On 25/04/13 23:43, hari jayaram wrote: > Hi > I did a > export RDBASE=/home/hari/RDKit_2012_09_1 > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib > > Then cd into the build directory > Run cmake .. > Then run make > > At around 24% I get the following error ( see below) > > I installed the Ubuntu blessed libboost-python1.49-dev > > Any ideas how to get around this. On a related noted the Ubuntu > synaptic package repository did have a rdkit library but it does not > work and complains > > >>> from rdkit import Chem > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/usr/local/lib/python2.7/dist-packages/rdkit/Chem/__init__.py", > line 18, in <module> > from rdkit import rdBase > ImportError: cannot import name rdBase
Hmm... AFAIR, synaptic packages should not use files in /usr/local. Do you still get the same problem if you have not defined PYTHONPATH, PYTHONHOME or LD_LIBRARY_PATH? > > > > Linking CXX static library libCatalogs_static.a > [ 24%] Built target Catalogs_static > Scanning dependencies of target GraphMol > [ 25%] Building CXX object > Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o > [ 25%] Building CXX object > Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o > In file included from > /usr/local/include/boost/thread/detail/platform.hpp:17:0, > from /usr/local/include/boost/thread/mutex.hpp:12, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11: > /usr/local/include/boost/config/requires_threads.hpp:29:4: error: > #error "Threading support unavaliable: it has been explicitly disabled > with BOOST_DISABLE_THREADS" > In file included from /usr/local/include/boost/thread/mutex.hpp:12:0, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11: > /usr/local/include/boost/thread/detail/platform.hpp:67:9: error: > #error "Sorry, no boost threads are available for this platform." > In file included from > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20:0, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11: > /usr/local/include/boost/thread/mutex.hpp:18:2: error: #error "Boost > threads unavailable on this platform" > In file included from > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15:0, > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11: > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:313:5: error: > ‘mutex’ in namespace ‘boost’ does not name a type > make[2]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o] > Error 1 > make[1]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/all] Error 2 > make: *** [all] Error 2 > > There are 2 issues here: 1) "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS" (Someone at Boost Central can't spell :-) I doubt that compiling Boost without threads was a good idea. 2) and as this the above is unusual, this error: "/home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:313:5: error: ‘mutex’ in namespace ‘boost’ does not name a type" was not trapped before. Ideally QueryOps (or anything else) should not use boost mutex if threads have been disabled (this might be a pain to code up). HTH, Paul. ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
