Failed to install pyhsmm on Mac

[DanqingZ]

Below is my problem, I tried all the methods of installing pyhsmm, but still cannot install it on my Mac.

danqing0703@Danqings-MacBook-Pro:~/pyhsmm/examples$ pip install pyhsmm
Collecting pyhsmm
Using cached pyhsmm-0.1.4.tar.gz
Requirement already satisfied (use --upgrade to upgrade): Cython>=0.20.1 in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): numpy in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): scipy in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): matplotlib in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): nose in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): pybasicbayes>=0.1.3 in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): six>=1.4 in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): pytz in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): pyparsing>=1.5.6 in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): mock in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): future in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from pybasicbayes>=0.1.3->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from mock->matplotlib->pyhsmm)
Requirement already satisfied (use --upgrade to upgrade): funcsigs in /Users/danqing0703/anaconda/lib/python2.7/site-packages (from mock->matplotlib->pyhsmm)
Building wheels for collected packages: pyhsmm
Running setup.py bdist_wheel for pyhsmm
Complete output from command /Users/danqing0703/anaconda/bin/python -c "import setuptools;file='/private/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-build-QaUnW3/pyhsmm/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" bdist_wheel -d /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/tmpsYliUapip-wheel-:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.5-x86_64-2.7
creating build/lib.macosx-10.5-x86_64-2.7/pyhsmm
copying pyhsmm/init.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm
copying pyhsmm/models.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm
copying pyhsmm/parallel.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm
creating build/lib.macosx-10.5-x86_64-2.7/pyhsmm/basic
copying pyhsmm/basic/init.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/basic
copying pyhsmm/basic/abstractions.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/basic
copying pyhsmm/basic/distributions.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/basic
copying pyhsmm/basic/models.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/basic
creating build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/init.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/hmm_states.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/hsmm_inb_states.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/hsmm_states.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/initial_state.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
copying pyhsmm/internals/transitions.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/internals
creating build/lib.macosx-10.5-x86_64-2.7/pyhsmm/plugins
copying pyhsmm/plugins/init.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/plugins
creating build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/init.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/general.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/plot.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/profiling.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/stats.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/testing.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
copying pyhsmm/util/text.py -> build/lib.macosx-10.5-x86_64-2.7/pyhsmm/util
running build_ext
building 'pyhsmm/internals.hmm_messages_interface' extension
creating build/temp.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/pyhsmm
creating build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals
gcc -fno-strict-aliasing -I/Users/danqing0703/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipyhsmm/deps/Eigen3 -I/Users/danqing0703/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/danqing0703/anaconda/include/python2.7 -c pyhsmm/internals/hmm_messages_interface.cpp -o build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals/hmm_messages_interface.o -O3 -std=c++11 -DNDEBUG -w -DHMM_TEMPS_ON_HEAP
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:276:
pyhsmm/deps/Eigen3/Eigen/src/Core/MathFunctions.h:357:18: error: no member named 'log1p' in namespace 'std'; did you mean 'log10'?
using std::log1p;
~~~~~^~~~~
log10
/usr/include/math.h:391:15: note: 'log10' declared here
extern double log10(double);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:324:
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:302:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:303:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:304:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:373:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:374:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:439:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:440:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:329:
pyhsmm/deps/Eigen3/Eigen/src/Core/PlainObjectBase.h:470:25: error: no member named 'move' in namespace 'std'
: m_storage( std::move(other.m_storage) )
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:222:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:331:
pyhsmm/deps/Eigen3/Eigen/src/Core/Array.h:134:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/internals/hmm_messages.h:224:18: note: in instantiation of template class 'Eigen::Matrix<int, -1, -1, 0, -1, -1>' requested here
MatrixXi args(M,T);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::base;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:144:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::coeffRef;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:378:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::m_storage;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:73:20: note: in instantiation of template class 'Eigen::Matrix<float, -1, -1, 1, -1, -1>' requested here
typedef typename PlainObjectType::Index Index;
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:32:31: note: in instantiation of template class 'Eigen::internal::traits<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
enum { has_direct_access = (traits::Flags & DirectAccessBit) ? 1 : 0,
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:109:32: note: in instantiation of template class 'Eigen::internal::accessors_level<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
int Level = internal::accessors_level::has_write_access ? WriteAccessors : ReadOnlyAccessors
^
