(Moving to devel mailing list)
You see the lines starting with gcc-4.2 and g++-4.2. Type these in
manually (copy+paste) and verify that you get the same error messages.
You may have to change to a particular directory first.
Then, in each line remove "-arch i386 -arch ppc" and see if they
compile without errors. As before, email any error messages here.
- Noel
On 13 October 2011 16:18, Chris Mayne <cgma...@gmail.com> wrote:
> oh yes, that's silly.
>
> $ VERBOSE=1 make _openbabel >& tmp.txt
> $ cat tmp.txt
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake"
> -H/Users/cmayne/openbabel/src/openbabel
> -B/Users/cmayne/openbabel/build/openbabel --check-build-system
> CMakeFiles/Makefile.cmake 0
> make -f CMakeFiles/Makefile2 _openbabel
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake"
> -H/Users/cmayne/openbabel/src/openbabel
> -B/Users/cmayne/openbabel/build/openbabel --check-build-system
> CMakeFiles/Makefile.cmake 0
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake" -E cmake_progress_start
> /Users/cmayne/openbabel/build/openbabel/CMakeFiles 21
> make -f CMakeFiles/Makefile2 scripts/CMakeFiles/_openbabel.dir/all
> make -f src/CMakeFiles/openbabel.dir/build.make
> src/CMakeFiles/openbabel.dir/depend
> cd /Users/cmayne/openbabel/build/openbabel && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E cmake_depends "Unix Makefiles"
> /Users/cmayne/openbabel/src/openbabel
> /Users/cmayne/openbabel/src/openbabel/src
> /Users/cmayne/openbabel/build/openbabel
> /Users/cmayne/openbabel/build/openbabel/src
> /Users/cmayne/openbabel/build/openbabel/src/CMakeFiles/openbabel.dir/DependInfo.cmake
> --color=
> make -f src/CMakeFiles/openbabel.dir/build.make
> src/CMakeFiles/openbabel.dir/build
> make[3]: Nothing to be done for `src/CMakeFiles/openbabel.dir/build'.
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake" -E cmake_progress_report
> /Users/cmayne/openbabel/build/openbabel/CMakeFiles 41 42 43 44 45 46 47 48
> 49 50 51 52 53 54 55 56 57 58 59 60 61
> [100%] Built target openbabel
> make -f scripts/CMakeFiles/_openbabel.dir/build.make
> scripts/CMakeFiles/_openbabel.dir/depend
> cd /Users/cmayne/openbabel/build/openbabel && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E cmake_depends "Unix Makefiles"
> /Users/cmayne/openbabel/src/openbabel
> /Users/cmayne/openbabel/src/openbabel/scripts
> /Users/cmayne/openbabel/build/openbabel
> /Users/cmayne/openbabel/build/openbabel/scripts
> /Users/cmayne/openbabel/build/openbabel/scripts/CMakeFiles/_openbabel.dir/DependInfo.cmake
> --color=
> make -f scripts/CMakeFiles/_openbabel.dir/build.make
> scripts/CMakeFiles/_openbabel.dir/build
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake" -E cmake_progress_report
> /Users/cmayne/openbabel/build/openbabel/CMakeFiles
> [100%] Generating
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp,
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && /usr/local/bin/swig
> -python -c++ -small -O -templatereduce -naturalvar
> -I/Users/cmayne/openbabel/src/openbabel/include
> -I/Users/cmayne/openbabel/build/openbabel/include -o
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp
> -outdir /Users/cmayne/openbabel/src/openbabel/scripts/python
> /Users/cmayne/openbabel/src/openbabel/scripts/openbabel-python.i
> /Users/cmayne/openbabel/src/openbabel/include/openbabel/isomorphism.h:159:
> Warning 325: Nested class not currently supported (Functor ignored)
> cd /Users/cmayne/openbabel/build/openbabel/scripts && /usr/bin/python2.6
> /Users/cmayne/openbabel/src/openbabel/scripts/python/setup.py build
> --build-lib=/Users/cmayne/openbabel/build/openbabel/scripts/pybuild
> running build
> running build_py
> copying openbabel.py ->
> /Users/cmayne/openbabel/build/openbabel/scripts/pybuild
> copying pybel.py -> /Users/cmayne/openbabel/build/openbabel/scripts/pybuild
> running build_ext
> building '_openbabel' extension
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os
> -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64
> -pipe -I/Users/cmayne/openbabel/src/openbabel/scripts/python/../../include
> -I../include
> -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
> -c /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp
> -o
> build/temp.macosx-10.6-universal-2.6/Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.o
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid for
> C/ObjC but not for C++
> In file included from
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3344:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryAtom::Matches(const
