On Aug 17, 2012, at 11:35 AM, Greg Landrum wrote: > Here is, hopefully, the last update on this topic. Apologies for the > verbosity.
I'm trying to build the latests from the new repository. Here's the message I get: [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o Linking CXX executable testDict ld: warning: path '/usr/lib/libpython2.7.dylib' following -L not a directory Undefined symbols for architecture x86_64: "boost::any RDKit::Dict::toany<std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >(std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >) const", referenced from: void RDKit::Dict::setVal<std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >(std::string const&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&) in testDict.cpp.o "std::vector<int, std::allocator<int> > RDKit::Dict::fromany<std::vector<int, std::allocator<int> > >(boost::any const&) const", referenced from: void RDKit::Dict::getVal<std::vector<int, std::allocator<int> > >(std::string const&, std::vector<int, std::allocator<int> >&) const in testDict.cpp.o "boost::any RDKit::Dict::toany<std::vector<int, std::allocator<int> > >(std::vector<int, std::allocator<int> >) const", referenced from: void RDKit::Dict::setVal<std::vector<int, std::allocator<int> > >(std::string const&, std::vector<int, std::allocator<int> >&) in testDict.cpp.o "int RDKit::Dict::fromany<int>(boost::any const&) const", referenced from: void RDKit::Dict::getVal<int>(std::string const&, int&) const in testDict.cpp.o "boost::any RDKit::Dict::toany<int>(int) const", referenced from: void RDKit::Dict::setVal<int>(std::string const&, int&) in testDict.cpp.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) Just in case, I rebuilt Boost to 1.50 , checked out the latest RDKit from 10 minutes, etc. This is deep into the mixture of C++ and OS-specific architecture I can't figure out. If it's of any help, -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is Clang 3.1.0 What gets me is that I was able to build RDKit on this same machine last week. BTW, a "make -k" keeps on going. It looks like the issue might be some subtle difference between gcc and clang. I say this because I see clang warnings which suggest that clang hasn't yet been used to compile RDKit. /Users/dalke/cvses/rdkit-code/Code/RDGeneral/StreamOps.h:50:32: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] for (unsigned int i = 0; i < size / 2; ++i) ~ ^ ~~~~~~~~ /Users/dalke/cvses/rdkit-code/Code/RDGeneral/StreamOps.h:81:12: note: in instantiation of function template specialization 'RDKit::SwapBytes<unsigned char, 1>' requested here return SwapBytes<T, sizeof(T)>(value); ^ /Users/dalke/cvses/rdkit-code/Code/RDGeneral/StreamOps.h:229:11: note: in instantiation of function template specialization 'RDKit::EndianSwapBytes<0, 0, unsigned char>' requested here loc = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(tloc); ^ /Users/dalke/cvses/rdkit-code/Code/DataStructs/SparseIntVect.h:333:7: note: in instantiation of function template specialization 'RDKit::streamRead<unsigned char>' requested here streamRead(ss,tVal); ^ /Users/dalke/cvses/rdkit-code/Code/DataStructs/SparseIntVect.h:317:11: note: in instantiation of function template specialization 'RDKit::SparseIntVect<int>::readVals<unsigned char>' requested here readVals<unsigned char>(ss);break; ^ /Users/dalke/cvses/rdkit-code/Code/DataStructs/SparseIntVect.h:295:7: note: in instantiation of member function 'RDKit::SparseIntVect<int>::initFromText' requested here initFromText(txt.c_str(),txt.length()); ^ /Users/dalke/cvses/rdkit-code/Code/DataStructs/testDatastructs.cpp:918:9: note: in instantiation of member function 'RDKit::SparseIntVect<int>::fromString' requested here iV2.fromString(pkl); ^ /Library/Python/2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API ... ^ 1 warning generated. Currently at 35% in the build process, and slowly advancing. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel