Hi James,
Many thanks for the quick answer. I'm afraid I'm already using the trunk:
brew install -v --HEAD rdkit --with-inchi
(revision 2148)
Regards,
George
On 9 October 2012 21:30, James Swetnam <jswet...@gmail.com> wrote:
> George-
>
> I believe you're running into an issue that was raised on the developer
> list. I submitted a patch for this issue, which has been applied in the
> SVN trunk. If you install from trunk you should be fine.
>
> Best
> James
>
> On Tue, Oct 9, 2012 at 12:52 PM, George Papadatos <gpapada...@gmail.com>wrote:
>
>> HI RDKitters,
>>
>> I get compilation errors when I try to build RDKit on a new Mountain Lion
>> Mac OS machine.
>> I've tried both Eddie's brew formula and manual installation with cmake.
>> I also tried both the beta 2012_09 versions and the 2012_06 one.
>> Apart from the system python, I use the python.org version (2.7.3)
>> I also used brew to build boost from source. I copied the error I get at
>> the bottom of this message.
>>
>> Has anyone had a similar problem? Any ideas for troubleshooting?
>>
>> Many thanks,
>>
>> George
>>
>>
>> Linking CXX shared library ../../lib/libGraphMol.dylib
>> cd /tmp/rdkit-urlC/Code/GraphMol &&
>> /usr/local/Cellar/cmake/2.8.9/bin/cmake -E cmake_link_script
>> CMakeFiles/GraphMol.dir/link.txt --verbose=1
>> /usr/local/Library/ENV/4.3/c++ -shared -compatibility_version 1.0.0
>> -current_version 2012.9.1 -o ../../lib/libGraphMol.2012.09.1pre.dylib
>> -install_name /tmp/rdkit-urlC/lib/libGraphMol.1.dylib
>> CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o
>> CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o
>> CMakeFiles/GraphMol.dir/MolOps.cpp.o
>> CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o
>> CMakeFiles/GraphMol.dir/RWMol.cpp.o
>> CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o
>> CMakeFiles/GraphMol.dir/atomic_data.cpp.o
>> CMakeFiles/GraphMol.dir/QueryOps.cpp.o
>> CMakeFiles/GraphMol.dir/MolPickler.cpp.o
>> CMakeFiles/GraphMol.dir/Canon.cpp.o
>> CMakeFiles/GraphMol.dir/AtomIterators.cpp.o
>> CMakeFiles/GraphMol.dir/BondIterators.cpp.o
>> CMakeFiles/GraphMol.dir/Aromaticity.cpp.o
>> CMakeFiles/GraphMol.dir/Kekulize.cpp.o
>> CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o
>> CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o
>> CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/RankAtoms.cpp.o
>> CMakeFiles/GraphMol.dir/Matrices.cpp.o
>> CMakeFiles/GraphMol.dir/Chirality.cpp.o
>> CMakeFiles/GraphMol.dir/RingInfo.cpp.o
>> CMakeFiles/GraphMol.dir/Conformer.cpp.o
>> -L/System/Library/Frameworks/Python.framework/Versions/2.7/Python
>> ../../lib/libRDGeometryLib.2012.09.1pre.dylib
>> ../../lib/libRDGeneral.2012.09.1pre.dylib
>> ../../lib/libDataStructs.2012.09.1pre.dylib
>> ../../lib/libRDGeneral.2012.09.1pre.dylib
>> Undefined symbols for architecture x86_64:
>> "boost::any RDKit::Dict::toany<boost::shared_array<double>
>> >(boost::shared_array<double>) const", referenced from:
>> void RDKit::Dict::setVal<boost::shared_array<double> >(std::string
>> const&, boost::shared_array<double>&) in Matrices.cpp.o
>> "boost::any RDKit::Dict::toany<boost::shared_array<int>
>> >(boost::shared_array<int>) const", referenced from:
>> void RDKit::Dict::setVal<boost::shared_array<int> >(std::string
>> const&, boost::shared_array<int>&) in Matrices.cpp.o
>> "boost::any RDKit::Dict::toany<std::string>(std::string) const",
>> referenced from:
>> void RDKit::Dict::setVal<std::string>(std::string const&,
>> std::string&) in Chirality.cpp.o
>> "boost::any RDKit::Dict::toany<std::list<int, std::allocator<int> >
>> >(std::list<int, std::allocator<int> >) const", referenced from:
>> void RDKit::Dict::setVal<std::list<int, std::allocator<int> >
>> >(std::string const&, std::list<int, std::allocator<int> >&) in Canon.cpp.o
>> "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 FindRings.cpp.o
>> "boost::any RDKit::Dict::toany<std::vector<std::string,
>> std::allocator<std::string> > >(std::vector<std::string,
>> std::allocator<std::string> >) const", referenced from:
