* What's the official state of Python module scipy in Cygwin? @ 2020-06-21 13:03 My Name 2020-06-21 17:51 ` Marco Atzeri 0 siblings, 1 reply; 11+ messages in thread From: My Name @ 2020-06-21 13:03 UTC (permalink / raw) To: cygwin IIRC, at one point I was able to use scipy in Cygwin, after a period of failed attempts. I believe that having installed gcc-fortran might have been part of the solution I stumbled upon. But now I'm back to being unable to install scipy in Cygwin. Is it supported officially? Or unsupported but sometimes possible? Thank you. ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 13:03 What's the official state of Python module scipy in Cygwin? My Name @ 2020-06-21 17:51 ` Marco Atzeri 2020-06-21 18:31 ` My Name 0 siblings, 1 reply; 11+ messages in thread From: Marco Atzeri @ 2020-06-21 17:51 UTC (permalink / raw) To: cygwin On 21.06.2020 15:03, My Name via Cygwin wrote: > IIRC, at one point I was able to use scipy in Cygwin, after a period of > failed attempts. I believe that having installed gcc-fortran might have > been part of the solution I stumbled upon. > > But now I'm back to being unable to install scipy in Cygwin. Is it > supported officially? Or unsupported but sometimes possible? > > Thank you. > -- partially supported ? pythonXX-numpy is available, except the 3.8 version for the time being as all the 3.8 packages are under deployment. All the rest is not, as no one has spent time to package them. What is the problem and on which package ? Regards Marco ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 17:51 ` Marco Atzeri @ 2020-06-21 18:31 ` My Name 2020-06-21 19:36 ` Brian Inglis 2020-06-21 19:40 ` Eliot Moss 0 siblings, 2 replies; 11+ messages in thread From: My Name @ 2020-06-21 18:31 UTC (permalink / raw) To: Marco Atzeri; +Cc: The Cygwin Mailing List (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. On Sun, Jun 21, 2020 at 10:52 AM Marco Atzeri via Cygwin <cygwin@cygwin.com> wrote: > On 21.06.2020 15:03, My Name via Cygwin wrote: > > IIRC, at one point I was able to use scipy in Cygwin, after a period of > > failed attempts. I believe that having installed gcc-fortran might have > > been part of the solution I stumbled upon. > > > > But now I'm back to being unable to install scipy in Cygwin. Is it > > supported officially? Or unsupported but sometimes possible? > > > > Thank you. > > -- > > > partially supported ? > > pythonXX-numpy is available, except the 3.8 version for the > time being as all the 3.8 packages are under deployment. > > All the rest is not, as no one has spent time to package them. > > What is the problem and on which package ? > > Regards > Marco > > > > -- > 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 > ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 18:31 ` My Name @ 2020-06-21 19:36 ` Brian Inglis 2020-06-21 19:47 ` Marco Atzeri 2020-06-21 23:28 ` My Name 2020-06-21 19:40 ` Eliot Moss 1 sibling, 2 replies; 11+ messages in thread From: Brian Inglis @ 2020-06-21 19:36 UTC (permalink / raw) To: cygwin 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.] ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 19:36 ` Brian Inglis @ 2020-06-21 19:47 ` Marco Atzeri 2020-06-21 22:47 ` My Name 2020-06-21 23:28 ` My Name 1 sibling, 1 reply; 11+ messages in thread From: Marco Atzeri @ 2020-06-21 19:47 UTC (permalink / raw) To: cygwin On 21.06.2020 21:36, Brian Inglis wrote: > 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.) >> > >> 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. > if Scipy requires just a BLAS, liblapack-devel should be enough for the compilation. libopenblas for compatibility reason provides only the shared library but I am not packing the headers. It helps to run faster any BLAS routine used by programs. ATLAS takes too long to compile and it does NOT provides multiprocessor libraries as OpenBlas. So no interest to package it for Cygwin from my side. Regards Marco ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 19:47 ` Marco Atzeri @ 2020-06-21 22:47 ` My Name 0 siblings, 0 replies; 11+ messages in thread From: My Name @ 2020-06-21 22:47 UTC (permalink / raw) To: Marco Atzeri; +Cc: The Cygwin Mailing List M.A., I tried your recipe first, because it involved the fewest packages, but it did not work for me. After installing cygwin64 as best I could, I executed this Windows batch file: ============================= setup-x86_64.exe -P liblapack-devel,gcc-core,gcc-fortran,python27,python37,python37-pip,python37-numpy,bzr,emacs-w32,aspell,aspell-en,octave ============================= That worked, except for an error message I often get at the end of installation, something about fonts I believe, though I failed to note the exact message. Then I did: ============================= $ python3.7 -m pip install scipy Collecting scipy Using cached scipy-1.5.0.tar.gz (25.6 MB) Installing build dependencies ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-m8_ieab2/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.18' 'numpy==1.14.5; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' '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'"'"'' 'pybind11>=2.4.3' cwd: None Complete output (351 lines): Ignoring numpy: markers 'python_version == "3.6" 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 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 wheel Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB) Collecting setuptools Using cached setuptools-47.3.1-py3-none-any.whl (582 kB) Collecting