[Rdkit-devel] "symbol(s) not found" on Mac OS X 10.7.3

[Andrew D. <da...@da...>]

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...@da...