yahmm not importing correctly on python 3.4

[anticorrelator]

I can successfully install yahmm using pip3, but none of the modules are loaded on import. The install works for python2.

osx 10.10.1 Cython (0.21.1) numpy (1.9.1) scipy (0.14.0) networkx (1.9.1) matplotlib (1.4.0) yahmm (1.1.1)

[jmschrei]

That's odd. Can you provide the logs of what happens when you try to use it with python 3.4?

[anmwinter]

I am having the same issue:

Aras-MacBook-Air:yahmm-master arakooser$ python3 Python 3.4.2 (v3.4.2:ab2c023a9432, Oct 5 2014, 20:42:22) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information.

from yahmm import * model = Model("5prime_ss_recog") Traceback (most recent call last): File "", line 1, in NameError: name 'Model' is not defined from yahmm import Model Traceback (most recent call last): File "", line 1, in ImportError: cannot import name 'Model'

[anmwinter]

Here is the log from the sudo pip3 install yahmm

Aras-MacBook-Air:yahmm-master arakooser$ sudo pip3 install yahmm Downloading/unpacking yahmm Downloading yahmm-1.1.1.zip (43kB): 43kB downloaded Running setup.py (path:/private/tmp/pip_build_root/yahmm/setup.py) egg_info for package yahmm

Requirement already satisfied (use --upgrade to upgrade): cython>=0.20.1 in /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages (from yahmm) Requirement already satisfied (use --upgrade to upgrade): numpy>=1.8.0 in /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages (from yahmm) Requirement already satisfied (use --upgrade to upgrade): scipy>=0.13.3 in /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages (from yahmm) Requirement already satisfied (use --upgrade to upgrade): networkx>=1.8.1 in /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages (from yahmm) Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.3.1 in /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages (from yahmm) Installing collected packages: yahmm Running setup.py install for yahmm cythoning yahmm/yahmm.pyx to yahmm/yahmm.c building 'yahmm.yahmm' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -I/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.4/include/python3.4m -c yahmm/yahmm.c -o build/temp.macosx-10.6-intel-3.4/yahmm/yahmm.o In file included from yahmm/yahmm.c:240: In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:17: In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804: /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it by " \