> OpenBabel::OBAtom*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:101:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryBond::Matches(const
> OpenBabel::OBBond*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:179:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = unsigned int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid for
> C/ObjC but not for C++
> In file included from
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3344:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryAtom::Matches(const
> OpenBabel::OBAtom*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:101:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryBond::Matches(const
> OpenBabel::OBBond*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:179:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = unsigned int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid for
> C/ObjC but not for C++
> In file included from
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3344:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryAtom::Matches(const
> OpenBabel::OBAtom*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:101:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryBond::Matches(const
> OpenBabel::OBBond*) const’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/../../include/openbabel/query.h:179:
> warning: comparison between signed and unsigned integer expressions
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = unsigned int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:
> In static member function ‘static Type swig::traits_as<Type,
> swig::value_category>::as(PyObject*, bool) [with Type = int]’:
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.cpp:3898:
> warning: ‘v’ may be used uninitialized in this function
> g++-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -arch i386 -arch ppc -arch
> x86_64
> build/temp.macosx-10.6-universal-2.6/Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel-python.o
> -L/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib
> -L/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64 -L../lib
> -lopenbabel -o
> /Users/cmayne/openbabel/build/openbabel/scripts/pybuild/_openbabel.so
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib' following
> -L not found
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64' following
> -L not found
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib' following
> -L not found
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64' following
> -L not found
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (ppc)
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib' following
> -L not found
> ld: warning: directory
> '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64' following
> -L not found
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo "import sys" > ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo "if sys.platform.find('linux') != -1:"
>>> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo " try:" >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo " import dl" >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo " except ImportError:" >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo " import DLFCN as dl" >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E echo "
> sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && cat
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel.py >> ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E copy ob.py
> /Users/cmayne/openbabel/src/openbabel/scripts/python/openbabel.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && "/Applications/CMake
> 2.8-5.app/Contents/bin/cmake" -E remove ob.py
> cd /Users/cmayne/openbabel/build/openbabel/scripts && install_name_tool
> -change /Users/cmayne/openbabel/build/openbabel/lib/libopenbabel.4.dylib
> /usr/local/bin/lib/libopenbabel.4.dylib
> /Users/cmayne/openbabel/build/openbabel/scripts/pybuild/_openbabel.so
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake" -E cmake_progress_report
> /Users/cmayne/openbabel/build/openbabel/CMakeFiles
> [100%] Built target _openbabel
> "/Applications/CMake 2.8-5.app/Contents/bin/cmake" -E cmake_progress_start
> /Users/cmayne/openbabel/build/openbabel/CMakeFiles 0
>
> On Thu, Oct 13, 2011 at 10:03 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> That should be "make[SPACE]_openbabel" :-)
>>
>> On 13 October 2011 15:31, Chris Mayne <cgma...@gmail.com> wrote:
>> > Thanks for not giving up on me!
