ghost commented 8 years ago

Hi,

I tried installing riboHMM using sudo python setup.py install but it always throws me error like following

Error compiling Cython file:
------------------------------------------------------------
...
    return x_final, optimized

@cython.boundscheck(False)
@cython.wraparound(False)
@cython.nonecheck(False)
cdef tuple alpha_func_grad(np.ndarray[np.float64_t, ndim=2] x, list data, list states, list frames, np.ndarray[np.float64_t, ndim=3] rescale, np.ndarray[np.float64_t, ndim=2] beta):
    ^
------------------------------------------------------------

ribohmm.pyx:1197:5: Function signature does not match previous declaration

Error compiling Cython file:
------------------------------------------------------------
...
    return func, gradient

@cython.boundscheck(False)
@cython.wraparound(False)
@cython.nonecheck(False)
cdef tuple alpha_func_grad_hess(np.ndarray[np.float64_t, ndim=2] x, list data, list states, list frames, np.ndarray[np.float64_t, ndim=3] rescale, np.ndarray[np.float64_t, ndim=2] beta):
    ^
------------------------------------------------------------

ribohmm.pyx:1265:5: Function signature does not match previous declaration
building 'ribohmm' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I. -I/usr/include/python2.7 -c ribohmm.c -o build/temp.linux-x86_64-2.7/ribohmm.o
ribohmm.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
 #error Do not use this file, it is the result of a failed Cython compilation.
  ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Any guidance in installing the riboHMM would be highly appreciable. Thanks in advance

mhassan commented 8 years ago

Were you able to resolve this? am stuck in the same lane

ghost commented 8 years ago

No........I tried even updating cython but still no use. As the paper published out recently I expect the author respond to the issues as soon as possible.

rajanil commented 8 years ago

Sorry, I seem to have missed this issue. The riboHMM release isn't complete yet; I expect to have a release within the week and will provide a full README on how to install, etc.

mhassan commented 8 years ago

Is the complete riboHMM out?

mjoppich commented 8 years ago

Any new info on when you can release?

Just curious :) (and leaving a reply so I don't miss it)

nonomono commented 8 years ago

I am getting a 'gcc' failed with exit 1 error could you please let me know what am I supposed to do to correct this issue, I have tried installing 'gcc' and 'python-dev' but they seem to be fine

error: command 'gcc' failed with exit status 1 (ribohmm) rr@rr-S2400SC:~/proj/riboHMM$ sudo apt-get install python-dev [sudo] password for rr: Reading package lists... Done Building dependency tree
Reading state information... Done python-dev is already the newest version (2.7.11-1). 0 upgraded, 0 newly installed, 0 to remove and 185 not upgraded. **(ribohmm) rr@rr-S2400SC:~/proj/riboHMM$ python setup.py build_ext --inplace running build_ext skipping 'seq.c' Cython extension (up-to-date) running build_ext skipping 'ribohmm.c' Cython extension (up-to-date) building 'ribohmm' extension gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include -I. -I/home/rr/anaconda2/envs/ribohmm/include/python2.7 -c ribohmm.c -o build/temp.linux-x86_64-2.7/ribohmm.o In file included from /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from ribohmm.c:274: /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

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

^ ribohmm.c:888:25: error: expected identifier or ‘(’ before ‘;’ token PyBoolObject _restrict; ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_10Transition___cinit’: ribohmm.c:18332:43: error: expected identifier before ‘restrict’ Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:774:24: note: in definition of macro ‘PyDECREF’ --((PyObject)(op))->ob_refcnt != 0) \ ^ ribohmm.c:18332:3: note: in expansion of macro ‘**Pyx_DECREF’ PyxDECREF(((PyObject )pyx_v_self->restrict)); ^ ribohmm.c:18332:43: error: expected identifier before ‘restrict’ Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:115:47: note: in definition of macro ‘Py_TYPE’

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

/home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:777:9: note: in expansion of macro ‘_Py_Dealloc’ _PyDealloc((PyObject )(op)); \ ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:18332:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:18332:43: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:764:45: note: in definition of macro ‘_Py_Dealloc’ (_Py_TYPE(op)->tpdealloc)((PyObject )(op))) ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:18332:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:18333:17: error: expected identifier before ‘restrict’ pyx_v_self->restrict = ((PyBoolObject )Py_True); ^ ribohmm.c: In function ‘pyx_f_7ribohmm_10Transition_update’: ribohmm.c:18696:64: error: expected identifier before ‘restrict’ pyx_t_1 = __Pyx_PyObject_IsTrue(((PyObject )pyx_v_self->restrict)); if ( ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c:19005:47: error: expected identifier before ‘restrict’ Pyx_INCREF(((PyObject *)pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:769:18: note: in definition of macro ‘PyINCREF’ ((PyObject)(op))->ob_refcnt++) ^ ribohmm.c:19005:7: note: in expansion of macro ‘Pyx_INCREF’ __Pyx_INCREF(((PyObject *)pyx_v_self->restrict)); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:99:0, from ribohmm.c:4: ribohmm.c:19007:76: error: expected identifier before ‘restrict’ yTuple_SET_ITEM(pyx_t_4, 4+pyx_t_13, ((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/tupleobject.h:54:75: note: in definition of macro ‘PyTuple_SET_ITEM’

