Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

yahmm not importing correctly on python 3.4 #41

Open
anticorrelator opened this issue Dec 14, 2014 · 15 comments
Open

yahmm not importing correctly on python 3.4 #41

anticorrelator opened this issue Dec 14, 2014 · 15 comments

Comments

@anticorrelator
Copy link

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
Copy link
Owner

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

@anmwinter
Copy link

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
Copy link

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
Copy link

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
Copy link
Owner

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

@anmwinter
Copy link

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

@anmwinter
Copy link

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
Copy link
Owner

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
Copy link

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
Copy link
Author

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

@jmschrei
Copy link
Owner

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
Copy link

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.

@nanaya-tachibana nanaya-tachibana mentioned this issue Jan 3, 2015
Merged
jmschrei pushed a commit that referenced this issue Jan 3, 2015
Merge pull request #42 from nanaya-tachibana/41
e1df030 
Fix issue #41: yahmm not importing correctly on python 3.4
@jmschrei
Copy link
Owner

jmschrei commented Jan 7, 2015

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

@anmwinter
Copy link

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

@jmschrei
Copy link
Owner

jmschrei commented May 4, 2015

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@anticorrelator @anmwinter @jmschrei