Matthew,
Thanks.
Yingfeng
On Tue, Jul 16, 2013 at 10:11 AM, Matthew Lardy <mla...@gmail.com> wrote:
> Yingfeng,
>
> That's really unfortunate! Hopefully, you can punch through this quickly!
>
> Best,
> Matthew
>
>
> On Tue, Jul 16, 2013 at 5:29 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> Matthew,
>>
>> No. I am just a regular user. The administrator has decided to update the
>> whole system, but I don't know when.
>>
>> Yingfeng
>>
>>
>> On Tue, Jul 16, 2013 at 1:08 AM, Matthew Lardy <mla...@gmail.com> wrote:
>>
>>> 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 <greg.land...@gmail.com>wrote:
>>>
>>>>
>>>> On Mon, Jul 15, 2013 at 7:49 AM, Yingfeng Wang <ywang...@gmail.com>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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>>>>
>>>
>>
>
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