define PyTuple_SET_ITEM(op, i, v) (((PyTupleObject *)(op))->ob_item[i] = v)

ribohmm.c:19141:70: error: expected identifier before ‘restrict’ pyx_t_1 = Pyx_PyObject_IsTrue(((PyObject )pyx_v_self->restrict)); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_10Transition_2reduce’: ribohmm.c:19308:43: error: expected identifier before ‘restrict’ PyxINCREF(((PyObject )pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:769:18: note: in definition of macro ‘PyINCREF’ ((PyObject)(op))->ob_refcnt++) ^ ribohmm.c:19308:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject )pyx_v_self->restrict)); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:99:0, from ribohmm.c:4: ribohmm.c:19310:61: error: expected identifier before ‘restrict’ PyTuple_SET_ITEM(pyx_t_2, 1, ((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/tupleobject.h:54:75: note: in definition of macro ‘PyTuple_SET_ITEM’

define PyTuple_SET_ITEM(op, i, v) (((PyTupleObject *)(op))->ob_item[i] = v)

In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_10Transition_8restrict_get’: ribohmm.c:19514:43: error: expected identifier before ‘restrict’ PyxINCREF(((PyObject )pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:769:18: note: in definition of macro ‘PyINCREF’ ((PyObject)(op))->ob_refcnt++) ^ ribohmm.c:19514:3: note: in expansion of macro ‘Pyx_INCREF’ Pyx_INCREF(((PyObject )pyx_v_self->restrict)); ^ ribohmm.c:19515:40: error: expected identifier before ‘restrict’ pyx_r = ((PyObject )pyx_v_self->restrict); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_10Transition_8restrict_2set’: ribohmm.c:19548:43: error: expected identifier before ‘restrict’ PyxDECREF(((PyObject )pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:774:24: note: in definition of macro ‘PyDECREF’ --((PyObject)(op))->ob_refcnt != 0) \ ^ ribohmm.c:19548:3: note: in expansion of macro ‘Pyx_DECREF’ PyxDECREF(((PyObject )pyx_v_self->restrict)); ^ ribohmm.c:19548:43: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:115:47: note: in definition of macro ‘Py_TYPE’

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

/home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:777:9: note: in expansion of macro ‘_Py_Dealloc’ _PyDealloc((PyObject )(op)); \ ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19548:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:19548:43: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject )__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:764:45: note: in definition of macro ‘_Py_Dealloc’ (_Py_TYPE(op)->tp_dealloc)((PyObject )(op))) ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19548:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:19549:17: error: expected identifier before ‘restrict’ pyx_v_self->restrict = ((PyBoolObject *)pyx_t_1); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_10Transition_8restrict_4del**’: ribohmm.c:19584:43: error: expected identifier before ‘restrict’ PyxDECREF(((PyObject )__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:774:24: note: in definition of macro ‘PyDECREF’ --((PyObject)(op))->ob_refcnt != 0) \ ^ ribohmm.c:19584:3: note: in expansion of macro ‘Pyx_DECREF’ PyxDECREF(((PyObject )pyx_v_self->restrict)); ^ ribohmm.c:19584:43: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:115:47: note: in definition of macro ‘Py_TYPE’

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

/home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:777:9: note: in expansion of macro ‘_Py_Dealloc’ _PyDealloc((PyObject )(op)); \ ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19584:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:19584:43: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_self->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:764:45: note: in definition of macro ‘_Py_Dealloc’ (_Py_TYPE(op)->tpdealloc)((PyObject )(op))) ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19584:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_self->restrict)); ^ ribohmm.c:19585:17: error: expected identifier before ‘restrict’ pyx_v_self->restrict = ((PyBoolObject )Py_None); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_4rebuild_Transition’: ribohmm.c:19812:40: error: expected identifier before ‘restrict’ Pyx_DECREF(((PyObject )pyx_v_t->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:774:24: note: in definition of macro ‘PyDECREF’ --((PyObject)(op))->ob_refcnt != 0) \ ^ ribohmm.c:19812:3: note: in expansion of macro ‘Pyx_DECREF’ PyxDECREF(((PyObject )pyx_v_t->restrict)); ^ ribohmm.c:19812:40: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)pyx_v_t->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:115:47: note: in definition of macro ‘Py_TYPE’

