On Mon, Jul 15, 2013 at 7:49 AM, Yingfeng Wang <[email protected]> wrote:
>
> I also tried boost 1.49.0, and met same problem. If necessary, I can try
> 1.51.
>
hmm, ok, so much for that idea. Let's try something else.
> On Sunday, July 14, 2013, Yingfeng Wang wrote:
>>
>>> I failed to install RDKit on CentOS.
>>>
>>> The error message is
>>>
>>> [ 85%] Built target MolChemicalFeatures
>>> Linking CXX executable testSLNParse
>>> [ 85%] Built target rdSLNParse
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to
>>> `std::__detail::_List_node_base::_M_unhook()@GLIBCXX_3.4.15'
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to
>>> `std::overflow_error::~overflow_error()@GLIBCXX_3.4.15'
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to
>>> `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)@GLIBCXX_3.4.15'
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to `std::ctype<char>::_M_widen_init()
>>> const@GLIBCXX_3.4.11'
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to
>>> `std::invalid_argument::~invalid_argument()@GLIBCXX_3.4.15'
>>> /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
>>> undefined reference to
>>> `std::__detail::_List_node_base::_M_transfer(std::__detail::_List_node_base*,
>>> std::__detail::_List_node_base*)@GLIBCXX_3.4.15'
>>> collect2: ld returned 1 exit status
>>> make[2]: *** [Code/GraphMol/SLNParse/testSLNParse] Error 1
>>> make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/all]
>>> Error 2
>>>
>>>
This error is happening during the build of the SLN parser. The easiest
"solution", if you aren't planning on using SLN, is to disable that part of
the build by providing cmake with the argument: -DRDK_BUILD_SLN_SUPPORT=OFF
and then re-running make.
If you want to find the real solution, I need a bit more information. It
looks like there is something strange/wrong about your boost.regex build
(it looks like it could be using a different version of libstdc++), so
we're going to have to track that down. Start with sending the output of
this command:
ldd /home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so
next look in the lib/ directory of wherever you're doing the RDKit build
and send the result of running ldd on one of the .so files in that
directory.
finally, do the following:
VERBOSE=1 make testSLNParse
and send the part of the (very long) output that includes the actual build
command and the error message. This will be towards the bottom of the
output and the build command will look something like this (the paths will
of course be completely different for you):
/usr/bin/c++ -O3 -DNDEBUG -Wl,-search_paths_first
-Wl,-headerpad_max_install_names CMakeFiles/testSLNParse.dir/test.cpp.o
-o testSLNParse -L/usr/local/lib
../../../lib/libSLNParse.2013.06.1beta1.dylib
../../../lib/libSmilesParse.2013.06.1beta1.dylib
../../../lib/libSubstructMatch.2013.06.1beta1.dylib
../../../lib/libGraphMol.2013.06.1beta1.dylib
../../../lib/libRDGeometryLib.2013.06.1beta1.dylib
../../../lib/libRDGeneral.2013.06.1beta1.dylib
/usr/local/lib/libboost_regex.dylib
../../../lib/libDataStructs.2013.06.1beta1.dylib
../../../lib/libRDGeneral.2013.06.1beta1.dylib -lpthread
-greg
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