conda build of Release_2016_09_2 on Kubuntu 16.10 64bit fails

[apahl]

Hi, the RDkit build of Release_2016_09_2 fails on Kubuntu 16.10 64bit with the following (not very informative) error:

[ 61%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so
[ 61%] Built target rdchem
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
Command failed: /bin/bash -x -e /home/pahl/anaconda3/conda-bld/work/conda_build.sh

The build of boost 1.56.0 by the respective recipe wass successful.

Any ideas?

Kind regards,
Axel

[rvianello]

the recipe runs make with the -j option, resulting in the parallel build of multiple modules, this may have the side effect that when an error occurs the actual diagnostic messages are output a bit before the compilation stops, and you may need to look for them in the preceding logs. Alternatively, you may try removing the -j option from the make command line in the recipes build.sh script.

I experienced some issues on Fedora 25 #37, it would be interesting to know if your problem is similar.

[apahl]

Looking further up in the log I found:

[ 58%] Linking CXX executable testSLNParse
../../../lib/libSLNParse.so.1.2016.09.2: undefined reference to `boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary[abi:cxx11](char const*, char const*) const'
../../../lib/libSLNParse.so.1.2016.09.2: undefined reference to `boost::re_detail::cpp_regex_traits_implementation<char>::transform[abi:cxx11](char const*, char const*) const'
collect2: error: ld returned 1 exit status
Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make:104: recipe for target 'Code/GraphMol/SLNParse/testSLNParse' failed
make[2]: *** [Code/GraphMol/SLNParse/testSLNParse] Error 1
CMakeFiles/Makefile2:7798: recipe for target 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all' failed
make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

[rvianello]

I have no quick ideas about how to solve this one, but if you are not interested in using the SLN parser you may try adding -D RDK_BUILD_SLN_SUPPORT=OFF on the cmake command line and see if the build proceeds to completion.

[apahl]

Hi Riccardo,
thanks a lot. Running a non-parallel build now gives this error, which looks very similar to yours:

In file included from /home/pahl/anaconda3/envs/_build/include/boost/config.hpp:61:0,
                 from /home/pahl/anaconda3/envs/_build/include/boost/cstdint.hpp:36,
                 from /home/pahl/anaconda3/envs/_build/include/boost/multiprecision/cpp_int.hpp:11,
                 from /home/pahl/anaconda3/conda-bld/work/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp:36:
/home/pahl/anaconda3/envs/_build/include/boost/multiprecision/cpp_int.hpp:181:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
/home/pahl/anaconda3/envs/_build/include/boost/multiprecision/cpp_int.hpp:401:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
/home/pahl/anaconda3/envs/_build/include/boost/multiprecision/cpp_int.hpp:548:4: error: right operand of shift expression ‘(1u << 63u)’ is >= than the precision of the left operand [-fpermissive]
    BOOST_STATIC_CONSTANT(limb_type, sign_bit_mask = 1u << (limb_bits - 1));
    ^
Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make:350: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o' failed
make[2]: *** [Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o] Error 1
CMakeFiles/Makefile2:3702: recipe for target 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all' failed
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
Command failed: /bin/bash -x -e /home/pahl/anaconda3/conda-bld/work/conda_build.sh

[apahl]

Closed.
See #37 (comment)