Cython>=0.29.18 Using cached Cython-0.29.20-py2.py3-none-any.whl (973 kB) Collecting numpy==1.14.5 Using cached numpy-1.14.5.zip (4.9 MB) Collecting pybind11>=2.4.3 Using cached pybind11-2.5.0-py2.py3-none-any.whl (296 kB) Using legacy setup.py install for numpy, since package 'wheel' is not installed. Installing collected packages: wheel, setuptools, Cython, numpy, pybind11 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/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-8tdeenwm/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-8tdeenwm/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-5f417uh8/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-m8_ieab2/overlay --compile --install-headers /tmp/pip-build-env-m8_ieab2/overlay/include/python3.7m/numpy cwd: /tmp/pip-install-8tdeenwm/numpy/ Complete output (326 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) blas_opt_info: blas_mkl_info: customize UnixCCompiler libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE blis_info: customize UnixCCompiler libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE openblas_info: customize UnixCCompiler customize UnixCCompiler libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] 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/'] NOT AVAILABLE atlas_3_10_blas_info: customize UnixCCompiler libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] 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/'] NOT AVAILABLE atlas_blas_info: customize UnixCCompiler libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE /tmp/pip-install-8tdeenwm/numpy/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() blas_info: customize UnixCCompiler customize UnixCCompiler C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 creating /tmp/tmpmrhhvsma/tmp creating /tmp/tmpmrhhvsma/tmp/tmpmrhhvsma compile options: '-I/usr/include -c' gcc: /tmp/tmpmrhhvsma/source.c gcc /tmp/tmpmrhhvsma/tmp/tmpmrhhvsma/source.o -L/usr/lib -lcblas -o /tmp/tmpmrhhvsma/a.out.exe /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status gcc /tmp/tmpmrhhvsma/tmp/tmpmrhhvsma/source.o -L/usr/lib -lblas -o /tmp/tmpmrhhvsma/a.out.exe customize UnixCCompiler FOUND: libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c define_macros = [('HAVE_CBLAS', None)] FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c /bin/sh: svnversion: command not found non-existing path in 'numpy/distutils': 'site.cfg' /bin/sh: svnversion: command not found F2PY Version 2 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 customize UnixCCompiler FOUND: libraries = ['lapack', 'lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = ['lapack', 'lapack', 'blas', 'blas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include'] /usr/lib/python3.7/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 creating build creating build/src.cygwin-3.1.5-x86_64-3.7 creating build/src.cygwin-3.1.5-x86_64-3.7/numpy creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/distutils building library "npymath" sources get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95']' customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize IntelVisualFCompiler Could not locate executable ifort Could not locate executable ifl customize AbsoftFCompiler Could not locate executable f90 customize CompaqVisualFCompiler Found executable /usr/bin/DF customize IntelItaniumVisualFCompiler Could not locate executable efl customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c gcc _configtest.o -o _configtest.exe success! removing: _configtest.c _configtest.o _configtest.exe C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch] 1 | int exp (void); | ^~~ _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’ +++ |+#include <math.h> 1 | int exp (void); gcc _configtest.o -o _configtest.exe success! removing: _configtest.c _configtest.o _configtest.exe creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath' to include_dirs. conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/ieee754.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h'] building library "npysort" sources creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/quicksort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/mergesort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/heapsort.c creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_partition.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private' to include_dirs. conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/selection.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_binsearch.h conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/binsearch.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_partition.h', 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_binsearch.h'] building extension "numpy.core._dummy" sources Generating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/include/numpy/config.h C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c _configtest.c:1:10: fatal error: Python.h: No such file or directory 1 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. _configtest.c:1:10: fatal error: Python.h: No such file or directory 1 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-8tdeenwm/numpy/setup.py", line 394, in <module> setup_package() File "/tmp/pip-install-8tdeenwm/numpy/setup.py", line 386, in setup_package setup(**metadata) File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/core.py", line 169, in setup return old_setup(**new_attr) File "/usr/lib/python3.7/site-packages/setuptools/__init__.py", line 144, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/install.py", line 62, in run r = self.setuptools_run() File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run return distutils_install.run(self) File "/usr/lib/python3.7/distutils/command/install.py", line 545, in run self.run_command('build') File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/build.py", line 47, in run old_build.run(self) File "/usr/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/build_src.py", line 148, in run self.build_sources() File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources self.build_extension_sources(ext) File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/build_src.py", line 324, in build_extension_sources sources = self.generate_sources(sources, ext) File "/tmp/pip-install-8tdeenwm/numpy/numpy/distutils/command/build_src.py", line 377, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 422, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 48, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 281, in check_types "install {0}-dev|{0}-devel.".format(python)) SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-8tdeenwm/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-8tdeenwm/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-5f417uh8/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-m8_ieab2/overlay --compile --install-headers /tmp/pip-build-env-m8_ieab2/overlay/include/python3.7m/numpy Check the logs for full command output. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-m8_ieab2/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.18' 'numpy==1.14.5; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' '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'"'"'' 'pybind11>=2.4.3' Check the logs for full command output. $ ============================= Next, as an experiment, I've tried something else that didn't work: ============================= $ python3.7 -m pip install -U numpy Collecting numpy Using cached numpy-1.19.0.zip (7.3 MB) 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/tmpz6kfi_qg cwd: /tmp/pip-install-r_cig5d6/numpy Complete output (245 lines): Processing numpy/random/_bounded_integers.pxd.in Processing numpy/random/bit_generator.pyx Processing numpy/random/mtrand.pyx Processing numpy/random/_bounded_integers.pyx.in Processing numpy/random/_common.pyx Processing numpy/random/_generator.pyx Processing numpy/random/_mt19937.pyx Processing numpy/random/_pcg64.pyx Processing numpy/random/_philox.pyx Processing numpy/random/_sfc64.pyx Cythonizing sources blas_opt_info: blas_mkl_info: customize UnixCCompiler libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE blis_info: libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE openblas_info: libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE atlas_3_10_blas_threads_info: Setting PTATLAS=ATLAS libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE atlas_3_10_blas_info: libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE accelerate_info: NOT AVAILABLE blas_info: C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 creating /tmp/tmp739jv32g/tmp creating /tmp/tmp739jv32g/tmp/tmp739jv32g compile options: '-I/usr/include -c' gcc: /tmp/tmp739jv32g/source.c gcc /tmp/tmp739jv32g/tmp/tmp739jv32g/source.o -L/usr/lib -lblas -o /tmp/tmp739jv32g/a.out.exe FOUND: libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c define_macros = [('HAVE_CBLAS', None)] FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c 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', '/usr/lib/'] NOT AVAILABLE openblas_lapack_info: libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE openblas_clapack_info: libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE flame_info: libraries flame not found in ['/usr/local/lib', '/usr/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 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 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 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 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: FOUND: libraries = ['lapack', 'lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['lapack', 'lapack', 'blas', 'blas'] library_dirs = ['/usr/lib'] language = c define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] include_dirs = ['/usr/include'] running dist_info running build_src build_src building py_modules sources creating build creating build/src.cygwin-3.1.5-x86_64-3.7 creating build/src.cygwin-3.1.5-x86_64-3.7/numpy creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/distutils building library "npymath" sources Could not locate executable g77 Could not locate executable f77 Could not locate executable ifort Could not locate executable ifl Could not locate executable f90 Could not locate executable efl creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath' to include_dirs. conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/ieee754.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h'] building library "npysort" sources creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_sort.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common' to include_dirs. creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/quicksort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/mergesort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/timsort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/heapsort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/radixsort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_partition.h conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/selection.