 ^
In file included from yahmm/yahmm.c:240:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:
/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: unused function '_import_array' [-Wunused-function]
_import_array(void)
^
In file included from yahmm/yahmm.c:241:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ufuncobject.h:317:
/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: unused function '_import_umath' [-Wunused-function]
_import_umath(void)
^
yahmm/yahmm.c:92793:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
static CYTHON_INLINE PyObject\* __Pyx_PyUnicode_FromString(const char\* c_str) {
                               ^
yahmm/yahmm.c:92933:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
static CYTHON_INLINE PyObject \* __Pyx_PyInt_FromSize_t(size_t ival) {
                                ^
yahmm/yahmm.c:88609:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function]
static CYTHON_INLINE void ___Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
                           ^
yahmm/yahmm.c:88618:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
                          ^
yahmm/yahmm.c:88623:27: warning: unused function '__Pyx_CyFunction_SetDefaultsKwDict' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
                          ^
yahmm/yahmm.c:88628:27: warning: unused function '__Pyx_CyFunction_SetAnnotationsDict' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
                          ^
yahmm/yahmm.c:88918:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                               ^
yahmm/yahmm.c:89280:26: warning: unused function '__Pyx_PyBytes_Equals' [-Wunused-function]
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject_ s1, PyObject\* s2, int equals) {
                         ^
yahmm/yahmm.c:90011:26: warning: unused function '__Pyx_GetBufferAndValidate' [-Wunused-function]
static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
                         ^
yahmm/yahmm.c:90045:27: warning: unused function '__Pyx_SafeReleaseBuffer' [-Wunused-function]
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer\* info) {
                          ^
yahmm/yahmm.c:91237:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
                                               ^
yahmm/yahmm.c:91247:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                             ^
yahmm/yahmm.c:91250:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91256:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91268:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91275:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
                                               ^
yahmm/yahmm.c:91281:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
                             ^
yahmm/yahmm.c:91284:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
                                               ^
yahmm/yahmm.c:91298:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                   ^
yahmm/yahmm.c:91357:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
                                                ^
yahmm/yahmm.c:91367:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                             ^
yahmm/yahmm.c:91370:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91376:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91388:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91395:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
                                                ^
yahmm/yahmm.c:91401:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
                             ^
yahmm/yahmm.c:91404:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
                                                ^
yahmm/yahmm.c:91418:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                    ^
yahmm/yahmm.c:91601:27: warning: function '__Pyx_PyInt_As_char' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject _x) {
                          ^
yahmm/yahmm.c:91696:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
                          ^
yahmm/yahmm.c:3223:26: warning: unused function '__pyx_f_5yahmm_5yahmm_pair_int_max' [-Wunused-function]
static CYTHON_INLINE int __pyx_f_5yahmm_5yahmm_pair_int_max(int __pyx_v_x, int __pyx_v_y) {
                         ^
yahmm/yahmm.c:71081:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {
                               ^
yahmm/yahmm.c:71131:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
                               ^
yahmm/yahmm.c:71181:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {
                               ^
yahmm/yahmm.c:71231:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {
                               ^
yahmm/yahmm.c:71281:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {
                               ^
yahmm/yahmm.c:72044:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]
static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {
                          ^
yahmm/yahmm.c:72132:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {
                               ^
41 warnings generated.
In file included from yahmm/yahmm.c:240:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:
/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
In file included from yahmm/yahmm.c:240:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:
/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: unused function '_import_array' [-Wunused-function]
_import_array(void)
^
In file included from yahmm/yahmm.c:241:
In file included from /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/ufuncobject.h:317:
/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: unused function '_import_umath' [-Wunused-function]
_import_umath(void)
^
yahmm/yahmm.c:92793:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
static CYTHON_INLINE PyObject_ __Pyx_PyUnicode_FromString(const char\* c_str) {
                               ^
yahmm/yahmm.c:92933:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
static CYTHON_INLINE PyObject \* __Pyx_PyInt_FromSize_t(size_t ival) {
                                ^
yahmm/yahmm.c:88609:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function]
static CYTHON_INLINE void ___Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
                           ^
yahmm/yahmm.c:88618:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
                          ^
yahmm/yahmm.c:88623:27: warning: unused function '__Pyx_CyFunction_SetDefaultsKwDict' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
                          ^
yahmm/yahmm.c:88628:27: warning: unused function '__Pyx_CyFunction_SetAnnotationsDict' [-Wunused-function]
static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
                          ^
yahmm/yahmm.c:88918:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                               ^
yahmm/yahmm.c:89280:26: warning: unused function '__Pyx_PyBytes_Equals' [-Wunused-function]
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject_ s1, PyObject\* s2, int equals) {
                         ^
yahmm/yahmm.c:90011:26: warning: unused function '__Pyx_GetBufferAndValidate' [-Wunused-function]
static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
                         ^
yahmm/yahmm.c:90045:27: warning: unused function '__Pyx_SafeReleaseBuffer' [-Wunused-function]
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer\* info) {
                          ^
yahmm/yahmm.c:90118:1: warning: unused function '__pyx_add_acquisition_count_locked' [-Wunused-function]
__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
yahmm/yahmm.c:90128:1: warning: unused function '__pyx_sub_acquisition_count_locked' [-Wunused-function]
__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
yahmm/yahmm.c:91237:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
                                               ^
yahmm/yahmm.c:91247:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                             ^
yahmm/yahmm.c:91250:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91256:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91268:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                               ^
yahmm/yahmm.c:91275:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
                                               ^
yahmm/yahmm.c:91281:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
                             ^
yahmm/yahmm.c:91284:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
                                               ^
yahmm/yahmm.c:91298:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                   ^
yahmm/yahmm.c:91357:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
                                                ^
yahmm/yahmm.c:91367:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                             ^
yahmm/yahmm.c:91370:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91376:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91388:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                ^
yahmm/yahmm.c:91395:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
                                                ^
yahmm/yahmm.c:91401:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]
    static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
                             ^
yahmm/yahmm.c:91404:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]
    static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
                                                ^
yahmm/yahmm.c:91418:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                    ^
yahmm/yahmm.c:91601:27: warning: function '__Pyx_PyInt_As_char' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) {
                          ^
yahmm/yahmm.c:91696:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
                          ^
yahmm/yahmm.c:3223:26: warning: unused function '__pyx_f_5yahmm_5yahmm_pair_int_max' [-Wunused-function]
static CYTHON_INLINE int __pyx_f_5yahmm_5yahmm_pair_int_max(int __pyx_v_x, int __pyx_v_y) {
                         ^
yahmm/yahmm.c:71081:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {
                               ^
yahmm/yahmm.c:71131:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
                               ^
yahmm/yahmm.c:71181:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {
                               ^
yahmm/yahmm.c:71231:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {
                               ^
yahmm/yahmm.c:71281:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {
                               ^
yahmm/yahmm.c:72044:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]
static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {
                          ^
yahmm/yahmm.c:72132:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {
                               ^
43 warnings generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.4/yahmm/yahmm.o -o build/lib.macosx-10.6-intel-3.4/yahmm/yahmm.so
changing mode of build/scripts-3.4/example.py from 644 to 755
changing mode of build/scripts-3.4/rainy_sunny_hmm.py from 644 to 755
changing mode of build/scripts-3.4/tied_state_hmm.py from 644 to 755
changing mode of build/scripts-3.4/infinite_hmm.py from 644 to 755
warning: yahmm/yahmm.pyx:2081:41: Index should be typed for more efficient access

