Re: [Rdkit-discuss] install RDKit on CentOS
Hi Yingfeng, I have not yet built the RDKit with boost 1.54.0. This makes it hard for me to know if the problem is the new version of boost, centos, or something with your configuration. Any chance that you can go back to an older version of boost like 1.51? -greg 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::ctypechar::_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 I tried cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 .. cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 -D Boost_USE_STATIC_LIBS=OFF.. cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 -D Boost_USE_STATIC_LIBS=OFF -D Boost_NO_SYSTEM_PATHS=ON .. Thanks. Yingfeng -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install RDKit on CentOS
Gianluca, I am using CentOS 5.8. But I am just a regular user. So I prefer to install RDkit by building it from source. Thanks. Yingfeng On Mon, Jul 15, 2013 at 5:51 AM, Gianluca Sforna gia...@gmail.com wrote: On Sun, Jul 14, 2013 at 10:57 PM, Yingfeng Wang ywang...@gmail.com wrote: I failed to install RDKit on CentOS. Which version of centos? I have packages for version 6 (64 bit) ready to install with yum in http://giallu.fedorapeople.org/rdkit-2013.03/el6-x86_64/ -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install RDKit on CentOS
Hi Greg, I just tried 1.51, and got same problem. Thanks. Yingfeng On Mon, Jul 15, 2013 at 7:49 AM, Yingfeng Wang ywang...@gmail.com wrote: Greg, I also tried boost 1.49.0, and met same problem. If necessary, I can try 1.51. Yingfeng On Mon, Jul 15, 2013 at 5:02 AM, Greg Landrum greg.land...@gmail.comwrote: Hi Yingfeng, I have not yet built the RDKit with boost 1.54.0. This makes it hard for me to know if the problem is the new version of boost, centos, or something with your configuration. Any chance that you can go back to an older version of boost like 1.51? -greg 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::ctypechar::_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 I tried cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 .. cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 -D Boost_USE_STATIC_LIBS=OFF.. cmake -D BOOST_ROOT=/home/yingfeng/software/boost/boost_1_54_0 -D Boost_USE_STATIC_LIBS=OFF -D Boost_NO_SYSTEM_PATHS=ON .. Thanks. Yingfeng -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install RDKit on CentOS
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::ctypechar::_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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] install RDKit on CentOS
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.comwrote: 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::ctypechar::_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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