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in Atom.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in FindRings.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in ROMol.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in MolPickler.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in Canon.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in
>> Aromaticity.cpp.o
>> void RDKit::Dict::setVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) in
>> MolDiscriminators.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
>> Chirality.cpp.o
>> "boost::any RDKit::Dict::toany<bool>(bool) const", referenced from:
>> void RDKit::Dict::setVal<bool>(std::string const&, bool&) in
>> Canon.cpp.o
>> void RDKit::Dict::setVal<bool>(std::string const&, bool&) in
>> AddHs.cpp.o
>> void RDKit::Dict::setVal<bool>(std::string const&, bool&) in
>> Chirality.cpp.o
>> "boost::any RDKit::Dict::toany<double>(double) const", referenced from:
>> void RDKit::Dict::setVal<double>(std::string const&, double&) in
>> MolDiscriminators.cpp.o
>> "boost::any RDKit::Dict::toany<int>(int) const", referenced from:
>> void RDKit::Dict::setVal<int>(std::string const&, int&) in
>> MolPickler.cpp.o
>> void RDKit::Dict::setVal<int>(std::string const&, int&) in
>> Aromaticity.cpp.o
>> void RDKit::Dict::setVal<int>(std::string const&, int&) in
>> AddHs.cpp.o
>> void RDKit::Dict::setVal<int>(std::string const&, int&) in
>> Chirality.cpp.o
>> "boost::any RDKit::Dict::toany<unsigned int>(unsigned int) const",
>> referenced from:
>> void RDKit::Dict::setVal<unsigned int>(std::string const&, unsigned
>> int&) in Canon.cpp.o
>> "boost::shared_array<double>
>> RDKit::Dict::fromany<boost::shared_array<double> >(boost::any const&)
>> const", referenced from:
>> void RDKit::Dict::getVal<boost::shared_array<double> >(std::string
>> const&, boost::shared_array<double>&) const in Matrices.cpp.o
>> "std::vector<std::vector<int, std::allocator<int> >,
>> std::allocator<std::vector<int, std::allocator<int> > > >
>> RDKit::Dict::fromany<std::vector<std::vector<int, std::allocator<int> >,
>> std::allocator<std::vector<int, std::allocator<int> > > > >(boost::any
>> const&) const", referenced from:
>> void RDKit::Dict::getVal<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>
>> > > >&) const in FindRings.cpp.o
>> "std::vector<std::string, std::allocator<std::string> >
>> RDKit::Dict::fromany<std::vector<std::string, std::allocator<std::string> >
>> >(boost::any const&) const", referenced from:
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> FindRings.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> ROMol.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> MolPickler.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> Canon.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> Aromaticity.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> MolDiscriminators.cpp.o
>> void RDKit::Dict::getVal<std::vector<std::string,
>> std::allocator<std::string> > >(std::string const&,
>> std::vector<std::string, std::allocator<std::string> >&) const in
>> AddHs.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
>> Chirality.cpp.o
>> "bool RDKit::Dict::fromany<bool>(boost::any const&) const", referenced
>> from:
>> void RDKit::Dict::getVal<bool>(std::string const&, bool&) const in
>> AddHs.cpp.o
>> void RDKit::Dict::getVal<bool>(std::string const&, bool&) const in
>> Chirality.cpp.o
>> "double RDKit::Dict::fromany<double>(boost::any const&) const",
>> referenced from:
>> void RDKit::Dict::getVal<double>(std::string const&, double&) const
>> in MolDiscriminators.cpp.o
>> "int RDKit::Dict::fromany<int>(boost::any const&) const", referenced
>> from:
>> void RDKit::Dict::getVal<int>(std::string const&, int&) const in
>> MolPickler.cpp.o
>> void RDKit::Dict::getVal<int>(std::string const&, int&) const in
>> AddHs.cpp.o
>> void RDKit::Dict::getVal<int>(std::string const&, int&) const in
>> Chirality.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)
>> make[2]: *** [lib/libGraphMol.2012.09.1pre.dylib] Error 1
>> make[1]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/all] Error 2
>> make: *** [all] Error 2
>> Error: Failure while executing: make
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
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