Results from trying to build `rank_filter` in `conda` without adding `-stdlib=libc++` to `CXXFLAGS` or `CXX_LDFLAGS`

rank_filter-build.log

$ conda build rank_filter
Removing old build directory
Removing old work directory
BUILD START: rank_filter-v0.1-np19py27_0
Fetching package metadata: ......
Solving package specifications: .
The following NEW packages will be INSTALLED:

    boost:      1.56.0-1           
    fftw:       3.3.4-0            
    hdf5:       1.8.14-0           
    jpeg:       8d-1               
    libpng:     1.5.13-1           
    libtiff:    4.0.2-1            
    nose:       1.3.6-py27_0       
    numpy:      1.9.2-py27_0       
    openssl:    1.0.1k-1           
    pip:        6.1.1-py27_0       
    python:     2.7.9-1            
    readline:   6.2-2              
    setuptools: 15.0-py27_0        
    sqlite:     3.8.4.1-1          
    tk:         8.5.18-0           
    vigra:      g14de6ac-np19py27_1
    zlib:       1.2.8-0            

Linking packages ...
[      COMPLETE      ]|###############################################################################################################################################################################################################| 100%
Removing old work directory
checkout: u'v0.1'
Cloning into '/zopt/conda/conda-bld/work'...
done.
Checking connectivity... done
Note: checking out 'v0.1'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 174f33a... Readme.md: Add Travis badge.
==> git log -n1 <==

commit 174f33a667b678695f086331acd6a297748e36eb
Author: John Kirkham <[email protected]>
Date:   Sat Jan 24 20:27:15 2015 -0500

    Readme.md: Add Travis badge.


==> git describe --tags --dirty <==

v0.1


==> git status <==

# HEAD detached at v0.1
nothing to commit, working directory clean


Package: rank_filter-v0.1-np19py27_0
source tree in: /zopt/conda/conda-bld/work
+++ dirname /Users/kirkhamj/Developer/ilastik-build-conda/rank_filter/build.sh
++ cd /Users/kirkhamj/Developer/ilastik-build-conda/rank_filter
++ pwd
+ CWD=/Users/kirkhamj/Developer/ilastik-build-conda/rank_filter
+ source /Users/kirkhamj/Developer/ilastik-build-conda/rank_filter/../common-vars.sh
+++ uname
++ [[ Darwin == \D\a\r\w\i\n ]]
++ DYLIB_EXT=dylib
+++ uname
++ [[ Darwin == \D\a\r\w\i\n ]]
++ LIBRARY_SEARCH_VAR=DYLD_FALLBACK_LIBRARY_PATH
++ export MACOSX_DEPLOYMENT_TARGET=10.7
++ MACOSX_DEPLOYMENT_TARGET=10.7
+++ uname
++ [[ Darwin == \D\a\r\w\i\n ]]
++ CXXFLAGS='-arch x86_64'
++ CXX_LDFLAGS='-arch x86_64'
+ RANK_FILTER_CXX_FLAGS='-stdlib=libc++ -arch x86_64'
+ RANK_FILTER_LDFLAGS='-arch x86_64'
++ pwd
+ SRC=/zopt/conda/conda-bld/work
+ mkdir -pv build
+ cd build
++ pwd
+ BLD=/zopt/conda/conda-bld/work/build
+ cmake /zopt/conda/conda-bld/work -DCMAKE_INSTALL_PREFIX=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh -DCMAKE_PREFIX_PATH=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh '-DCMAKE_SHARED_LINKER_FLAGS=-arch x86_64' '-DCMAKE_CXX_LINK_FLAGS=-stdlib=libc++ -arch x86_64' '-DCMAKE_CXX_FLAGS=-stdlib=libc++ -arch x86_64' -DBOOST_ROOT=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh -DVIGRA_ROOT=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh -DPYTHON_EXECUTABLE=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/bin/python
-- The C compiler identification is Clang 5.0.0
-- The CXX compiler identification is Clang 5.0.0
CMake Warning at /Applications/CMake 2.8-12.app/Contents/share/cmake-2.8/Modules/Platform/Darwin.cmake:143 (message):
  CMAKE_OSX_DEPLOYMENT_TARGET is '10.7' but the matching SDK does not exist
  at:

   "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk"

  Instead using SDK:

   "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk"

  matching the host OS X version.
Call Stack (most recent call first):
  /Applications/CMake 2.8-12.app/Contents/share/cmake-2.8/Modules/CMakeSystemSpecificInformation.cmake:36 (include)
  CMakeLists.txt:22 (project)


-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- 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
-- Found PythonInterp: /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/bin/python (found version "2.7.9") 
-- Found Python
--   > includes:          /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/include/python2.7
--   > library path:      /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib
--   > site-packages:     /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib/python2.7/site-packages
-- Boost version: 1.56.0
-- Found the following Boost libraries:
--   container
--   python
-- Found VIGRA
--   > includes:                 /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/include
--   > libraries:                /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib
--   > vigranumpy site-package:  /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib/python2.7/site-packages/vigra
--   > vigranumpycore library:   /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib/python2.7/site-packages/vigra/vigranumpycore.so
-- Found VIGRA: /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh  
-- Found Numpy
--   > includes:      /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib/python2.7/site-packages/numpy/core/include
-- Found Nose
--   > nose.core:      /zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib/python2.7/site-packages/nose/core.pyc
-- Configuring done
-- Generating done
-- Build files have been written to: /zopt/conda/conda-bld/work/build
+ eval DYLD_FALLBACK_LIBRARY_PATH=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib make -j8
++ DYLD_FALLBACK_LIBRARY_PATH=/zopt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeh/lib
++ make -j8
Scanning dependencies of target cxxtest
[ 50%] Building CXX object CMakeFiles/cxxtest.dir/test/test_rank_filter.cxx.o
Linking CXX executable bin/cxxtest.out
[ 50%] Built target cxxtest
Scanning dependencies of target check
Entering test suite RankFilterTestSuite
All (18) tests passed in test suite RankFilterTestSuite
Leaving test suite RankFilterTestSuite

[ 50%] Built target check
Scanning dependencies of target rank_filter
[100%] Building CXX object CMakeFiles/rank_filter.dir/src/rank_filter_py.cxx.o
Linking CXX shared library slib/rank_filter.so
Undefined symbols for architecture x86_64:
  "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:
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<double>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<double>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<3u, vigra::Singleband<double>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<2u, vigra::Singleband<double>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<1u, vigra::Singleband<double>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<5u, vigra::Singleband<float>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.o
      boost::python::api::object boost::python::detail::make_function_aux<vigra::NumpyAnyArray (*)(vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> >, mpl_::int_<5> >(vigra::NumpyAnyArray (*)(vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag>), boost::python::default_call_policies const&, boost::mpl::vector6<vigra::NumpyAnyArray, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> const&, unsigned long, double, int, vigra::NumpyArray<4u, vigra::Singleband<float>, vigra::StridedArrayTag> > const&, std::__1::pair<boost::python::detail::keyword const*, boost::python::detail::keyword const*> const&, mpl_::int_<5>) in rank_filter_py.cxx.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]: *** [slib/rank_filter.so] Error 1
make[1]: *** [CMakeFiles/rank_filter.dir/all] Error 2
make: *** [all] Error 2
Command failed: /bin/bash -x -e /Users/kirkhamj/Developer/ilastik-build-conda/rank_filter/build.sh