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_
>> 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.
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> 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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