deepdrive
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pyarrow breaks the install.py using python3.9
What should I do? Is there some timeline for a diff and patch?
root@77d2c138cf98:/home/shyamal/deepdrive# python3.9 -m pip install -r requirements.txt
Collecting scipy
Using cached scipy-1.5.4-cp39-cp39-manylinux1_x86_64.whl (25.8 MB)
Requirement already satisfied: numpy in /usr/local/lib/python3.9/dist-packages (from -r requirements.txt (line 2)) (1.19.4)
Collecting h5py
Using cached h5py-3.1.0-cp39-cp39-manylinux1_x86_64.whl (4.4 MB)
Collecting gym
Using cached gym-0.17.3.tar.gz (1.6 MB)
Collecting arrow
Using cached arrow-0.17.0-py2.py3-none-any.whl (50 kB)
Requirement already satisfied: pytest-xdist in /usr/local/lib/python3.9/dist-packages (from -r requirements.txt (line 6)) (2.1.0)
Collecting requests
Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting clint
Using cached clint-0.5.1.tar.gz (29 kB)
Requirement already satisfied: Pillow in /usr/lib/python3/dist-packages (from -r requirements.txt (line 9)) (3.1.2)
Collecting boto
Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting future
Using cached future-0.18.2.tar.gz (829 kB)
Collecting pyzmq
Using cached pyzmq-19.0.2-cp39-cp39-manylinux1_x86_64.whl (1.1 MB)
Collecting gputil
Using cached GPUtil-1.4.0.tar.gz (5.5 kB)
Collecting joblib
Using cached joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting cloudpickle
Using cached cloudpickle-1.6.0-py3-none-any.whl (23 kB)
Collecting pyarrow
Using cached pyarrow-1.0.1.tar.gz (1.3 MB)
Installing build dependencies ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.9 /usr/local/lib/python3.9/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-888juo_9/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'cython >= 0.29' 'numpy==1.14.5; python_version<'"'"'3.7'"'"'' 'numpy==1.16.0; python_version>='"'"'3.7'"'"'' setuptools setuptools_scm wheel
cwd: None
Complete output (710 lines):
Ignoring numpy: markers 'python_version < "3.7"' don't match your environment
Collecting cython>=0.29
Using cached Cython-0.29.21-cp39-cp39-manylinux1_x86_64.whl (1.9 MB)
Collecting numpy==1.16.0
Using cached numpy-1.16.0.zip (5.1 MB)
Collecting setuptools
Using cached setuptools-50.3.2-py3-none-any.whl (785 kB)
Collecting setuptools_scm
Using cached setuptools_scm-4.1.2-py2.py3-none-any.whl (27 kB)
Collecting wheel
Using cached wheel-0.35.1-py2.py3-none-any.whl (33 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: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/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 /tmp/pip-wheel-sl6959pr
cwd: /tmp/pip-install-ma35s7ou/numpy/
Complete output (336 lines):
Running from numpy source directory.
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/misc_util.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
return is_string(s) and ('*' in s or '?' is s)
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
blis_info:
customize UnixCCompiler
libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_info:
customize UnixCCompiler
libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_info:
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
blas_info:
customize UnixCCompiler
libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/bin/sh: 1: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_lapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_clapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
customize UnixCCompiler
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
/usr/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.linux-x86_64-3.9
creating build/src.linux-x86_64-3.9/numpy
creating build/src.linux-x86_64-3.9/numpy/distutils
building library "npymath" sources
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgfortran
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize NAGFCompiler
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PathScaleFCompiler
Could not locate executable pathf95
customize NAGFORCompiler
Could not locate executable nagfor
don't know how to compile Fortran code on platform 'posix'
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
int exp (void);
^
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
_configtest.o: In function `main':
/tmp/pip-install-ma35s7ou/numpy/_configtest.c:6: undefined reference to `exp'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o _configtest.o.d
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
int exp (void);
^
x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
creating build/src.linux-x86_64-3.9/numpy/core
creating build/src.linux-x86_64-3.9/numpy/core/src
creating build/src.linux-x86_64-3.9/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h
adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_complex.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
building library "npysort" sources
creating build/src.linux-x86_64-3.9/numpy/core/src/common
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h
adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
creating build/src.linux-x86_64-3.9/numpy/core/src/npysort
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/heapsort.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/selection.c
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h
conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/binsearch.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
building extension "numpy.core._dummy" sources
Generating build/src.linux-x86_64-3.9/numpy/core/include/numpy/config.h
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 415, in <module>
setup_package()
File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 407, in setup_package
setup(**metadata)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 179, in run
self.run_command('build')
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 423, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 47, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 279, in check_types
raise SystemError(
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
----------------------------------------
ERROR: Failed building wheel for numpy
Running setup.py clean for numpy
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
cwd: /tmp/pip-install-ma35s7ou/numpy
Complete output (10 lines):
Running from numpy source directory.
`setup.py clean` is not supported, use one of the following instead:
- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
files that aren't checked into the git repo)
Add `--force` to your command to use it anyway if you must (unsupported).
----------------------------------------
ERROR: Failed cleaning build dir for numpy
Failed to build numpy
Installing collected packages: cython, numpy, setuptools, setuptools-scm, wheel
Running setup.py install for numpy: started
Running setup.py install for numpy: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-40loq39b/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-888juo_9/overlay --compile --install-headers /tmp/pip-build-env-888juo_9/overlay/include/python3.9/numpy
cwd: /tmp/pip-install-ma35s7ou/numpy/
Complete output (327 lines):
Running from numpy source directory.
Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:
- `pip install .` (from a git repo or downloaded source
release)
- `pip install numpy` (last NumPy release on PyPi)
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
blis_info:
customize UnixCCompiler
libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_info:
customize UnixCCompiler
libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_info:
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
blas_info:
customize UnixCCompiler
libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/bin/sh: 1: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_lapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_clapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
customize UnixCCompiler
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running install
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
building library "npymath" sources
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgfortran
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize NAGFCompiler
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PathScaleFCompiler
Could not locate executable pathf95
customize NAGFORCompiler
Could not locate executable nagfor
don't know how to compile Fortran code on platform 'posix'
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
int exp (void);
^
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
_configtest.o: In function `main':
/tmp/pip-install-ma35s7ou/numpy/_configtest.c:6: undefined reference to `exp'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o _configtest.o.d
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
int exp (void);
^
x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
building library "npysort" sources
adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
building extension "numpy.core._dummy" sources
Generating build/src.linux-x86_64-3.9/numpy/core/include/numpy/config.h
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
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/usr/include/python3.9 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 415, in <module>
setup_package()
File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 407, in setup_package
setup(**metadata)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/install.py", line 62, in run
r = self.setuptools_run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run
return distutils_install.run(self)
File "/usr/lib/python3.9/distutils/command/install.py", line 590, in run
self.run_command('build')
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 423, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 47, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 279, in check_types
raise SystemError(
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-40loq39b/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-888juo_9/overlay --compile --install-headers /tmp/pip-build-env-888juo_9/overlay/include/python3.9/numpy Check the logs for full command output.
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.9 /usr/local/lib/python3.9/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-888juo_9/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'cython >= 0.29' 'numpy==1.14.5; python_version<'"'"'3.7'"'"'' 'numpy==1.16.0; python_version>='"'"'3.7'"'"'' setuptools setuptools_scm wheel Check the logs for full command output.
i have the same issue
I have the same issue with python 3.8
same here. does anyone have a fix for it?