[cctbxbb] Boost Import Error
Magnus Andersson
magnus.andersson at scilifelab.se
Wed Jun 4 05:15:04 PDT 2014
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
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20140604/7806dc90/attachment-0001.htm>
More information about the cctbxbb
mailing list