Description
Hi, I'm running into issues installing this via pip on Python 3.9, despite having few of the requirements already satisfied (see the first lines of the log below):
➜ pip install sklearn-pandas
Collecting sklearn-pandas
Using cached sklearn_pandas-2.0.3-py2.py3-none-any.whl (10 kB)
Requirement already satisfied: numpy>=1.18.1 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from sklearn-pandas) (1.19.2)
Requirement already satisfied: pandas>=1.0.5 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from sklearn-pandas) (1.1.3)
Requirement already satisfied: scipy>=1.4.1 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from sklearn-pandas) (1.5.2)
Requirement already satisfied: python-dateutil>=2.7.3 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from pandas>=1.0.5->sklearn-pandas) (2.8.1)
Requirement already satisfied: numpy>=1.18.1 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from sklearn-pandas) (1.19.2)
Requirement already satisfied: pytz>=2017.2 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from pandas>=1.0.5->sklearn-pandas) (2020.4)
Requirement already satisfied: six>=1.5 in /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas>=1.0.5->sklearn-pandas) (1.15.0)
Collecting scikit-learn>=0.23.0
Using cached scikit-learn-0.23.2.tar.gz (7.2 MB)
Installing build dependencies ... error
ERROR: Command errored out with exit status 1:
command: /Users/xxx/miniconda3/envs/omni/bin/python /Users/xxx/miniconda3/envs/omni/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/jx/z4vcr3393j537mmdc9jg1gsc0000gn/T/pip-build-env-vq1ymb5n/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.28.5' 'numpy==1.13.3; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation == '"'"'CPython'"'"'' 'numpy==1.14.0; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation != '"'"'CPython'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'scipy>=0.19.1'
cwd: None
Complete output (2494 lines):
Ignoring numpy: markers 'python_version == "3.6" and platform_system != "AIX" and platform_python_implementation == "CPython"' don't match your environment
Ignoring numpy: markers 'python_version == "3.6" and platform_system != "AIX" and platform_python_implementation != "CPython"' don't match your environment
Ignoring numpy: markers 'python_version == "3.7" and platform_system != "AIX"' don't match your environment
Ignoring numpy: markers 'python_version == "3.6" and platform_system == "AIX"' don't match your environment
Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
Ignoring numpy: markers 'python_version >= "3.8" and platform_system == "AIX"' don't match your environment
Collecting Cython>=0.28.5
Using cached Cython-0.29.21-py2.py3-none-any.whl (974 kB)
Collecting numpy==1.17.3
Using cached numpy-1.17.3.zip (6.4 MB)
Collecting scipy>=0.19.1
Using cached scipy-1.5.4-cp39-cp39-macosx_10_9_x86_64.whl (29.1 MB)
Collecting setuptools
Using cached setuptools-51.0.0-py3-none-any.whl (785 kB)
Collecting wheel
Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
Building wheels for collected packages: numpy
Building wheel for numpy (setup.py): started
Building wheel for numpy (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /Users/xxx/miniconda3/envs/omni/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/jx/z4vcr3393j537mmdc9jg1gsc0000gn/T/pip-install-vpubhwxv/numpy_c9b5b84c35144de6b143a5317b9f20b6/setup.py'"'"'; __file__='"'"'/private/var/folders/jx/z4vcr3393j537mmdc9jg1gsc0000gn/T/pip-install-vpubhwxv/numpy_c9b5b84c35144de6b143a5317b9f20b6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/jx/z4vcr3393j537mmdc9jg1gsc0000gn/T/pip-wheel-02k93ojp
cwd: /private/var/folders/jx/z4vcr3393j537mmdc9jg1gsc0000gn/T/pip-install-vpubhwxv/numpy_c9b5b84c35144de6b143a5317b9f20b6/
Complete output (2291 lines):
Running from numpy source directory.
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/Users/xxx/miniconda3/envs/omni/lib']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/usr/local/include', '/Users/xxx/miniconda3/envs/omni/include']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/Users/xxx/miniconda3/envs/omni/lib']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/usr/local/include', '/Users/xxx/miniconda3/envs/omni/include']
/bin/sh: svnversion: command not found
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/Users/xxx/miniconda3/envs/omni/lib']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/usr/local/include', '/Users/xxx/miniconda3/envs/omni/include']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/Users/xxx/miniconda3/envs/omni/lib']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/usr/local/include', '/Users/xxx/miniconda3/envs/omni/include']
/Users/xxx/miniconda3/envs/omni/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.macosx-10.9-x86_64-3.9
creating build/src.macosx-10.9-x86_64-3.9/numpy
creating build/src.macosx-10.9-x86_64-3.9/numpy/distutils
building library "npymath" sources
get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize NAGFCompiler
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64 -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/xxx/miniconda3/envs/omni/include/python3.9 -c'
clang: _configtest.c
clang -arch x86_64 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64 -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/xxx/miniconda3/envs/omni/include/python3.9 -c'
clang: _configtest.c
_configtest.c:1:5: warning: incompatible redeclaration of library function 'exp' [-Wincompatible-library-redeclaration]
int exp (void);
^
_configtest.c:1:5: note: 'exp' is a builtin with type 'double (double)'
1 warning generated.
clang -arch x86_64 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
creating build/src.macosx-10.9-x86_64-3.9/numpy/core
creating build/src.macosx-10.9-x86_64-3.9/numpy/core/src
creating build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h
adding 'build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath/npy_math_complex.c
None - nothing done with h_files = ['build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
building library "npysort" sources
creating build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_sort.h
adding 'build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common' to include_dirs.
creating build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/timsort.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/heapsort.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/radixsort.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_partition.h
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/selection.c
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_binsearch.h
conv_template:> build/src.macosx-10.9-x86_64-3.9/numpy/core/src/npysort/binsearch.c
None - nothing done with h_files = ['build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.macosx-10.9-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
building extension "numpy.core._dummy" sources
Generating build/src.macosx-10.9-x86_64-3.9/numpy/core/include/numpy/config.h
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64 -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/xxx/miniconda3/envs/omni/include/python3.9 -c'
clang: _configtest.c
success!
removing: _configtest.c _configtest.o _configtest.o.d
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64 -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/xxx/miniconda3/envs/omni/include/python3.9 -c'
clang: _configtest.c
_configtest.c:1:10: fatal error: 'endian.h' file not found
#include <endian.h>
^~~~~~~~~~
1 error generated.
failure.
removing: _configtest.c _configtest.o
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64 -fPIC -O2 -isystem /Users/xxx/miniconda3/envs/omni/include -arch x86_64
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/xxx/miniconda3/envs/omni/include/python3.9 -c'
clang: _configtest.c
_configtest.c:1:10: fatal error: 'sys/endian.h' file not found
#include <sys/endian.h>
...
and the error log goes on for many pages and prohibits pasting here