search

Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
Other
98 stars 36 forks source link

cannot cache function 'log_beta' #5

Open jatintalwar opened 5 years ago

jatintalwar commented 5 years ago

Hello,

I am getting this error when i try to run PyClone (0.13.1) on centos7 i have installed all the required packages form python (including numba, 0.41.0).

Do you know why is this error being given? I am not so familiar with numba and the jit function that is used here.

PyClone -h

Traceback (most recent call last): File "/usr/bin/PyClone", line 9, in load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')() File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 378, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2566, in load_entry_point return ep.load() File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load entry = import(self.module_name, globals(),globals(), ['name']) File "build/bdist.linux-x86_64/egg/pyclone/cli.py", line 7, in File "build/bdist.linux-x86_64/egg/pyclone/run.py", line 21, in File "build/bdist.linux-x86_64/egg/pyclone/pyclone_beta_binomial.py", line 21, in File "build/bdist.linux-x86_64/egg/pyclone/math_utils.py", line 26, in File "/usr/lib64/python2.7/site-packages/numba/decorators.py", line 191, in wrapper disp.enable_caching() File "/usr/lib64/python2.7/site-packages/numba/dispatcher.py", line 566, in enable_caching self._cache = FunctionCache(self.py_func) File "/usr/lib64/python2.7/site-packages/numba/caching.py", line 614, in init self._impl = self._impl_class(py_func) File "/usr/lib64/python2.7/site-packages/numba/caching.py", line 349, in init "for file %r" % (qualname, source_path)) RuntimeError: cannot cache function 'log_beta': no locator available for file 'build/bdist.linux-x86_64/egg/pyclone/math_utils.py'

pawelqs commented 4 years ago

Hi @jatintalwar, I have encountered the same error. Did you solve it?

omula commented 4 years ago

You have to install it using pip and not python. In case you end up with an egg file (zipped) it won't work due to numba caching.

renyongzhe commented 4 years ago

You have to install it using pip and not python. In case you end up with an egg file (zipped) it won't work due to numba caching.

how to install pyclone using pip?

omula commented 4 years ago

IIRC:

  1. Clone the repo.
  2. Enter to the folder.
  3. pip install .
mark-welsh commented 4 years ago

^^^ this worked for me. I installed dependencies manually using pyenv/pip and received the same error after running python setup.py install for PyClone

running pip install . instead worked just fine