Mail Archives: cygwin/2020/06/21/15:37:46
| X-Recipient: | archive-cygwin AT delorie DOT com
|
| X-Original-To: | cygwin AT cygwin DOT com
|
| Delivered-To: | cygwin AT cygwin DOT com
|
| DMARC-Filter: | OpenDMARC Filter v1.3.2 sourceware.org 22DA5388F042
|
| Authentication-Results: | sourceware.org; dmarc=none (p=none dis=none)
|
| header.from=SystematicSw.ab.ca
|
| Authentication-Results: | sourceware.org;
|
| spf=none smtp.mailfrom=brian DOT inglis AT systematicsw DOT ab DOT ca
|
| X-Authority-Analysis: | v=2.3 cv=ecemg4MH c=1 sm=1 tr=0
|
| a=kiZT5GMN3KAWqtYcXc+/4Q==:117 a=kiZT5GMN3KAWqtYcXc+/4Q==:17
|
| a=IkcTkHD0fZMA:10 a=FP58Ms26AAAA:8 a=ozQi6Qy7AAAA:8 a=8pif782wAAAA:8
|
| a=YfKmt1VHORM4D0PU1pgA:9 a=QEXdDO2ut3YA:10 a=5011TGWGUjXZ4oUQxJtK:22
|
| Subject: | Re: What's the official state of Python module scipy in Cygwin?
|
| To: | cygwin AT cygwin DOT com
|
| References: | <CAGUd5DX9ke=DTSbafeZFAmLAAHcrAtagM-se4EwYgOKKEK6qsQ AT mail DOT gmail DOT com>
|
| <86888556-a7c2-501f-c734-f0085ea6bdf5 AT gmail DOT com>
|
| <CAGUd5DUnQU3i2U9qnfa68ZhP6vXCUxyeFRVsHPaSOs-5UDj94w AT mail DOT gmail DOT com>
|
| From: | Brian Inglis <Brian DOT Inglis AT SystematicSw DOT ab DOT ca>
|
| Autocrypt: | addr=Brian DOT Inglis AT SystematicSw DOT ab DOT ca; prefer-encrypt=mutual;
|
| keydata=
|
| mDMEXopx8xYJKwYBBAHaRw8BAQdAnCK0qv/xwUCCZQoA9BHRYpstERrspfT0NkUWQVuoePa0
|
| LkJyaWFuIEluZ2xpcyA8QnJpYW4uSW5nbGlzQFN5c3RlbWF0aWNTdy5hYi5jYT6IlgQTFggA
|
| PhYhBMM5/lbU970GBS2bZB62lxu92I8YBQJeinHzAhsDBQkJZgGABQsJCAcCBhUKCQgLAgQW
|
| AgMBAh4BAheAAAoJEB62lxu92I8Y0ioBAI8xrggNxziAVmr+Xm6nnyjoujMqWcq3oEhlYGAO
|
| WacZAQDFtdDx2koSVSoOmfaOyRTbIWSf9/Cjai29060fsmdsDLg4BF6KcfMSCisGAQQBl1UB
|
| BQEBB0Awv8kHI2PaEgViDqzbnoe8B9KMHoBZLS92HdC7ZPh8HQMBCAeIfgQYFggAJhYhBMM5
|
| /lbU970GBS2bZB62lxu92I8YBQJeinHzAhsMBQkJZgGAAAoJEB62lxu92I8YZwUBAJw/74rF
|
| IyaSsGI7ewCdCy88Lce/kdwX7zGwid+f8NZ3AQC/ezTFFi5obXnyMxZJN464nPXiggtT9gN5
|
| RSyTY8X+AQ==
|
| Organization: | Systematic Software
|
| Message-ID: | <15e60aa4-000e-2d15-7704-186d594fbfd4@SystematicSw.ab.ca>
|
| Date: | Sun, 21 Jun 2020 13:36:55 -0600
|
| User-Agent: | Mozilla/5.0 (Windows NT 10.0; WOW64; rv:68.0) Gecko/20100101
|
| Thunderbird/68.9.0
|
| MIME-Version: | 1.0
|
| In-Reply-To: | <CAGUd5DUnQU3i2U9qnfa68ZhP6vXCUxyeFRVsHPaSOs-5UDj94w@mail.gmail.com>
|
| X-CMAE-Envelope: | MS4wfBBjT9DN0fMtf+4i9Bgvs4ilc/EN8khYoMFJI2r4KT1u1ju+aT6yf7kgfj/gCgo+zYZfO03FApSApC1EczshNlIWSaURl+S26pc8KOuJ010uwacp0E29
|
| zBNY7RI560SoeU/pohoIaHA0/0+YuFSHoVWYNTnwPNzW+KBQPwIvcGkaGvA2HCefrKMSsgEMtXrvMA==
|
| X-Spam-Status: | No, score=-9.3 required=5.0 tests=BAYES_00, BODY_8BITS,
|
| KAM_DMARC_STATUS, KAM_LAZY_DOMAIN_SECURITY, RCVD_IN_DNSWL_LOW,
|
| RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL, SPF_HELO_NONE, SPF_NONE,
|
| TXREP autolearn=no autolearn_force=no version=3.4.2
|
| X-Spam-Checker-Version: | SpamAssassin 3.4.2 (2018-09-13) on
|
| server2.sourceware.org
|
| X-BeenThere: | cygwin AT cygwin DOT com
|
| X-Mailman-Version: | 2.1.29
|
| List-Id: | General Cygwin discussions and problem reports <cygwin.cygwin.com>
|
| List-Unsubscribe: | <http://cygwin.com/mailman/options/cygwin>,
|
| <mailto:cygwin-request AT cygwin DOT com?subject=unsubscribe>
|
| List-Archive: | <https://cygwin.com/pipermail/cygwin/>
|
| List-Post: | <mailto:cygwin AT cygwin DOT com>
|
| List-Help: | <mailto:cygwin-request AT cygwin DOT com?subject=help>
|
| List-Subscribe: | <http://cygwin.com/mailman/listinfo/cygwin>,
|
| <mailto:cygwin-request AT cygwin DOT com?subject=subscribe>
|
| Reply-To: | cygwin AT cygwin DOT com
|
| Errors-To: | cygwin-bounces AT cygwin DOT com
|
| Sender: | "Cygwin" <cygwin-bounces AT cygwin DOT com>
|
| X-MIME-Autoconverted: | from base64 to 8bit by delorie.com id 05LJbRuX022455
|
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.]
--
Problem reports: https://cygwin.com/problems.html
FAQ: https://cygwin.com/faq/
Documentation: https://cygwin.com/docs.html
Unsubscribe info: https://cygwin.com/ml/#unsubscribe-simple
- Raw text -