Install issue OS X 10.10.5

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Ken Yocum

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Sep 30, 2015, 3:54:20 PM9/30/15
to bob-devel
After installing prerequisites using brew, 

pip install bob

Final error:
  ImportError: dlopen(/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/_logging.so, 2): Symbol not found: __ZN3bob4core16AutoOutputDeviceC1ERKSs
      Referenced from: /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/_logging.so
      Expected in: dynamic lookup


Any ideas?


Ken



Full output:

Collecting bob
  Using cached bob-2.0.5.zip
Requirement already satisfied (use --upgrade to upgrade): setuptools in /Users/kyocum/anaconda/envs/faceivector/lib/python2.7/site-packages (from bob)
Collecting bob.extension==2.0.8 (from bob)
  Downloading bob.extension-2.0.8.zip (142kB)
    100% |████████████████████████████████| 143kB 946kB/s
Collecting bob.blitz==2.0.7 (from bob)
Collecting bob.core==2.0.4 (from bob)
Collecting bob.io.base==2.0.6 (from bob)
  Using cached bob.io.base-2.0.6.zip
    Complete output from command python setup.py egg_info:

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/temp/easy_install-OIE0AV/bob.blitz-2.0.7/.eggs/bob.extension-2.0.8-py2.7.egg

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/.eggs/bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg
    Searching for bob.extension
    Best match: bob.extension 2.0.8
    Processing bob.extension-2.0.8.zip
    Writing /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/temp/easy_install-7C88jM/bob.extension-2.0.8/setup.cfg
    Running bob.extension-2.0.8/setup.py -q bdist_egg --dist-dir /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/temp/easy_install-7C88jM/bob.extension-2.0.8/egg-dist-tmp-3W6fvM
    creating /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/.eggs/bob.extension-2.0.8-py2.7.egg
    Extracting bob.extension-2.0.8-py2.7.egg to /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/.eggs

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/.eggs/bob.extension-2.0.8-py2.7.egg
    Re-run cmake no build system arguments
    -- The C compiler identification is AppleClang 7.0.0.7000072
    -- The CXX compiler identification is AppleClang 7.0.0.7000072
    -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
    -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
    -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core
    /usr/local/Cellar/cmake/3.3.2/bin/cmake -H/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core -B/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core --check-build-system CMakeFiles/Makefile.cmake 0
    /usr/local/Cellar/cmake/3.3.2/bin/cmake -E cmake_progress_start /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/progress.marks
    /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all
    /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/bob_core.dir/build.make CMakeFiles/bob_core.dir/depend
    cd /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core && /usr/local/Cellar/cmake/3.3.2/bin/cmake -E cmake_depends "Unix Makefiles" /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/bob_core.dir/DependInfo.cmake --color=
    Dependee "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/bob_core.dir/DependInfo.cmake" is newer than depender "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/bob_core.dir/depend.internal".
    Dependee "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles/bob_core.dir/depend.internal".
    Scanning dependencies of target bob_core
    /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/bob_core.dir/build.make CMakeFiles/bob_core.dir/build
    [ 50%] Building CXX object CMakeFiles/bob_core.dir/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/bob/core/cpp/logging.cpp.o
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++   -DBLITZ_VERSION=\"0.10\" -DHAVE_BLITZ=1 -DNO_IMPORT_ARRAY=1 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -DPY_ARRAY_UNIQUE_SYMBOL=BOB_NUMPY_C_API -Dbob_core_EXPORTS -std=c++0x -pedantic -Wall -pthread -Qunused-arguments -m64 -O3 -g0 -DNDEBUG -mtune=generic  -fPIC -I/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/bob/core/include -I/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/.eggs/bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg/bob/blitz/include -isystem /Users/kyocum/anaconda/envs/faceivector/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -isystem /usr/local/Cellar/blitz/0.10/include    -o CMakeFiles/bob_core.dir/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/bob/core/cpp/logging.cpp.o -c /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/bob/core/cpp/logging.cpp
    [100%] Linking CXX shared library /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/lib.macosx-10.5-x86_64-2.7/bob/core/libbob_core.dylib
    /usr/local/Cellar/cmake/3.3.2/bin/cmake -E cmake_link_script CMakeFiles/bob_core.dir/link.txt --verbose=1
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++  -std=c++0x -pedantic -Wall -pthread -Qunused-arguments -m64 -O3 -g0 -DNDEBUG -mtune=generic  -dynamiclib -Wl,-headerpad_max_install_names  -o /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/lib.macosx-10.5-x86_64-2.7/bob/core/libbob_core.dylib -install_name @rpath/libbob_core.dylib CMakeFiles/bob_core.dir/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/bob/core/cpp/logging.cpp.o  -L/usr/local/Cellar/blitz/0.10/lib -lboost_system-mt -lboost_iostreams-mt -lboost_filesystem-mt -lblitz -Wl,-rpath,/usr/local/Cellar/blitz/0.10/lib
    [100%] Built target bob_core
    /usr/local/Cellar/cmake/3.3.2/bin/cmake -E cmake_progress_start /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-1NaxMC/bob.core-2.0.4/build/build_cmake/bob_core/CMakeFiles 0
    zip_safe flag not set; analyzing archive contents...
    bob.core.__init__: module references __file__

