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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