Hello again,
Success at last! I managed to build rdkit using brew and boost 1.49.
I think the cause of the problem was a strange combination of Mountain
Lion, boost 1.51 and not up-to-date rdkit svn repo in HomeBrew.
So to summarise:
brew update
brew uninstall boost
brew versions boost
cd /usr/local
git checkout e40bc41 /usr/local/Library/Formula/boost.rb #version 1.49.0
cd
brew install boost --build-from-source
brew untap edc/homebrew-rdkit
brew tap edc/homebrew-rdkit
brew uninstall rdkit
brew install --HEAD rdkit
Thanks for all the tips,
George
On 10 October 2012 12:32, George Papadatos <gpapada...@gmail.com> wrote:
> Hi Greg,
>
> I built boost 1.49 from source and tried again. There is now a similar
> error but elsewhere:
>
> 44%] Building CXX object
> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o
> Linking CXX shared library ../../../lib/libSmilesParse.dylib
> ld: warning: path
> '//Library/Frameworks/Python.framework/Versions/2.7/Python' following -L
> not a directory
> Undefined symbols for architecture x86_64:
> "yysmarts_parse(char const*, std::vector<RDKit::RWMol*,
> std::allocator<RDKit::RWMol*> >*, void*)", referenced from:
> RDKit::(anonymous namespace)::smarts_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "yysmiles_parse(char const*, std::vector<RDKit::RWMol*,
> std::allocator<RDKit::RWMol*> >*, std::list<unsigned int,
> std::allocator<unsigned int> >*, void*)", referenced from:
> RDKit::(anonymous namespace)::smiles_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "yysmarts_lex_init(void**)", referenced from:
> RDKit::(anonymous namespace)::smarts_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "yysmiles_lex_init(void**)", referenced from:
> RDKit::(anonymous namespace)::smiles_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "setup_smarts_string(std::string const&, void*)", referenced from:
> RDKit::(anonymous namespace)::smarts_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "setup_smiles_string(std::string const&, void*)", referenced from:
> RDKit::(anonymous namespace)::smiles_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "yysmarts_lex_destroy(void*)", referenced from:
> RDKit::(anonymous namespace)::smarts_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "yysmiles_lex_destroy(void*)", referenced from:
> RDKit::(anonymous namespace)::smiles_parse(std::string const&,
> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >&) in
> SmilesParse.cpp.o
> "_yysmarts_debug", referenced from:
> RDKit::SmartsToMol(std::string, int, bool, std::map<std::string,
> std::string, std::less<std::string>, std::allocator<std::pair<std::string
> const, std::string> > >*) in SmilesParse.cpp.o
> "_yysmiles_debug", referenced from:
> RDKit::SmilesToMol(std::string, int, bool, std::map<std::string,
> std::string, std::less<std::string>, std::allocator<std::pair<std::string
> const, std::string> > >*) in SmilesParse.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/libSmilesParse.2012.09.1beta.dylib] Error 1
> make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all]
> Error 2
> make: *** [all] Error 2
>
>
> On 10 October 2012 02:35, Greg Landrum <greg.land...@gmail.com> wrote:
>
>> Just an FYI, not sure if it's relevant or not: I have not yet done an
>> rdkit build with boost 1.51, so I am not sure that the problem isn't there
>>
>> -greg
>>
>>
>>
>> On Tuesday, October 9, 2012, George Papadatos 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:
>>>
>>>
>
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