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg
    Searching for bob.blitz
    Best match: bob.blitz 2.0.7
    Processing bob.blitz-2.0.7.zip
    Writing /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-ab0Ls3/bob.blitz-2.0.7/setup.cfg
    Running bob.blitz-2.0.7/setup.py -q bdist_egg --dist-dir /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-ab0Ls3/bob.blitz-2.0.7/egg-dist-tmp-JkglK1

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-ab0Ls3/bob.blitz-2.0.7/.eggs/bob.extension-2.0.8-py2.7.egg
    creating /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg
    Extracting bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg to /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg
    Searching for bob.extension
    Best match: bob.extension 2.0.8
    Processing bob.extension-2.0.8.zip
    Writing /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-yFY6_G/bob.extension-2.0.8/setup.cfg
    Running bob.extension-2.0.8/setup.py -q bdist_egg --dist-dir /var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/easy_install-yFY6_G/bob.extension-2.0.8/egg-dist-tmp-spRnWB
    creating /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.extension-2.0.8-py2.7.egg
    Extracting bob.extension-2.0.8-py2.7.egg to /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs

    Installed /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.extension-2.0.8-py2.7.egg
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/setup.py", line 181, in <module>
        boost_modules = boost_modules,
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.blitz-2.0.7-py2.7-macosx-10.5-x86_64.egg/bob/blitz/extension.py", line 52, in __init__
        BobExtension.__init__(self, *args, **kwargs)
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.extension-2.0.8-py2.7.egg/bob/extension/__init__.py", line 291, in __init__
        bob_includes, bob_libraries, bob_library_dirs = get_bob_libraries(self.bob_packages)
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.extension-2.0.8-py2.7.egg/bob/extension/__init__.py", line 185, in get_bob_libraries
        pkg = importlib.import_module(package)
      File "/Users/kyocum/anaconda/envs/faceivector/lib/python2.7/importlib/__init__.py", line 37, in import_module
        __import__(name)
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/__init__.py", line 6, in <module>
        from . import log
      File "/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/log.py", line 11, in <module>
        from ._logging import reset
    ImportError: dlopen(/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/_logging.so, 2): Symbol not found: __ZN3bob4core16AutoOutputDeviceC1ERKSs
      Referenced from: /private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/_logging.so
      Expected in: dynamic lookup

André Anjos

unread,
Oct 3, 2015, 12:32:42 AM10/3/15
to bob-...@googlegroups.com

On Wed, Sep 30, 2015 at 9:54 PM, Ken Yocum <kyo...@gmail.com> wrote:
  ImportError: dlopen(/private/var/folders/gf/cqllgwgn4wj6ytvnvjdqphd00000gq/T/pip-build-hdbF7j/bob.io.base/.eggs/bob.core-2.0.4-py2.7-macosx-10.5-x86_64.egg/bob/core/_logging.so, 2): Symbol not found: __ZN3bob4core16AutoOutputDeviceC1ERKSs

It is difficult to say as we don't use brew ourselves (btw, the release of Bob 2.x on MacPorts is now eminent).

The symbol resolves to: bob::core::AutoOutputDevice::AutoOutputDevice(std::string const&), which is properly defined at logging.cpp (https://github.com/bioidiap/bob.core/blob/master/bob/core/cpp/logging.cpp).

My guess is that there is something wrong with the linking of this package.

Best, A


--
Dr. André Anjos
Idiap Research Institute
Centre du Parc - rue Marconi 19
CH-1920 Martigny, Suisse
Phone: +41 27 721 7763
Fax: +41 27 721 7712
http://andreanjos.org

mka...@sas.upenn.edu

unread,
Nov 20, 2015, 5:16:53 PM11/20/15
to bob-devel
I've tried it with buildout as well... same error.  Is there another way to install?

 File "/Users/mkapes/.virtualenvs/pyth3/lib/python3.4/site-packages/bob/core/__init__.py", line 6, in <module>

    from . import log

  File "/Users/mkapes/.virtualenvs/pyth3/lib/python3.4/site-packages/bob/core/log.py", line 11, in <module>

    from ._logging import reset

ImportError: dlopen(/Users/mkapes/.virtualenvs/pyth3/lib/python3.4/site-packages/bob/core/_logging.so, 2): Symbol not found: __ZN3bob4core16AutoOutputDeviceC1ERKSs

  Referenced from: /Users/mkapes/.virtualenvs/pyth3/lib/python3.4/site-packages/bob/core/_logging.so

  Expected in: flat namespace

 in /Users/mkapes/.virtualenvs/pyth3/lib/python3.4/site-packages/bob/core/_logging.so

bob.buildout.extension: An error occurred when trying to install bob.io.base 2.0.6. Look above this message for any errors that were output by easy_install.

While:

  Installing scripts.

  Getting distribution for 'bob.learn.linear'.

  Getting distribution for 'bob.io.base'.

Error: Couldn't install: bob.io.base 2.0.6


Thanks...
--mk
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