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

/home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:777:9: note: in expansion of macro ‘_Py_Dealloc’ _PyDealloc((PyObject )(op)); \ ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19812:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_t->restrict)); ^ ribohmm.c:19812:40: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_t->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:764:45: note: in definition of macro ‘_Py_Dealloc’ (_Py_TYPE(op)->tpdealloc)((PyObject )(op))) ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:19812:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_t->restrict)); ^ ribohmm.c:19813:14: error: expected identifier before ‘restrict’ pyx_v_t->restrict = ((PyBoolObject *)pyx_t_1); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_pf_7ribohmm_14learn_parameters’: ribohmm.c:46962:49: error: expected identifier before ‘restrict’ Pyx_DECREF(((PyObject )pyx_v_transition->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:774:24: note: in definition of macro ‘PyDECREF’ --((PyObject)(op))->ob_refcnt != 0) \ ^ ribohmm.c:46962:3: note: in expansion of macro ‘__Pyx_DECREF’ PyxDECREF(((PyObject )pyx_v_transition->restrict)); ^ ribohmm.c:46962:49: error: expected identifier before ‘restrict’ Pyx_DECREF(((PyObject )__pyx_v_transition->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:115:47: note: in definition of macro ‘Py_TYPE’

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

/home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:777:9: note: in expansion of macro ‘_Py_Dealloc’ _PyDealloc((PyObject )(op)); \ ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:46962:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_transition->restrict)); ^ ribohmm.c:46962:49: error: expected identifier before ‘restrict’ __Pyx_DECREF(((PyObject *)__pyx_v_transition->restrict)); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:764:45: note: in definition of macro ‘_Py_Dealloc’ (_Py_TYPE(op)->tpdealloc)((PyObject )(op))) ^ ribohmm.c:1085:27: note: in expansion of macro ‘Py_DECREF’

define __Pyx_DECREF(r) Py_DECREF(r)

ribohmm.c:46962:3: note: in expansion of macro ‘Pyx_DECREF’ __Pyx_DECREF(((PyObject *)pyx_v_transition->restrict)); ^ ribohmm.c:46963:23: error: expected identifier before ‘restrict’ pyx_v_transition->restrict = ((PyBoolObject )Py_False); ^ ribohmm.c: In function ‘__pyx_tp_new_7ribohmm_Transition’: ribohmm.c:51711:6: error: expected identifier before ‘restrict’ p->restrict = ((PyBoolObject )Py_None); Py_INCREF(Py_None); ^ In file included from /home/rr/anaconda2/envs/ribohmm/include/python2.7/Python.h:80:0, from ribohmm.c:4: ribohmm.c: In function ‘pyx_tp_dealloc_7ribohmm_Transition’: ribohmm.c:51728:15: error: expected identifier before ‘restrict’ Py_CLEAR(p->restrict); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:816:13: note: in definition of macro ‘Py_CLEAR’ if (op) { \ ^ ribohmm.c:51728:15: error: expected identifier before ‘restrict’ Py_CLEAR(p->restrict); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:817:46: note: in definition of macro ‘Py_CLEAR’ PyObject _py_tmp = (PyObject )(op); \ ^ ribohmm.c:51728:15: error: expected identifier before ‘restrict’ Py_CLEAR(p->restrict); ^ /home/rr/anaconda2/envs/ribohmm/include/python2.7/object.h:818:14: note: in definition of macro ‘Py_CLEAR’ (op) = NULL; \ ^ ribohmm.c: In function ‘pyx_tp_traverse_7ribohmm_Transition’: ribohmm.c:51737:10: error: expected identifier before ‘restrict’ if (p->restrict) { ^ ribohmm.c:51738:29: error: expected identifier before ‘restrict’ e = (v)(((PyObject)p->restrict), a); if (e) return e; ^ ribohmm.c: In function ‘pyx_tp_clear_7ribohmmTransition’: ribohmm.c:51752:24: error: expected identifier before ‘restrict’ tmp = ((PyObject)p->restrict); ^ ribohmm.c:51753:6: error: expected identifier before ‘restrict’ p->restrict = ((PyBoolObject *)Py_None); Py_INCREF(Py_None); ^ In file included from /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from ribohmm.c:274: ribohmm.c: At top level: /home/rr/anaconda2/envs/ribohmm/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1448:1: warning: ‘_import_array’ defined but not used [-Wunused-function] _import_array(void) ^ error: command 'gcc' failed with exit status 1** (ribohmm) rr@rr-S2400SC:~/proj/riboHMM$ sudo apt-get install gcc Reading package lists... Done Building dependency tree
Reading state information... Done gcc is already the newest version (4:5.3.1-1ubuntu1). gcc set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 185 not upgraded.

