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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