[cctbxbb] Boost Import Error

[Magnus Andersson]

Hi,
> I think the problem is that it is picking up libboost_python.dylib that was supplied with the system (in /usr/local/lib), and not the one that was used in compilation (in $LIBTBX_BUILD/lib). Could you check that there is a libboost_python.dylib in this directory?

Yes, it's there.

> What happens if you change the search order for the linker (if this was Linux, export DYLIB_LIBRARY_PATH=$LIBTBX_BUILD/lib:$DYLIB_LIBRARY_PATH would work, but on the Mac I do not know).
> 

I assume $LIBTBX_BUILD is /Users/magnus/Downloads/cctbx_build/

in my case,

but what is $DYLIB_LIBRARY_PATH?

> It would probably be easier for you to rebuild the cctbx Python bindings with the Python you want to use, and then all things would work.

I think that's what I'm trying to do. I want to avoid the cctbx wrapper and therefore are launching python from my /opt/local/bin install where I keep all the rest of the modules I need. It is only cctbx that causes trouble. So I try to get "my" python to accept it.

Thanks for you help in this matter - I appreciate it, 

Magnus


> It only takes 10-20 minutes to compile even on a vintage computer.
> 
> BW, Gabor
> 
> On 2014-06-04 13:15, Magnus Andersson wrote:
>> Thanks Luc,
>> I have now updated by PYTHONPATH as you suggested:
>> export
>> PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib
>> , which indeed makes my /opt/local/bin/python2.7 find boost. However,
>> now I get a new error message, which is a little harder to interpret:
>> import iotbx.pdb
>> File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py",
>> line 2, in <module>
>> from cctbx.array_family import flex
>> File
>> "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py",
>> line 2, in <module>
>> import scitbx.array_family.flex
>> File
>> "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py",
>> line 2, in <module>
>> import boost.optional # import dependency
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py",
>> line 2, in <module>
>> import boost.python
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
>> line 57, in <module>
>> ext = import_ext("boost_python_meta_ext")
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
>> line 36, in import_ext
>> + [" "+p for p in sys.path]))
>> ImportError: __import__("boost_python_meta_ext"):
>> dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so,
>> 2): Symbol not found:
>> boost::python::objects::function_object(boost::python::objects::py_function
>> const&, std::__1::pair<boost::python::detail::keyword const*,
>> boost::python::detail::keyword const*> const&)
>> Referenced from:
>> /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
>> Expected in: /usr/local/lib/libboost_python.dylib
>> in /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
>> sys.path:
>> /Users/magnus/Documents/TR-WAXS/magnus_testing/PyWAXS
>> /Users/magnus/.venvburrito/lib/python/distribute-0.6.32-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenv-1.8.4-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenvwrapper-3.6-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/stevedore-0.8-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenv_clone-0.2.4-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python
>> /Users/magnus/Downloads/cctbx_sources
>> /opt/local/bin
>> /Users/magnus/Downloads/cctbx_build/lib
>> /Users/magnus/Downloads/cctbx_sources/boost_adaptbx
>> /Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath
>> /usr/local/lib
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC
>> /Library/Python/2.7/site-packages
>> I don't know how to deal with this - any suggestions?
>> Thanks,
>> Magnus
>> On 03 Jun 2014, at 23:44, Luc Bourhis <luc_j_bourhis at mac.com> wrote:
>>>> Suggestions?
>>> If you want to do it by hand, you need to parrot what cctbx.python
>>> does. You need to set the following environment variables:
>>> 1. LIBTBX_BUILD
>>> that must be the path of cctbx_build next to cctbx_sources or
>>> cctbx_project
>>> 2. PYTHONPATH
>>> at the very least it shall contain
>> $LIBTBX_BUILD/lib:$CCTBXSRC:$CCTBXSRC/boost_adaptbx:$CCTBXSRC/libtbx/pythonpath
>>> where $CCTBXSRC is the full path of cctbx_sources or cctbx_project
>>> 3. DYLD_LIBRARY_PATH
>>> It shall contain $LIBTBX_BUILD/lib
>>> Best wishes,
>>> Luc
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>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
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