I encountered the follow error when running python3.7 setup.py build_ext --inplace in the /fastStructure/vars folder. Compilation worked fine in the /fastStructure/ folder...
Would appreciate any help to get this working!
running build_ext
skipping 'utils.c' Cython extension (up-to-date)
Compiling allelefreq.pyx because it changed.
Compiling marglikehood.pyx because it changed.
[1/2] Cythonizing allelefreq.pyx
/u/yxeng/.local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: ./allelefreq.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
# use an iterative fixed-point solver to update parameter estimates.
var_beta, var_gamma = self._unconstrained_solver(Dvarbeta, Dvargamma)
# if a variable violates positivity constraint,
# set it to an estimate from the previous update
bad_beta = reduce(utils.OR,[(var_beta<=0),np.isnan(var_beta)])
^
------------------------------------------------------------
allelefreq.pyx:148:19: undeclared name not builtin: reduce
Traceback (most recent call last):
File "setup.py", line 25, in <module>
ext_modules = cythonize(ext_modules)
File "/u/yxeng/.local/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1115, in cythonize
cythonize_one(*args)
File "/u/yxeng/.local/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: allelefreq.pyx
I encountered the follow error when running
python3.7 setup.py build_ext --inplace
in the/fastStructure/vars
folder. Compilation worked fine in the/fastStructure/
folder...Would appreciate any help to get this working!