Error in installing numpy
mitlearn opened this issue · comments
While trying install numpy via custom-cont.init.d script but failed. Then I tried install manually, it return msg
root@7536f3269223:/config# pip3 install numpy==1.19
Collecting numpy==1.19
Downloading numpy-1.19.0.zip (7.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 6.6 MB/s eta 0:00:00 Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [237 lines of output]
Running from numpy source directory.
setup.py:460: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
run_build = parse_setuppy_commands()
Cythonizing sources
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_mt19937.pyx
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/tools/cythonize.py:73: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
required_version = LooseVersion('0.29.14')
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(cython_version) < required_version:
Processing numpy/random/_generator.pyx
Processing numpy/random/_philox.pyx
Processing numpy/random/_bounded_integers.pyx.in
Processing numpy/random/_common.pyx
Processing numpy/random/_sfc64.pyx
Processing numpy/random/bit_generator.pyx
Processing numpy/random/_pcg64.pyx
Processing numpy/random/mtrand.pyx
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
blis_info:
libraries blis not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_info:
libraries satlas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/system_info.py:1914: UserWarning:
Optimized (vendor) Blas libraries are not found.
Falls back to netlib Blas library which has worse performance.
A better performance should be easily gained by switching
Blas library.
if self._calc_info(blas):
blas_info:
libraries blas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/system_info.py:1914: 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.
if self._calc_info(blas):
blas_src_info:
NOT AVAILABLE
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/system_info.py:1914: 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.
if self._calc_info(blas):
NOT AVAILABLE
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_clapack_info:
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
flame_info:
libraries flame not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib']
NOT AVAILABLE
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/system_info.py:1748: 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.
return getattr(self, '_calc_info_{}'.format(name))()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/system_info.py:1748: 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.
return getattr(self, '_calc_info_{}'.format(name))()
NOT AVAILABLE
numpy_linalg_lapack_lite:
FOUND:
language = c
define_macros = [('HAVE_BLAS_ILP64', None), ('BLAS_SYMBOL_SUFFIX', '64_')]
/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py:275: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running dist_info
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
Could not locate executable gfortran
Could not locate executable f95
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable lf95
Could not locate executable pgfortran
Could not locate executable f90
Could not locate executable f77
Could not locate executable fort
Could not locate executable efort
Could not locate executable efc
Could not locate executable g77
Could not locate executable g95
Could not locate executable pathf95
Could not locate executable nagfor
don't know how to compile Fortran code on platform 'posix'
Traceback (most recent call last):
File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 188, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 281, in run_setup
super(_BuildMetaLegacyBackend,
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 174, in run_setup
exec(compile(code, file, 'exec'), locals())
File "setup.py", line 489, in <module>
setup_package()
File "setup.py", line 481, in setup_package
setup(**metadata)
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1229, in run_command
super().run_command(command)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 35, in run
egg_info.run()
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/command/egg_info.py", line 24, in run
self.run_command("build_src")
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1229, in run_command
super().run_command(command)
File "/tmp/pip-build-env-7sgmtvhm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/command/build_src.py", line 144, in run
self.build_sources()
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/command/build_src.py", line 155, in build_sources
self.build_library_sources(*libname_info)
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/command/build_src.py", line 288, in build_library_sources
sources = self.generate_sources(sources, (lib_name, build_info))
File "/tmp/pip-install-8m_yt9m7/numpy_9a517ae298db4061840b5b16a4cae074/numpy/distutils/command/build_src.py", line 378, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 655, in get_mathlib_info
raise RuntimeError("Broken toolchain: cannot link a simple C program")
RuntimeError: Broken toolchain: cannot link a simple C program
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
It seems to required gcc dependency, so if possible pre-compile&install numpy while building docker, it would be solved.
Thanks in advanced.
Solved after apk add build-base python3-dev manually