> wrote:
>>
>>> 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_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
>>>>
>>>> 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_iarchive>::load_override(boost::a
>>>>>> rchive::class_name_type&)'
>>>>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>>>>>> reference to `boost::archive::archive_excep
>>>>>> tion::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.
>>>>>>>
>>>>>>> ------------------------------------------------------------
>>>>>>> ------------------
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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