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

[James S. <jsw...@gm...>]

Looks like you're trying to link against a 32-bit shared library?

file -L /path/to/boost/shared/libraries*

Should tell you the architecture of your boost 1.5

On Wed, Aug 22, 2012 at 3:17 AM, Andrew Dalke <da...@da...>wrote:

> 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...
>
>
>
>
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