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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