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:105:12: note: in instantiation of default argument for 'MapBase<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' required here
: public MapBase<Map<PlainObjectType, MapOptions, StrideType> >
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/internals/hmm_messages.h:31:24: note: in instantiation of template class 'Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> >' requested here
NPMatrix eA(A,M,M);
^
pyhsmm/internals/hmm_messages.h:260:12: note: in instantiation of function template specialization 'hmm::messages_backwards_log' requested here
{ hmm::messages_backwards_log(M,T,A,aBl,betal); }
^
pyhsmm/internals/hmm_messages_interface.cpp:2961:15: note: in instantiation of member function 'hmmc<float, int>::messages_backwards_log' requested here
__pyx_v_ref.messages_backwards_log((__pyx_v_A.shape[0]), (__pyx_v_aBl.shape[0]), (&(((float *) ( / dim=1 / ((char *) (((float *) ( / dim=0 / (__pyx_v_A.data + __pyx_t_1 * __pyx_v_A.strides[0]) )) + __pyx_t_2)) )))), (&(((float ) ( / dim=1 / ((char *) (((float *) ( / dim=0 _/ (__pyx_v_aBl.data + __pyx_t_3 * __pyx_v_aBl.strides[0]) )) + __pyx_t_4)) )))), (&(___Pyx_BufPtrCContig2d(float *, __pyx_pybuffernd_betal.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_betal.diminfo[0].strides, __pyx_t_6, __pyx_pybuffernd_betal.diminfo[1].strides))));
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
using Base::base;
^~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'gcc' failed with exit status 1

---

Failed building wheel for pyhsmm
Failed to build pyhsmm
Installing collected packages: pyhsmm
Running setup.py install for pyhsmm
Complete output from command /Users/danqing0703/anaconda/bin/python -c "import setuptools, tokenize;file='/private/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-build-QaUnW3/pyhsmm/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-5FdwS0-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
running build_ext
building 'pyhsmm/internals.hmm_messages_interface' extension
gcc -fno-strict-aliasing -I/Users/danqing0703/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipyhsmm/deps/Eigen3 -I/Users/danqing0703/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/danqing0703/anaconda/include/python2.7 -c pyhsmm/internals/hmm_messages_interface.cpp -o build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals/hmm_messages_interface.o -O3 -std=c++11 -DNDEBUG -w -DHMM_TEMPS_ON_HEAP
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:276:
pyhsmm/deps/Eigen3/Eigen/src/Core/MathFunctions.h:357:18: error: no member named 'log1p' in namespace 'std'; did you mean 'log10'?
using std::log1p;
~~~~~^~~~~
log10
/usr/include/math.h:391:15: note: 'log10' declared here
extern double log10(double);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:324:
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:302:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:303:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:304:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:373:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:374:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:439:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:440:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:329:
pyhsmm/deps/Eigen3/Eigen/src/Core/PlainObjectBase.h:470:25: error: no member named 'move' in namespace 'std'
: m_storage( std::move(other.m_storage) )
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:222:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:331:
pyhsmm/deps/Eigen3/Eigen/src/Core/Array.h:134:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/internals/hmm_messages.h:224:18: note: in instantiation of template class 'Eigen::Matrix<int, -1, -1, 0, -1, -1>' requested here
MatrixXi args(M,T);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::base;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:144:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::coeffRef;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:378:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<int, -1, -1, 0, -1, -1>'
using Base::m_storage;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:73:20: note: in instantiation of template class 'Eigen::Matrix<float, -1, -1, 1, -1, -1>' requested here
typedef typename PlainObjectType::Index Index;
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:32:31: note: in instantiation of template class 'Eigen::internal::traits<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
enum { has_direct_access = (traits::Flags & DirectAccessBit) ? 1 : 0,
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:109:32: note: in instantiation of template class 'Eigen::internal::accessors_level<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
int Level = internal::accessors_level::has_write_access ? WriteAccessors : ReadOnlyAccessors
^
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:105:12: note: in instantiation of default argument for 'MapBase<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' required here
: public MapBase<Map<PlainObjectType, MapOptions, StrideType> >
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/internals/hmm_messages.h:31:24: note: in instantiation of template class 'Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> >' requested here
NPMatrix eA(A,M,M);
^
pyhsmm/internals/hmm_messages.h:260:12: note: in instantiation of function template specialization 'hmm::messages_backwards_log' requested here
{ hmm::messages_backwards_log(M,T,A,aBl,betal); }
^
pyhsmm/internals/hmm_messages_interface.cpp:2961:15: note: in instantiation of member function 'hmmc<float, int>::messages_backwards_log' requested here
__pyx_v_ref.messages_backwards_log((__pyx_v_A.shape[0]), (__pyx_v_aBl.shape[0]), (&(((float *) ( / dim=1 / ((char *) (((float *) ( / dim=0 / (__pyx_v_A.data + __pyx_t_1 * __pyx_v_A.strides[0]) )) + __pyx_t_2)) )))), (&(((float ) ( / dim=1 / ((char *) (((float *) ( / dim=0 _/ (__pyx_v_aBl.data + __pyx_t_3 * __pyx_v_aBl.strides[0]) )) + __pyx_t_4)) )))), (&(___Pyx_BufPtrCContig2d(float *, __pyx_pybuffernd_betal.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_betal.diminfo[0].strides, __pyx_t_6, __pyx_pybuffernd_betal.diminfo[1].strides))));
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:279:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of 'Matrix<float, -1, -1, 1, -1, -1>'
using Base::base;
^~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/Users/danqing0703/anaconda/bin/python -c "import setuptools, tokenize;file='/private/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-build-QaUnW3/pyhsmm/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-5FdwS0-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T/pip-build-QaUnW3/pyhsmm

