Hi Yingfeng,
Forgive me if I am jumping in without knowing all that you have tried, but
did you try pulling boost with Yum? I was able to get RDKit, and the Java
wrappers, to cleanly compile on CentOS 6.4 with that flavor of boost.
Matt
On Mon, Jul 15, 2013 at 9:39 PM, Greg Landrum <[email protected]>wrote:
>
> 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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