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_binsearch.h conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/binsearch.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_sort.h', 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_partition.h', 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/common/npy_binsearch.h'] building library "npyrandom" sources building extension "numpy.core._multiarray_tests" sources creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/multiarray conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/multiarray/_multiarray_tests.c building extension "numpy.core._multiarray_umath" sources 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() /tmp/pip-install-r_cig5d6/numpy/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): /usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) 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-mh_sorol/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-mh_sorol/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-mh_sorol/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 489, in <module> setup_package() File "setup.py", line 481, in setup_package setup(**metadata) File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/core.py", line 169, in setup return old_setup(**new_attr) File "/tmp/pip-build-env-mh_sorol/overlay/lib/python3.7/site-packages/setuptools/__init__.py", line 161, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-build-env-mh_sorol/overlay/lib/python3.7/site-packages/setuptools/command/dist_info.py", line 31, in run egg_info.run() File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/command/egg_info.py", line 24, in run self.run_command("build_src") File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/command/build_src.py", line 144, in run self.build_sources() File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/command/build_src.py", line 161, in build_sources self.build_extension_sources(ext) File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/command/build_src.py", line 318, in build_extension_sources sources = self.generate_sources(sources, ext) File "/tmp/pip-install-r_cig5d6/numpy/numpy/distutils/command/build_src.py", line 378, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 428, 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 286, in check_types "install {0}-dev|{0}-devel.".format(python)) SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpz6kfi_qg Check the logs for full command output. $ ============================= And finally: ============================= $ python3.7 -m pip install -U liblapack-devel ERROR: Could not find a version that satisfies the requirement liblapack-devel (from versions: none) ERROR: No matching distribution found for liblapack-devel $ ============================= Next I'll try the longer recipes recommended in this thread. Best regards On Sun, Jun 21, 2020 at 12:47 PM Marco Atzeri via Cygwin <cygwin@cygwin.com> wrote: > On 21.06.2020 21:36, Brian Inglis wrote: > > 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.) > >> > > > > >> 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. > > > > if Scipy requires just a BLAS, liblapack-devel should be enough for > the compilation. > > libopenblas for compatibility reason provides only the shared library > but I am not packing the headers. It helps to run faster any BLAS > routine used by programs. > > ATLAS takes too long to compile and it does NOT provides multiprocessor > libraries as OpenBlas. So no interest to package it for Cygwin from > my side. > > > Regards > Marco > > > -- > 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 > ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 19:36 ` Brian Inglis 2020-06-21 19:47 ` Marco Atzeri @ 2020-06-21 23:28 ` My Name 1 sibling, 0 replies; 11+ messages in thread From: My Name @ 2020-06-21 23:28 UTC (permalink / raw) To: The Cygwin Mailing List B.I., thank you, but your recipe did not work for me: ================== $ python3.7 -m pip install scipy Collecting scipy Using cached scipy-1.5.0.tar.gz (25.6 MB) Installing build dependencies ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-u0tmgezi/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.18' 'numpy==1.14.5; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' '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'"'"'' 'pybind11>=2.4.3' cwd: None Complete output (351 lines): Ignoring numpy: markers 'python_version == "3.6" 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 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 wheel Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB) Collecting setuptools Using cached setuptools-47.3.1-py3-none-any.whl (582 kB) Collecting Cython>=0.29.18 Using cached Cython-0.29.20-py2.py3-none-any.whl (973 kB) Collecting numpy==1.14.5 Using cached numpy-1.14.5.zip (4.9 MB) Collecting pybind11>=2.4.3 Using cached pybind11-2.5.0-py2.py3-none-any.whl (296 kB) Using legacy setup.py install for numpy, since package 'wheel' is not installed. Installing collected packages: wheel, setuptools, Cython, numpy, pybind11 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/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wizs3z2z/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-wizs3z2z/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-qmbtrkjp/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-u0tmgezi/overlay --compile --install-headers /tmp/pip-build-env-u0tmgezi/overlay/include/python3.7m/numpy cwd: /tmp/pip-install-wizs3z2z/numpy/ Complete output (326 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) blas_opt_info: blas_mkl_info: customize UnixCCompiler libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE blis_info: customize UnixCCompiler libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE openblas_info: customize UnixCCompiler customize UnixCCompiler libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] 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/'] NOT AVAILABLE atlas_3_10_blas_info: customize UnixCCompiler libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] 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/'] NOT AVAILABLE atlas_blas_info: customize UnixCCompiler libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/'] NOT AVAILABLE /tmp/pip-install-wizs3z2z/numpy/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() blas_info: customize UnixCCompiler customize UnixCCompiler C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 creating /tmp/tmploe9v3xi/tmp creating /tmp/tmploe9v3xi/tmp/tmploe9v3xi compile options: '-I/usr/include -c' gcc: /tmp/tmploe9v3xi/source.c gcc /tmp/tmploe9v3xi/tmp/tmploe9v3xi/source.o -L/usr/lib -lcblas -o /tmp/tmploe9v3xi/a.out.exe /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status gcc /tmp/tmploe9v3xi/tmp/tmploe9v3xi/source.o -L/usr/lib -lblas -o /tmp/tmploe9v3xi/a.out.exe customize UnixCCompiler FOUND: libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c define_macros = [('HAVE_CBLAS', None)] FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = ['blas', 'blas'] library_dirs = ['/usr/lib'] include_dirs = ['/usr/include'] language = c /bin/sh: svnversion: command not found non-existing path in 'numpy/distutils': 'site.cfg' /bin/sh: svnversion: command not found F2PY Version 2 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 customize UnixCCompiler FOUND: libraries = ['lapack', 'lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = ['lapack', 'lapack', 'blas', 'blas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include'] /usr/lib/python3.7/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 creating build creating build/src.cygwin-3.1.5-x86_64-3.7 creating build/src.cygwin-3.1.5-x86_64-3.7/numpy creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/distutils building library "npymath" sources get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95']' customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize IntelVisualFCompiler Could not locate executable ifort Could not locate executable ifl customize AbsoftFCompiler Could not locate executable f90 customize CompaqVisualFCompiler Found executable /usr/bin/DF customize IntelItaniumVisualFCompiler Could not locate executable efl customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c gcc _configtest.o -o _configtest.exe success! removing: _configtest.c _configtest.o _configtest.exe C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch] 1 | int exp (void); | ^~~ _configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’ +++ |+#include <math.h> 1 | int exp (void); gcc _configtest.o -o _configtest.exe success! removing: _configtest.c _configtest.o _configtest.exe creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath' to include_dirs. conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/ieee754.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npymath/npy_math_internal.h'] building library "npysort" sources creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/quicksort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/mergesort.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/heapsort.c creating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_partition.h adding 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private' to include_dirs. conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/selection.c conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_binsearch.h conv_template:> build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/npysort/binsearch.c None - nothing done with h_files = ['build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_partition.h', 'build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/src/private/npy_binsearch.h'] building extension "numpy.core._dummy" sources Generating build/src.cygwin-3.1.5-x86_64-3.7/numpy/core/include/numpy/config.h C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/build=/usr/src/debug/python37-3.7.7-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/python/python37/python37-3.7.7-1.x86_64/src/Python-3.7.7=/usr/src/debug/python37-3.7.7-1 compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.7m -c' gcc: _configtest.c _configtest.c:1:10: fatal error: Python.h: No such file or directory 1 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. _configtest.c:1:10: fatal error: Python.h: No such file or directory 1 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-wizs3z2z/numpy/setup.py", line 394, in <module> setup_package() File "/tmp/pip-install-wizs3z2z/numpy/setup.py", line 386, in setup_package setup(**metadata) File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/core.py", line 169, in setup return old_setup(**new_attr) File "/usr/lib/python3.7/site-packages/setuptools/__init__.py", line 144, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/install.py", line 