>> > I figured out the version problem -- it was installing into
>> > /usr/local/bin/bin instead of /usr/local/bin
>> >
>> > The requested information:
>> >
>> > $ touch ../../src/openbabel/scripts/openbabel-python.i
>> > $ VERBOSE=1 make_openbabel >& tmp.txt
>> > $ cat tmp.txt
>> > -bash: make_openbabel: command not found
>> >
>> > $ grep -i python CMakeCache.txt > tmp2.txt
>> > $ cat tmp2.txt
>> > //Build Python bindings
>> > PYTHON_BINDINGS:BOOL=ON
>> > PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.6
>> >
>> > PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Headers
>> > PYTHON_LIBRARY:FILEPATH=/usr/lib/libpython2.6.dylib
>> > //Details about finding PythonInterp
>> >
>> > FIND_PACKAGE_MESSAGE_DETAILS_PythonInterp:INTERNAL=[/usr/bin/python2.6][v()]
>> > //Details about finding PythonLibs
>> >
>> > FIND_PACKAGE_MESSAGE_DETAILS_PythonLibs:INTERNAL=[/usr/lib/libpython2.6.dylib][/System/Library/Frameworks/Python.framework/Headers][v()]
>> > //ADVANCED property for variable: PYTHON_EXECUTABLE
>> > PYTHON_EXECUTABLE-ADVANCED:INTERNAL=1
>> > //ADVANCED property for variable: PYTHON_INCLUDE_DIR
>> > PYTHON_INCLUDE_DIR-ADVANCED:INTERNAL=1
>> > //Path to where Python.h is found (deprecated)
>> >
>> > PYTHON_INCLUDE_PATH:INTERNAL=/System/Library/Frameworks/Python.framework/Headers
>> > //ADVANCED property for variable: PYTHON_LIBRARY
>> > PYTHON_LIBRARY-ADVANCED:INTERNAL=1
>> >
>> >
>> >
>> >
>> > On Thu, Oct 13, 2011 at 7:34 AM, Noel O'Boyle <baoille...@gmail.com>
>> > wrote:
>> >>
>> >> On 12 October 2011 15:47, Chris Mayne <cgma...@gmail.com> wrote:
>> >> > I cleared everything out and reran cmake with the following flags
>> >> > (i.e.
>> >> > leaving the -DPYTHON_PATH out):
>> >> >
>> >> > $ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/bin ../../src/openbabel
>> >> > -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
>> >> > -DSWIG_EXECUTABLE=/usr/local/bin/swig
>> >> > -DEIGEN2_INCLUDE_DIR=/usr/local/include/eigen2
>> >> > -DEIGEN3_INCLUDE_DIR=/usr/local/include/eigen3
>> >> >
>> >> > the only warning was:
>> >> >
>> >> > CMake Warning:
>> >> > Manually-specified variables were not used by the project:
>> >> >
>> >> > EIGEN2_INCLUDE_DIR
>> >> >
>> >> > I then issued "make" which yielded these warnings:
>> >> >
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib'
>> >> > following
>> >> > -L not found
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64'
>> >> > following
>> >> > -L not found
>> >> > ld: warning: in ../lib/libopenbabel.dylib, file was built for
>> >> > unsupported
>> >> > file format which is not the architecture being linked (i386)
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib'
>> >> > following
>> >> > -L not found
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64'
>> >> > following
>> >> > -L not found
>> >> > ld: warning: in ../lib/libopenbabel.dylib, file was built for
>> >> > unsupported
>> >> > file format which is not the architecture being linked (ppc)
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib'
>> >> > following
>> >> > -L not found
>> >> > ld: warning: directory
>> >> > '/Users/cmayne/openbabel/src/openbabel/scripts/python/../../lib64'
>> >> > following
>> >> > -L not found
>> >> > [100%] Built target _openbabel
>> >> >
>> >> >
>> >> > It would seem that this is where the python problems are coming up.
>> >>
>> >> Ok. Let's get to the bottom of this. Try "touch
>> >> ../../src/openbabel/scripts/openbabel-python.i" and then "VERBOSE=1
>> >> make _openbabel >& tmp.txt". This will give us the command lines that
>> >> are causing the problem. Also, it would be good to know which Python
>> >> are you linking against. Try "grep -i python CMakeCache.txt >
>> >> tmp2.txt".
>> >>
>> >> - Noel
>> >
>> >
>
>
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