nonomono commented 8 years ago

My package list: (ribohmm) rr@rr-S2400SC:~/proj/riboHMM$ conda list

packages in environment at /home/rr/anaconda2/envs/ribohmm:

# _nb_ext_conf 0.2.0 py27_0
alabaster 0.7.8 py27_0
anaconda-client 1.4.0 py27_0
anaconda custom py27_0
anaconda-navigator 1.2.1 py27_0
argcomplete 1.0.0 py27_1
astropy 1.2.1 np111py27_0
babel 2.3.3 py27_0
backports 1.0 py27_0
backports_abc 0.4 py27_0
beautifulsoup4 4.4.1 py27_0
bcftools 1.3.1 0 bioconda htslib 1.3.1 1 bioconda pysam 0.9.1 py27_1 bioconda samtools 1.3.1 4 bioconda bitarray 0.8.1 py27_0
blaze 0.10.1 py27_0
bokeh 0.12.0 py27_0
boto 2.40.0 py27_0
bottleneck 1.1.0 np111py27_0
cairo 1.12.18 6
cdecimal 2.3 py27_2
cffi 1.6.0 py27_0
chest 0.2.3 py27_0
click 6.6 py27_0
cloudpickle 0.2.1 py27_0
clyent 1.2.2 py27_0
colorama 0.3.7 py27_0
configobj 5.0.6 py27_0
configparser 3.5.0b2 py27_1
contextlib2 0.5.3 py27_0
cryptography 1.4 py27_0
curl 7.49.0 0
cvxopt 1.1.8 py27_3
cycler 0.10.0 py27_0
cython 0.24.1 py27_0
cytoolz 0.8.0 py27_0
dask 0.10.0 py27_0
datashape 0.5.2 py27_0
decorator 4.0.10 py27_0
dill 0.2.5 py27_0
docutils 0.12 py27_2
dynd-python 0.7.2 py27_0
entrypoints 0.2.2 py27_0
enum34 1.1.6 py27_0
et_xmlfile 1.0.1 py27_0
fastcache 1.0.2 py27_1
flask 0.11.1 py27_0
flask-cors 2.1.2 py27_0
fontconfig 2.11.1 6
freetype 2.5.5 1
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_0
futures 3.0.5 py27_0
get_terminal_size 1.0.0 py27_0
gevent 1.1.1 py27_0
greenlet 0.4.10 py27_0
grin 1.2.1 py27_3
h5py 2.6.0 np111py27_1
hdf5 1.8.16 0
heapdict 1.0.0 py27_1
idna 2.1 py27_0
imagesize 0.7.1 py27_0
ipaddress 1.0.16 py27_0
ipykernel 4.3.1 py27_0
ipython 4.2.0 py27_0
ipython_genutils 0.1.0 py27_0
ipywidgets 4.1.1 py27_0
itsdangerous 0.24 py27_0
jbig 2.1 0
jdcal 1.2 py27_1
jedi 0.9.0 py27_1
jinja2 2.8 py27_1
jpeg 8d 1
jsonschema 2.5.1 py27_0
jupyter 1.0.0 py27_3
jupyter_client 4.3.0 py27_0
jupyter_console 4.1.1 py27_0
jupyter_core 4.1.0 py27_0
libdynd 0.7.2 0
libffi 3.2.1 0
libgfortran 3.0.0 1
libpng 1.6.22 0
libsodium 1.0.10 0
libtiff 4.0.6 2
libxml2 2.9.2 0
libxslt 1.1.28 0
llvmlite 0.11.0 py27_0
locket 0.2.0 py27_1
lxml 3.6.0 py27_0
markupsafe 0.23 py27_2
matplotlib 1.5.1 np111py27_0
mistune 0.7.2 py27_0
mkl 11.3.3 0
mkl-service 1.1.2 py27_2
mpmath 0.19 py27_1
multipledispatch 0.4.8 py27_0
nb_anacondacloud 1.1.0 py27_0
nb_conda 1.1.0 py27_0
nb_conda_kernels 1.0.3 py27_0
nbconvert 4.2.0 py27_0
nbformat 4.0.1 py27_0
nbpresent 3.0.2 py27_0
networkx 1.11 py27_0
nltk 3.2.1 py27_0
nose 1.3.7 py27_1
notebook 4.2.1 py27_0
numba 0.26.0 np111py27_0
numexpr 2.6.0 np111py27_0
numpy 1.11.1 py27_0
odo 0.5.0 py27_1
