Hi
I'm trying to install phylo_utils but I'm getting the following error:
running install
/usr/local/lib/python2.7/dist-packages/setuptools-12.3-py2.7.egg/pkg_resources/init.py:2512: PEP440Warning: 'distribute (0.6.24dev-r0)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.
PEP440Warning,
/usr/local/lib/python2.7/dist-packages/setuptools-12.3-py2.7.egg/pkg_resources/init.py:2512: PEP440Warning: 'python-debian (0.1.21-nmu2-bpo70-1)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.
PEP440Warning,
running bdist_egg
running egg_info
creating phylo_utils.egg-info
writing requirements to phylo_utils.egg-info/requires.txt
writing phylo_utils.egg-info/PKG-INFO
writing top-level names to phylo_utils.egg-info/top_level.txt
writing dependency_links to phylo_utils.egg-info/dependency_links.txt
writing manifest file 'phylo_utils.egg-info/SOURCES.txt'
reading manifest file 'phylo_utils.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'phylo_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/init.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/likelihood.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/markov.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/models.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/seq_to_partials.py -> build/lib.linux-x86_64-2.7/phylo_utils
running build_ext
cythoning extensions/likcalc.pyx to extensions/likcalc.c
Error compiling Cython file:
...
cdef double LOG_SCALE_VALUE = np.log(SCALE_THRESHOLD)
cdef extern from "discrete_gamma.h":
int DiscreteGamma(double* freqK, double* rK, double alpha, double beta, int K, int UseMedian) nogil
cpdef int _discrete_gamma(double[:] freqK, double[:] rK, double alpha, double beta, int K, int UseMedian) nogil:
^
extensions/likcalc.pyx:18:33: Expected an identifier or literal
building 'phylo_utils.likcalc' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/extensions
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/pymodules/python2.7/numpy/core/include -I/usr/include/python2.7 -c extensions/likcalc.c -o build/temp.linux-x86_64-2.7/extensions/likcalc.o
extensions/likcalc.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1
With fixed width text the arrow indicated the problem is under the text "double[:]" but I can't get it to show that correctly here.
All the best
David
Hi
I'm trying to install phylo_utils but I'm getting the following error:
running install
/usr/local/lib/python2.7/dist-packages/setuptools-12.3-py2.7.egg/pkg_resources/init.py:2512: PEP440Warning: 'distribute (0.6.24dev-r0)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.
PEP440Warning,
/usr/local/lib/python2.7/dist-packages/setuptools-12.3-py2.7.egg/pkg_resources/init.py:2512: PEP440Warning: 'python-debian (0.1.21-nmu2-bpo70-1)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.
PEP440Warning,
running bdist_egg
running egg_info
creating phylo_utils.egg-info
writing requirements to phylo_utils.egg-info/requires.txt
writing phylo_utils.egg-info/PKG-INFO
writing top-level names to phylo_utils.egg-info/top_level.txt
writing dependency_links to phylo_utils.egg-info/dependency_links.txt
writing manifest file 'phylo_utils.egg-info/SOURCES.txt'
reading manifest file 'phylo_utils.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'phylo_utils.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/init.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/likelihood.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/markov.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/models.py -> build/lib.linux-x86_64-2.7/phylo_utils
copying phylo_utils/seq_to_partials.py -> build/lib.linux-x86_64-2.7/phylo_utils
running build_ext
cythoning extensions/likcalc.pyx to extensions/likcalc.c
Error compiling Cython file:
...
cdef double LOG_SCALE_VALUE = np.log(SCALE_THRESHOLD)
cdef extern from "discrete_gamma.h":
int DiscreteGamma(double* freqK, double* rK, double alpha, double beta, int K, int UseMedian) nogil
cpdef int _discrete_gamma(double[:] freqK, double[:] rK, double alpha, double beta, int K, int UseMedian) nogil:
^
extensions/likcalc.pyx:18:33: Expected an identifier or literal
building 'phylo_utils.likcalc' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/extensions
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/pymodules/python2.7/numpy/core/include -I/usr/include/python2.7 -c extensions/likcalc.c -o build/temp.linux-x86_64-2.7/extensions/likcalc.o
extensions/likcalc.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1
With fixed width text the arrow indicated the problem is under the text "double[:]" but I can't get it to show that correctly here.
All the best
David