[DanqingZ]

My gcc and g++ version

danqing0703@Danqings-MacBook-Pro:~/pyhsmm/examples$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix

danqing0703@Danqings-MacBook-Pro:~/pyhsmm/examples$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix

[mattjj]

That g++ isn't really g++, it's actually symlinked to Clang. Try passing --with-old-clang when you run the setup.py script (or equivalently adding '-stdlib=libc++' to CXXFLAGS and LDFLAGS) or installing g++.

[mattjj]

This is really a problem with compiling Eigen against a non-C++11 standard library (as came up e.g. here). It looks like the current version of Eigen might check if log1p is available in the standard library being compiled against. Maybe I can update Eigen (or, even better, have setup.py download the latest version) and some of these compilation issues will go away (since other people have gotten stuck here too).

[DanqingZ]

Hi thanks for the reply. But I am wondering what do you mean by passing "--with-old-lang"?? I tried python setup.py build_ext --inplace --with-cython --with-old-clang.But got the followings:

danqing0703@airbears2-10-142-147-19:~/Desktop/pyhsmm$ python setup.py build_ext --inplace --with-cython --with-old-clang
Compiling pyhsmm/internals/hmm_messages_interface.pyx because it changed.
Compiling pyhsmm/internals/hsmm_messages_interface.pyx because it changed.
Compiling pyhsmm/util/cstats.pyx because it changed.
Cythonizing pyhsmm/internals/hmm_messages_interface.pyx
Cythonizing pyhsmm/internals/hsmm_messages_interface.pyx
Cythonizing pyhsmm/util/cstats.pyx
/Users/danqing0703/anaconda/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running build_ext
building 'pyhsmm.internals.hmm_messages_interface' extension
creating build
creating build/temp.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/pyhsmm
creating build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals
gcc -fno-strict-aliasing -I/Users/danqing0703/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipyhsmm/deps/Eigen3/ -I/Users/danqing0703/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/danqing0703/anaconda/include/python2.7 -c pyhsmm/internals/hmm_messages_interface.cpp -o build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals/hmm_messages_interface.o -std=c++11 -O3 -w -DNDEBUG -DHMM_TEMPS_ON_HEAP -stdlib=libc++
clang: error: invalid deployment target for -stdlib=libc++ (requires OS X 10.7 or later)
error: command 'gcc' failed with exit status 1

[DanqingZ]

I tried to install pyhsmm many times on my Mac, but these compiling problems always occur...

[mattjj]

Like I said, the problem is really with compiling Eigen and isn't specific to pyhsmm, and those problems are in turn stemming from Clang having problems compiling C++11 with the correct C++11 standard library. As you can see, your most recent error is about Clang trying to build for legacy OS X versions.

The easiest solution would be to stop using Clang and use g++.

Btw check out #23 and #30 for other times this issue has come up. A comment in #23 mentions passing the -mmacosx-version-min=10.7 flag to fix your current error, but if it were me I'd avoid all these challenges by using g++!

[DanqingZ]

Hi I used "brew install gcc48" to install g++:
danqing0703@airbears2-10-142-147-19:~/Desktop/pyhsmm$ gcc-4.8 --version
gcc-4.8 (Homebrew gcc48 4.8.4) 4.8.4
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

But I still have the same error: command 'gcc' failed with exit status 1

[mattjj]

Is the compilation using the gcc version you just installed? My guess is it's not. Two ways to remedy that: either symlink the gcc-4.8 binary onto your PATH as gcc (before the current gcc symlink or replacing it) or just prefix the setup.py command with CXX=gcc-4.8, something like

CXX=gcc-4.8 setup.py build_ext install --with-cython

(assuming you're using bash or zsh and not fish).