changing mode of /Library/Frameworks/Python.framework/Versions/3.4/bin/example.py to 755
changing mode of /Library/Frameworks/Python.framework/Versions/3.4/bin/infinite_hmm.py to 755
changing mode of /Library/Frameworks/Python.framework/Versions/3.4/bin/rainy_sunny_hmm.py to 755
changing mode of /Library/Frameworks/Python.framework/Versions/3.4/bin/tied_state_hmm.py to 755

Successfully installed yahmm Cleaning up...

[anmwinter]

I am getting the same behavior and errors using sudo install pip yahmm

I am running OS X 10.9 with the latest X-code and command line tools.

[jmschrei]

Alright, I need to look into this. Thanks for providing the logs. Can you see if it works on Python 3.2?

[anmwinter]

Let me see if I can get Python 3.2 going tonight! And I'll give it a try.

[anmwinter]

Does this have something to do with how Cython, yahmm, and clang interact? I just realized gcc is gone from the latest X-Codes.

[jmschrei]

My initial hypotheses are either (1) that, or (2) I did not upload YAHMM to PyPI in a manner that pip3 can download. Let me know what the results are, because Travis says it works on 3.2, which will narrow down the problem.

[anmwinter]

Weirdly it's working under 2.7 just fine now.

I am having some trouble getting pip 3.2 to install and point to the python 3.2 directories. It keeps installing in the 3.4.

I'll let you know if I get it working.

[anticorrelator]

I get basically the same log as above when pip3 installing yahmm. FWIW I had gcc installed via brew (4.9.2)

[jmschrei]

As an additional test, can you try manually installing yahmm by cloning the repo or downloading the zip, and putting the files in whatever your Python path is? That will let me know if there's an issue with getting the files to you or the files themselves.

[anmwinter]

I failed to get pip-3.2 working correctly so I can't test that out. Sorry.

I'll try and move the yahmm files into my python path once I figure out where everything is installing to.

[jmschrei]

Did this change have an effect on your ability to install?

[anmwinter]

I tried and didn't see a change but I may have the wrong python path. I still need to check on that.

[jmschrei]

I got extremely busy and have not had time to focus on this issue. Can anyone comment on if this is still a problem?