openpyxl 2.3.2 py27_0
openssl 1.0.2h 1
pandas 0.18.1 np111py27_0
partd 0.3.4 py27_0
patchelf 0.9 0
path.py 8.2.1 py27_0
pathlib2 2.1.0 py27_0
patsy 0.4.1 py27_0
pep8 1.7.0 py27_0
pexpect 4.0.1 py27_0
pickleshare 0.7.2 py27_0
pillow 3.2.0 py27_1
pip 8.1.2 py27_0
pixman 0.32.6 0
ply 3.8 py27_0
psutil 4.3.0 py27_0
ptyprocess 0.5.1 py27_0
py 1.4.31 py27_0
pyasn1 0.1.9 py27_0
pycairo 1.10.0 py27_0
pycosat 0.6.1 py27_1
pycparser 2.14 py27_1
pycrypto 2.6.1 py27_4
pycurl 7.43.0 py27_0
pyflakes 1.2.3 py27_0
pygments 2.1.3 py27_0
pyopenssl 0.16.0 py27_0
pyparsing 2.1.4 py27_0
pyqt 4.11.4 py27_3
pytables 3.2.2 np111py27_4
pytest 2.9.2 py27_0
python 2.7.12 1
python-dateutil 2.5.3 py27_0
pytz 2016.4 py27_0
pyyaml 3.11 py27_4
pyzmq 15.2.0 py27_1
qt 4.8.7 3
qtconsole 4.2.1 py27_0
qtpy 1.0.2 py27_0
libgcc 4.8.5 1 r ncurses 5.9 8 r readline 6.2 2
redis 3.2.0 0
redis-py 2.10.5 py27_0
requests 2.10.0 py27_0
rope 0.9.4 py27_1
scikit-image 0.12.3 np111py27_1
scikit-learn 0.17.1 np111py27_2
scipy 0.18.1 np111py27_0
setuptools 23.0.0 py27_0
simplegeneric 0.8.1 py27_1
singledispatch 3.4.0.3 py27_0
sip 4.16.9 py27_0
six 1.10.0 py27_0
snowballstemmer 1.2.1 py27_0
sockjs-tornado 1.0.3 py27_0
sphinx 1.4.1 py27_0
sphinx_rtd_theme 0.1.9 py27_0
spyder 2.3.9 py27_0
sqlalchemy 1.0.13 py27_0
sqlite 3.13.0 0
ssl_match_hostname 3.4.0.2 py27_1
statsmodels 0.6.1 np111py27_1
sympy 1.0 py27_0
terminado 0.6 py27_0
tk 8.5.18 0
toolz 0.8.0 py27_0
tornado 4.3 py27_1
traitlets 4.2.1 py27_0
unicodecsv 0.14.1 py27_0
werkzeug 0.11.10 py27_0
wheel 0.29.0 py27_0
xlrd 1.0.0 py27_0
xlsxwriter 0.9.2 py27_0
xlwt 1.1.2 py27_0
xz 5.2.2 0
yaml 0.1.6 0
zeromq 4.1.4 0
zlib 1.2.8 3

rajanil / riboHMM

Installation problem #1

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

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

define __Pyx_DECREF(r) Py_DECREF(r)

define __Pyx_DECREF(r) Py_DECREF(r)

define PyTuple_SET_ITEM(op, i, v) (((PyTupleObject *)(op))->ob_item[i] = v)

define PyTuple_SET_ITEM(op, i, v) (((PyTupleObject *)(op))->ob_item[i] = v)

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

define __Pyx_DECREF(r) Py_DECREF(r)

define __Pyx_DECREF(r) Py_DECREF(r)

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

define __Pyx_DECREF(r) Py_DECREF(r)

define __Pyx_DECREF(r) Py_DECREF(r)

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

define __Pyx_DECREF(r) Py_DECREF(r)

define __Pyx_DECREF(r) Py_DECREF(r)

define PyTYPE(ob) (((PyObject)(ob))->ob_type)

define __Pyx_DECREF(r) Py_DECREF(r)

define __Pyx_DECREF(r) Py_DECREF(r)

packages in environment at /home/rr/anaconda2/envs/ribohmm: