On 2020-06-21 12:31, My Name via Cygwin wrote:
> (M.A., I've figured out how to reply to the Cygwin Mailing List on these.
> If you'd like me to remove your name from the list of addressees in my
> future emails, please let me know? I have not found comprehensive docs for
> this mailing-list software, so I'm clueless.)
>
> I was delighted when Numpy first showed up as an official Cygwin Package
> and am using Numpy in Python 3.7 in Cygwin now. I've realized that the
> latest Cygwin versions of Python (now 3.8) are often incomplete, but that's
> no problem for me. I'm also able to use Sympy in Cygwin by installing Sympy
> via Pip in python3.7 in Cygwin.
>
> Scipy includes functions outside Numpy and Sympy that would be useful to me
> at least, and I regularly rely on JupyterLab; so for those, I've been
> resorting to Windows 10 versions of Python3.
>
> I should have clarified in my original post in this thread, when I did
> happen to have success installing full Scipy in Cygwin, it was with this
> command:
>
> $ python3.7 -m pip install scipy
>
> When I did have that success installing Scipy in Cygwin, I later realized
> that whether Cygwin package gcc-fortran was installed locally made a
> difference. Without gcc-fortran installed locally, the pip command would
> fail to install Scipy. When I run that pip command now, I don't comprehend
> the output, but I recognize that the Scipy installation has failed, even
> though I do have Cygwin's gcc-fortran installed:
>
> ==================================
> $ python3.7 -m pip install scipy
> Collecting scipy
> Downloading scipy-1.5.0.tar.gz (25.6 MB)
> |████████████████████████████████| 25.6 MB 11.8 MB/s
> Installing build dependencies ... done
> Getting requirements to build wheel ... done
> Preparing wheel metadata ... error
> ERROR: Command errored out with exit status 1:
> command: /usr/bin/python3.7
> /usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py
> prepare_metadata_for_build_wheel /tmp/tmpc3ao3jht
> cwd: /tmp/pip-install-593dlngp/scipy
> Complete output (137 lines):
> lapack_opt_info:
> lapack_mkl_info:
> customize UnixCCompiler
> libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib',
> '/usr/lib/']
> NOT AVAILABLE
>
> openblas_lapack_info:
> customize UnixCCompiler
> customize UnixCCompiler
> libraries openblas not found in ['/usr/local/lib', '/usr/lib',
> '/usr/lib/']
> NOT AVAILABLE
>
> openblas_clapack_info:
> customize UnixCCompiler
> customize UnixCCompiler
> libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib',
> '/usr/lib/']
> NOT AVAILABLE
>
> atlas_3_10_threads_info:
> Setting PTATLAS=ATLAS
> customize UnixCCompiler
> libraries tatlas,tatlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries lapack_atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries tatlas,tatlas not found in /usr/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/
> <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
> NOT AVAILABLE
>
> atlas_3_10_info:
> customize UnixCCompiler
> libraries satlas,satlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries lapack_atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries satlas,satlas not found in /usr/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/
> <class 'numpy.distutils.system_info.atlas_3_10_info'>
> NOT AVAILABLE
>
> atlas_threads_info:
> Setting PTATLAS=ATLAS
> customize UnixCCompiler
> libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries lapack_atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries ptf77blas,ptcblas,atlas not found in /usr/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/
> <class 'numpy.distutils.system_info.atlas_threads_info'>
> NOT AVAILABLE
>
> atlas_info:
> customize UnixCCompiler
> libraries f77blas,cblas,atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries lapack_atlas not found in /usr/local/lib
> customize UnixCCompiler
> libraries f77blas,cblas,atlas not found in /usr/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/
> <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/']
> NOT AVAILABLE
>
> lapack_src_info:
> NOT AVAILABLE
>
> NOT AVAILABLE
>
> setup.py:462: UserWarning: Unrecognized setuptools command ('dist_info
> --egg-base /tmp/pip-modern-metadata-ib3nkeed'), proceeding with generating
> Cython sources and expanding templates
> ' '.join(sys.argv[1:])))
> Running from SciPy source directory.
>
> /tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
> 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()
>
> /tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
> 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()
>
> /tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624:
> 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()
> Traceback (most recent call last):
> File
> "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
> 280, in <module>
> main()
> File
> "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
> 263, in main
> json_out['return_val'] = hook(**hook_input['kwargs'])
> File
> "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line
> 133, in prepare_metadata_for_build_wheel
> return hook(metadata_directory, config_settings)
> File
> "/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
> line 157, in prepare_metadata_for_build_wheel
> self.run_setup()
> File
> "/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
> line 249, in run_setup
> self).run_setup(setup_script=setup_script)
> File
> "/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/setuptools/build_meta.py",
> line 142, in run_setup
> exec(compile(code, __file__, 'exec'), locals())
> File "setup.py", line 583, in <module>
> setup_package()
> File "setup.py", line 579, in setup_package
> setup(**metadata)
> File
> "/tmp/pip-build-env-znryb617/overlay/lib/python3.7/site-packages/numpy/distutils/core.py",
> line 135, in setup
> config = configuration()
> File "setup.py", line 477, in configuration
> raise NotFoundError(msg)
> numpy.distutils.system_info.NotFoundError: No lapack/blas resources
> found.
> ----------------------------------------
> ERROR: Command errored out with exit status 1: /usr/bin/python3.7
> /usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py
> prepare_metadata_for_build_wheel /tmp/tmpc3ao3jht Check the logs for full
> command output.
> Going by an old memory of mine, I recall that parts of Scipy rely on BLAS,
> https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms, and I read
> somewhere that that dependency adds to the difficulty of porting Scipy to
> new platforms.
Try installing or upgrading liblapack-devel liblapack-doc libopenblas
openblas-doc and see how far that gets you.
I remember coming across atlas elsewhere, but only know it provides some tuned
BLAS and LAPACK routines.
--
Take care. Thanks, Brian Inglis, Calgary, Alberta, Canada
This email may be disturbing to some readers as it contains
too much technical detail. Reader discretion is advised.
[Data in IEC units and prefixes, physical quantities in SI.]
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