George-
My templating fix was submitted as 2155, and HEAD in SVN is at 2234.
I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD
James
On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos <gpapada...@gmail.com
<mailto:gpapada...@gmail.com>> wrote:
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
<mailto: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 <mailto: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
<http://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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