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Unable to install ezstructure
Hello, I'm trying to install ezstructure and this is the output:
Collecting ezstructure
Using cached ezstructure-1.0.1.tar.gz (22 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in ./mambaforge/envs/serpe/lib/python3.11/site-packages (from ezstructure) (1.24.2)
Collecting scipy (from ezstructure)
Obtaining dependency information for scipy from https://files.pythonhosted.org/packages/b8/46/1d255bb55e63de02f7b2f3a2f71b59b840db21d61ff7cd41edbfc2da448a/scipy-1.11.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached scipy-1.11.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (59 kB)
Using cached scipy-1.11.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.2 MB)
Building wheels for collected packages: ezstructure
Building wheel for ezstructure (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for ezstructure (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [196 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/ezstructure
copying ezstructure/io.py -> build/lib.linux-x86_64-cpython-311/ezstructure
copying ezstructure/__init__.py -> build/lib.linux-x86_64-cpython-311/ezstructure
copying ezstructure/structure.py -> build/lib.linux-x86_64-cpython-311/ezstructure
copying ezstructure/distruct.py -> build/lib.linux-x86_64-cpython-311/ezstructure
copying ezstructure/chooseK.py -> build/lib.linux-x86_64-cpython-311/ezstructure
creating build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/__init__.py -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/allelefreq.pxd -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/admixprop.pxd -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/admixprop.h -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/marglikehood.h -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
copying ezstructure/vars/allelefreq.h -> build/lib.linux-x86_64-cpython-311/ezstructure/vars
running build_ext
/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-p_2nf1e1/ezstructure_599fb8c833a84d499640900ede3cabb9/ezstructure/vars/utils.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling ezstructure/vars/utils.pyx because it changed.
[1/1] Cythonizing ezstructure/vars/utils.pyx
building 'ezstructure.vars.utils' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/ezstructure
creating build/temp.linux-x86_64-cpython-311/ezstructure/vars
gcc -pthread -B /home/marcob/mambaforge/envs/serpe/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/marcob/mambaforge/envs/serpe/include -fPIC -O2 -isystem /home/marcob/mambaforge/envs/serpe/include -fPIC -I/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/numpy/core/include -I/home/marcob/mambaforge/envs/serpe/include/python3.11 -c ezstructure/vars/utils.c -o build/temp.linux-x86_64-cpython-311/ezstructure/vars/utils.o
In file included from /tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from ezstructure/vars/utils.c:1106:
/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
gcc -pthread -B /home/marcob/mambaforge/envs/serpe/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/marcob/mambaforge/envs/serpe/lib -Wl,-rpath-link,/home/marcob/mambaforge/envs/serpe/lib -L/home/marcob/mambaforge/envs/serpe/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/marcob/mambaforge/envs/serpe/lib -Wl,-rpath-link,/home/marcob/mambaforge/envs/serpe/lib -L/home/marcob/mambaforge/envs/serpe/lib build/temp.linux-x86_64-cpython-311/ezstructure/vars/utils.o -o build/lib.linux-x86_64-cpython-311/ezstructure/vars/utils.cpython-311-x86_64-linux-gnu.so
/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-p_2nf1e1/ezstructure_599fb8c833a84d499640900ede3cabb9/ezstructure/vars/admixprop.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np
cimport allelefreq as af
^
------------------------------------------------------------
ezstructure/vars/admixprop.pxd:3:8: 'allelefreq.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray alpha, var, xi
cdef list oldvar
cdef copy(self)
cdef require(self)
cdef update(self, np.ndarray[np.uint8_t, ndim=2] G, af.AlleleFreq pi)
^
------------------------------------------------------------
ezstructure/vars/admixprop.pxd:26:56: 'AlleleFreq' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef list oldvar
cdef copy(self)
cdef require(self)
cdef update(self, np.ndarray[np.uint8_t, ndim=2] G, af.AlleleFreq pi)
cdef square_update(self, np.ndarray[np.uint8_t, ndim=2] G, af.AlleleFreq pi)
^
------------------------------------------------------------
ezstructure/vars/admixprop.pxd:27:63: 'AlleleFreq' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
"""
self.var = np.require(self.var, dtype=np.float64, requirements='C')
self.xi = np.require(self.xi, dtype=np.float64, requirements='C')
cdef update(self, np.ndarray[np.uint8_t, ndim=2] G, af.AlleleFreq pi):
^
------------------------------------------------------------
ezstructure/vars/admixprop.pyx:58:56: 'AlleleFreq' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
else:
self.var = self.alpha + self.var
self.xi = np.exp(digamma(self.var)-digamma(utils.insum(self.var,[1])))
self.require()
cdef square_update(self, np.ndarray[np.uint8_t, ndim=2] G, af.AlleleFreq pi):
^
------------------------------------------------------------
ezstructure/vars/admixprop.pyx:84:63: 'AlleleFreq' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
pi : instance of `AlleleFreq`
"""
self.var = np.zeros((self.N,self.K), dtype=np.float64)
Q_update(<np.uint8_t*>G.data, <double*> pi.zetabeta.data, <double*> pi.zetagamma.data, <double*> self.xi.data, <double*> self.var.data, self.N, pi. L, self.K)
^
------------------------------------------------------------
ezstructure/vars/admixprop.pyx:74:38: Python objects cannot be cast to pointers of primitive types
Error compiling Cython file:
------------------------------------------------------------
...
pi : instance of `AlleleFreq`
"""
self.var = np.zeros((self.N,self.K), dtype=np.float64)
Q_update(<np.uint8_t*>G.data, <double*> pi.zetabeta.data, <double*> pi.zetagamma.data, <double*> self.xi.data, <double*> self.var.data, self.N, pi. L, self.K)
^
------------------------------------------------------------
ezstructure/vars/admixprop.pyx:74:66: Python objects cannot be cast to pointers of primitive types
Compiling ezstructure/vars/admixprop.pyx because it changed.
[1/1] Cythonizing ezstructure/vars/admixprop.pyx
Traceback (most recent call last):
File "/home/marcob/mambaforge/envs/serpe/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/marcob/mambaforge/envs/serpe/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/marcob/mambaforge/envs/serpe/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 416, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 401, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 24, in <module>
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 346, in run
self.run_command("build")
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/Cython/Distutils/build_ext.py", line 122, in build_extension
new_ext = cythonize(
^^^^^^^^^^
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-0qfn83c1/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: ezstructure/vars/admixprop.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for ezstructure
Failed to build ezstructure
ERROR: Could not build wheels for ezstructure, which is required to install pyproject.toml-based projects
I'm running Ubuntu 22.04.2 LTS on WSL2 on Windows 11.
Python version=3.11.0
Wheel version=0.41.0
Numpy version=1.24.2
Thank you
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