Hi George,
I'm not familiar with Mac, but I noticed those two lines in your output:
-- Found PythonLibs:
> //Library/Frameworks/Python.framework/Versions/2.7/Python (found version
> "2.7.3")
> -- Found PythonInterp:
> /Library/Frameworks/Python.framework/Versions/2.7/bin/python (found version
> "2.7.3")
And the error occurs when using the 1st one to do the linking.
That '//' at the beginning seem odd to me, I think it should be '/'. Though
in Linux '//' is the same as '/' from what tested.
Maybe someone with a bit more knowledge about Macs can help a bit here.
Regards,
Christos
On Wed, Oct 10, 2012 at 1:03 AM, George Papadatos <gpapada...@gmail.com>wrote:
> Hi James,
>
> You're right. I checked out the true HEAD which is 2234 but it still
> failed!
> This is the make log:
>
> MS-Verdun:build georgep$ cmake -D PYTHON_LIBRARY=/${PYTHON_ROOT}/Python
> -DPYTHON_INCLUDE_DIR=${PYTHON_ROOT}/Headers .. 2>&1 | tee cmake.log
> -- The C compiler identification is GNU 4.2.1
> -- The CXX compiler identification is Clang 4.1.0
> -- Checking whether C compiler has -isysroot
> -- Checking whether C compiler has -isysroot - yes
> -- Checking whether C compiler supports OSX deployment target flag
> -- Checking whether C compiler supports OSX deployment target flag - yes
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- Found PythonLibs:
> //Library/Frameworks/Python.framework/Versions/2.7/Python (found version
> "2.7.3")
> -- Found PythonInterp:
> /Library/Frameworks/Python.framework/Versions/2.7/bin/python (found version
> "2.7.3")
> -- Boost version: 1.51.0
> -- Found the following Boost libraries:
> -- python
> -- Found BISON: /usr/bin/bison
> -- Found FLEX: /usr/bin/flex
> -- Looking for include file pthread.h
> -- Looking for include file pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - found
> -- Found Threads: TRUE
> -- Boost version: 1.51.0
> -- Found the following Boost libraries:
> -- regex
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /Users/georgep/rdkit/rdkit-code/build
>
> *and the error is:*
>
> Linking CXX shared library ../../lib/libGraphMol.dylib
> ld: warning: path
> '//Library/Frameworks/Python.framework/Versions/2.7/Python' following -L
> not a directory
> Undefined symbols for architecture x86_64:
> "boost::system::system_category()", referenced from:
> __GLOBAL__I_a in QueryAtom.cpp.o
> __GLOBAL__I_a in QueryBond.cpp.o
> __GLOBAL__I_a in ROMol.cpp.o
> __GLOBAL__I_a in QueryOps.cpp.o
> boost::mutex::mutex() in MolPickler.cpp.o
> __GLOBAL__I_a in MolPickler.cpp.o
> __GLOBAL__I_a in AtomIterators.cpp.o
> ...
> "boost::system::generic_category()", referenced from:
> __GLOBAL__I_a in QueryAtom.cpp.o
> __GLOBAL__I_a in QueryBond.cpp.o
> __GLOBAL__I_a in ROMol.cpp.o
> __GLOBAL__I_a in QueryOps.cpp.o
> __GLOBAL__I_a in MolPickler.cpp.o
> __GLOBAL__I_a in AtomIterators.cpp.o
> __GLOBAL__I_a in AddHs.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.2012.09.1beta.dylib] Error 1
> make[1]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/all] Error 2
> make: *** [all] Error 2
>
> Any more ideas?
>
> Regards,
>
> George
>
>
>
>
> On 9 October 2012 22:33, James Swetnam <jswet...@gmail.com> wrote:
>
>> 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>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> 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
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Don't let slow site performance ruin your business. Deploy New Relic
>>>>> APM
>>>>> Deploy New Relic app performance management and know exactly
>>>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>>>> http://p.sf.net/sfu/newrelic-dev2dev
>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>>
>>>>
>>>
>>
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Christos Kannas
Researcher
Ph.D Student
e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/>
kannas.chris...@ucy.ac.cy
kannas.chris...@cs.ucy.ac.cy
chriskan...@gmail.com
Mob: (+357) 99530608
------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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