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 <[email protected]> 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 <[email protected]> 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 <[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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>>
>
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