Re: [Rdkit-discuss] Problems with building RDKit on Linux
Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost (by conda) is : /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/include/boost:/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib BTW, one of the system administrators of our cluster is trying to build rdkit from source and he didn't succeed either, he got the following problems: [ 2%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o /netscr/deep/installs/RDKit/rdkit-Release_2015_03_1/Code/RDBoost/python_streambuf.h: In member function 'virtual int boost_adaptbx::python::streambuf::underflow()': /netscr/deep/installs/RDKit/rdkit-Release_2015_03_1/Code/RDBoost/python_streambuf.h:223: error: 'PyBytes_AsStringAndSize' was not declared in this scope make[2]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o] Error 1 make[1]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all] Error 2 make: *** [all] Error 2 Any suggestion ? Raul From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk] Sent: Friday, March 18, 2016 3:11 PM To: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Problems with building RDKit on Linux On 17/03/2016 18:00, Mendez Giraldez, Raul wrote: > Hi everybody, > > I'm trying to build RDKit on Red Hat Enterprise Linux Server release > 5.11 and I get the following problem after trying to import rdkit libraries: > > > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > Anaconda is brought to you by Continuum Analytics. > Please check out: http://continuum.io/thanks and https://anaconda.org > >>> from rdkit import Chem > Traceback (most recent call last): >File "", line 1, in >File > "/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/Chem/__init__.py", > line 18, in > from rdkit import rdBase > ImportError: > /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/../../../libboost_thread.so.1.56.0: > undefined symbol: > _ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep > >>> > > > > There seems to be a problem with the boost libraries. Any suggestion ? Yes, it seems to me that the libraries that you are finding at runtime are not those against which rdkit was linked at compile time. Are you using LD_LIBRARY_PATH? -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problems with building RDKit on Linux
Hi everybody, I'm trying to build RDKit on Red Hat Enterprise Linux Server release 5.11 and I get the following problem after trying to import rdkit libraries: [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org >>> from rdkit import Chem Traceback (most recent call last): File "", line 1, in File "/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/Chem/__init__.py", line 18, in from rdkit import rdBase ImportError: /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/../../../libboost_thread.so.1.56.0: undefined symbol: _ZGVZN5boost16exception_detail27get_static_exception_objectINS0_14bad_exception_EEENS_13exception_ptrEvE2ep >>> There seems to be a problem with the boost libraries. Any suggestion ? Thanks so much in advance, Raul Raul Mendez Giraldez, PhD Dept. Epidemiology UNC School of Public Health Phone: 919-966-4596 137 East Franklin Street, 306G CVS Plaza Building Chapel Hill, NC 27599 - 8050 USA -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problems with building RDKit on Linux
Thanks Paul. I'm letting the system administrator know. Raul From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk] Sent: Friday, March 18, 2016 3:53 PM To: RDKit Discuss Subject: Re: [Rdkit-discuss] Problems with building RDKit on Linux On 18/03/2016 19:23, Mendez Giraldez, Raul wrote: > Yes, I think so Paul. my $LD_LIBRARY_PATH points towards the installed boost > (by conda) is : > > /nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/include/boost:/nas02/home/r/m/rmendez/Work/Software/miniconda/envs/my-rdkit-env/lib > > BTW, one of the system administrators of our cluster is trying to build rdkit > from source and he didn't succeed either, he got the following problems: > > [ 2%] Building CXX object > Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o > /netscr/deep/installs/RDKit/rdkit-Release_2015_03_1/Code/RDBoost/python_streambuf.h: > In member function 'virtual int > boost_adaptbx::python::streambuf::underflow()': > /netscr/deep/installs/RDKit/rdkit-Release_2015_03_1/Code/RDBoost/python_streambuf.h:223: > error: 'PyBytes_AsStringAndSize' was not declared in this scope > make[2]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o] Error 1 > make[1]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all] Error 2 > make: *** [all] Error 2 > PyBytes_AsStringAndSize should be part of basic Python. I am using Python-2.7.11 and it's defined/redefine in Include/bytesobject.h Paul. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