[DanqingZ]

Hi , thanks! I tried your command line:
~/Desktop/pyhsmm$ CXX=gcc-4.8 python setup.py build_ext install --with-cython

But still have the same problems..

/Users/danqing0703/anaconda/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running build_ext
building 'pyhsmm.internals.hmm_messages_interface' extension
gcc -fno-strict-aliasing -I/Users/danqing0703/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipyhsmm/deps/Eigen3/ -I/Users/danqing0703/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/danqing0703/anaconda/include/python2.7 -c pyhsmm/internals/hmm_messages_interface.cpp -o build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals/hmm_messages_interface.o -std=c++11 -O3 -w -DNDEBUG -DHMM_TEMPS_ON_HEAP
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:276:
pyhsmm/deps/Eigen3/Eigen/src/Core/MathFunctions.h:357:18: error: no member named 'log1p' in namespace 'std'; did you mean 'log10'?
using std::log1p;
~~~~~^~~~~
log10
/usr/include/math.h:391:15: note: 'log10' declared here
extern double log10(double);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:324:
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:302:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:303:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:304:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:373:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:374:21: error: no member named 'move' in namespace 'std'
, m_cols(std::move(other.m_cols))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:439:21: error: no member named 'move' in namespace 'std'
: m_data(std::move(other.m_data))
~~~~~^
pyhsmm/deps/Eigen3/Eigen/src/Core/DenseStorage.h:440:21: error: no member named 'move' in namespace 'std'
, m_rows(std::move(other.m_rows))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:329:
pyhsmm/deps/Eigen3/Eigen/src/Core/PlainObjectBase.h:470:25: error: no member named 'move' in namespace 'std'
: m_storage( std::move(other.m_storage) )
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:222:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:331:
pyhsmm/deps/Eigen3/Eigen/src/Core/Array.h:134:19: error: no member named 'move' in namespace 'std'
: Base(std::move(other))
~~~~~^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/internals/hmm_messages.h:224:18: note: in instantiation of template class 'Eigen::Matrix<int, -1, -1, 0, -1, -1>' requested here
MatrixXi args(M,T);
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<int, -1, -1, 0, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<int, -1, -1, 0, -1, -1>'
using Base::base;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:144:11: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<int, -1, -1, 0, -1, -1>'
using Base::coeffRef;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:378:11: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<int, -1, -1, 0, -1, -1>'
using Base::m_storage;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:403:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::derived;
^~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:73:20: note: in instantiation of template class 'Eigen::Matrix<float, -1, -1, 1, -1, -1>' requested here
typedef typename PlainObjectType::Index Index;
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:32:31: note: in instantiation of template class
'Eigen::internal::traits<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
enum { has_direct_access = (traits::Flags & DirectAccessBit) ? 1 : 0,
^
pyhsmm/deps/Eigen3/Eigen/src/Core/util/ForwardDeclarations.h:109:32: note: in instantiation of template class
'Eigen::internal::accessors_level<Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1, Eigen::Stride<0, 0> > >' requested here
int Level = internal::accessors_level::has_write_access ? WriteAccessors : ReadOnlyAccessors
^
pyhsmm/deps/Eigen3/Eigen/src/Core/Map.h:105:12: note: in instantiation of default argument for 'MapBase<Eigen::Map<Eigen::Matrix<float, -1, -1,
1, -1, -1>, 1, Eigen::Stride<0, 0> > >' required here
: public MapBase<Map<PlainObjectType, MapOptions, StrideType> >
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/internals/hmm_messages.h:31:24: note: in instantiation of template class 'Eigen::Map<Eigen::Matrix<float, -1, -1, 1, -1, -1>, 1,
Eigen::Stride<0, 0> >' requested here
NPMatrix eA(A,M,M);
^
pyhsmm/internals/hmm_messages.h:260:12: note: in instantiation of function template specialization 'hmm::messages_backwards_log' requested
here
{ hmm::messages_backwards_log(M,T,A,aBl,betal); }
^
pyhsmm/internals/hmm_messages_interface.cpp:2977:15: note: in instantiation of member function 'hmmc<float, int>::messages_backwards_log'
