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_
>> 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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>>
>>
>
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