requested here
__pyx_v_ref.messages_backwards_log((__pyx_v_A.shape[0]), (__pyx_v_aBl.shape[0]), (&(((float *) ( / dim=1 */ ((char *) (((float *) ( /...
^
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:139:5: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<float, -1, -1, 1, -1, -1>'
EIGEN_DENSE_PUBLIC_INTERFACE(Matrix)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pyhsmm/deps/Eigen3/Eigen/src/Core/util/Macros.h:404:9: note: expanded from macro 'EIGEN_DENSE_PUBLIC_INTERFACE'
using Base::const_cast_derived;
^~~~~~
In file included from pyhsmm/internals/hmm_messages_interface.cpp:286:
In file included from pyhsmm/internals/hmm_messages.h:4:
In file included from pyhsmm/deps/Eigen3/Eigen/Core:330:
pyhsmm/deps/Eigen3/Eigen/src/Core/Matrix.h:143:11: error: using declaration refers into 'Base::', which is not a base class of
'Matrix<float, -1, -1, 1, -1, -1>'
using Base::base;
^~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'gcc' failed with exit status 1

[mattjj]

It's still calling 'gcc'. Try doing this instead:

CC=gcc-4.8 setup.py build_ext install --with-cython

You may need to iterate on this to get the command right. It's nothing pyhsmm-specific; it's just about using the compiler you installed. (There may even be a way to get brew to select which compiler to use by default; that's how macports does it.)

[DanqingZ]

Sorry I am quite new to compiling issues and only encounter this problem when installing pyhsmm...could you provide some more hints on how to get this work? Like how to choose the right compiler? I think "CXX='g++-4.8'" and "CC=gcc-4.8" seems to be calling the 'gcc', but there are other new bugs that I do not know what to do...

danqing0703@airbears2-10-142-147-19:~/Desktop/pyhsmm$ CXX='g++-4.8' python setup.py build_ext install --with-cython
/Users/danqing0703/anaconda/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running build_ext
building 'pyhsmm.internals.hmm_messages_interface' extension
gcc-4.8 -fno-strict-aliasing -I/Users/danqing0703/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipyhsmm/deps/Eigen3/ -I/Users/danqing0703/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/danqing0703/anaconda/include/python2.7 -c pyhsmm/internals/hmm_messages_interface.cpp -o build/temp.macosx-10.5-x86_64-2.7/pyhsmm/internals/hmm_messages_interface.o -std=c++11 -O3 -w -DNDEBUG -DHMM_TEMPS_ON_HEAP
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121426:expecting string instruction after rep' /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121451:expecting string instruction afterrep'
/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121501:expecting string instruction after rep' /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121838:expecting string instruction afterrep'
/var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121863:expecting string instruction after rep' /var/folders/3h/t2d82x_163d9sh0rph_wgrw00000gn/T//cchczRJe.s:121913:expecting string instruction afterrep'
error: command 'gcc-4.8' failed with exit status 1

[mattjj]

I haven't seen that error before. Maybe your binutils is old. Can you verify that you can build binaries with this new gcc-4.8 using -O3, or perhaps try updating your binutils (if brew didn't do that for you)?

You probably only run into these problems in pyhsmm because I used C++11 when I wrote it. A lot of friendlier software supports older compilers and toolchains, but this is just research code :).

[mattjj]

Btw, I just pushed to master a new setup.py which attempts to download Eigen automatically. Since it's a newer Eigen version, it might solve some compilation problems, but since I changed several things it might break more than it fixes. I'll try to test things with Clang and sort them out when I get a chance, but I'm not sure when that will be.

[mattjj]

I was able to build pyhsmm using clang on the current master (5524043). My clang version is

○ clang++ -v
Apple LLVM version 7.0.0 (clang-700.1.76)
Target: x86_64-apple-darwin15.0.0
Thread model: posix

and I built it with my shell's equivalent of

CC=clang++ python setup.py build_ext --inplace

Maybe the new version of Eigen that the new setup.py file downloads solves these compilation issues, or maybe it just works on El Capitan. Let me know if you give it a shot.

[DanqingZ]

It works!! Thanks so much!!

[mattjj]

No problem :) sorry my code gave you a headache for a while.

[mathDR]

Pretty baller fix bro. And timely!!!

Sent from my iPhone

On Nov 2, 2015, at 19:29, Matthew Johnson notifications@github.com wrote:

Closed #52.

—
Reply to this email directly or view it on GitHub.

[mattjj]

Thanks, @mathDR !