62, in run r = self.setuptools_run() File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run return distutils_install.run(self) File "/usr/lib/python3.7/distutils/command/install.py", line 545, in run self.run_command('build') File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/build.py", line 47, in run old_build.run(self) File "/usr/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/build_src.py", line 148, in run self.build_sources() File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources self.build_extension_sources(ext) File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/build_src.py", line 324, in build_extension_sources sources = self.generate_sources(sources, ext) File "/tmp/pip-install-wizs3z2z/numpy/numpy/distutils/command/build_src.py", line 377, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 422, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 48, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 281, in check_types "install {0}-dev|{0}-devel.".format(python)) SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wizs3z2z/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-wizs3z2z/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-qmbtrkjp/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-u0tmgezi/overlay --compile --install-headers /tmp/pip-build-env-u0tmgezi/overlay/include/python3.7m/numpy Check the logs for full command output. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-u0tmgezi/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.18' 'numpy==1.14.5; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' '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'"'"'' 'pybind11>=2.4.3' Check the logs for full command output. $ ================== On Sun, Jun 21, 2020 at 12:37 PM Brian Inglis < Brian.Inglis@systematicsw.ab.ca> wrote: > 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 > ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 18:31 ` My Name 2020-06-21 19:36 ` Brian Inglis @ 2020-06-21 19:40 ` Eliot Moss 2020-06-21 21:09 ` Marco Atzeri 2020-06-21 23:16 ` My Name 1 sibling, 2 replies; 11+ messages in thread From: Eliot Moss @ 2020-06-21 19:40 UTC (permalink / raw) Cc: The Cygwin Mailing List You need to install openblas (and lapack, if openblas does not install it). You also need gcc, g++, and gfortran for building various components, and the suitable python-devel and python-pip packages. I further have the suitable python tkinter, six, and wheel packages installed from cygwin. I am finding that building scipy takes quite a while (a lot of long C and Fortran optimizing compilations). Above, when I say "suitable", I mean python37 (or whatever). scipy built for me under 3.7 just now, and I am starting a 3.8 build, which will require a local build of numpy, I believe, tediously longer :-) ... Regards - Eliot Moss ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 19:40 ` Eliot Moss @ 2020-06-21 21:09 ` Marco Atzeri 2020-06-21 23:16 ` My Name 1 sibling, 0 replies; 11+ messages in thread From: Marco Atzeri @ 2020-06-21 21:09 UTC (permalink / raw) To: cygwin On 21.06.2020 21:40, Eliot Moss wrote: > You need to install openblas (and lapack, if openblas does not install it). > > You also need gcc, g++, and gfortran for building various components, and > the suitable python-devel and python-pip packages. I further have the > suitable python tkinter, six, and wheel packages installed from cygwin. > > I am finding that building scipy takes quite a while (a lot of long > C and Fortran optimizing compilations). > > Above, when I say "suitable", I mean python37 (or whatever). scipy > built for me under 3.7 just now, and I am starting a 3.8 build, which > will require a local build of numpy, I believe, tediously longer :-) ... > > Regards - Eliot Moss Hi Elliot, in which order scipy builds the subpackages ? And how long takes the build of numpy ? Regards Marco ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 19:40 ` Eliot Moss 2020-06-21 21:09 ` Marco Atzeri @ 2020-06-21 23:16 ` My Name 2020-06-22 2:38 ` My Name 1 sibling, 1 reply; 11+ messages in thread From: My Name @ 2020-06-21 23:16 UTC (permalink / raw) To: moss; +Cc: The Cygwin Mailing List E.M., Can you please clarify several points you make? - In the Cygwin installer, I find no "lapack", but searching the installer for that term does return "liblapack". Would that Cygwin package suffice? If not, how would you suggest I install it? - In the Cygwin installer, I find no "openblas", but searching the installer for that term does return "libopenblas" (and the Cygwin installer tells me I already have v 0.3.9-1 installed). Does that suffice? - In the Cygwin installer, I find no "gcc", "g++", or "gfortran", but searching the installer for those terms does return "gcc-core", "gcc-g++", "libgfortran4", and "libgfortran5". Can you please tell me the exact spellings of the packages that worked for you? I lack the background to interpret your informal descriptions. - In the Cygwin installer, I find Packages with names of the form "python37-" followed respectively by "tkinter", "six", and "wheel", and I'm pretty confident that the long names I've found are what you're describing. Are you saying that these three are necessary for installing scipy, or that they're possibly necessary, and you're not sure? Since you had recent success installing scipy, I'd like to try your recipe, but could use exact spellings if you have time. Thank you. On Sun, Jun 21, 2020 at 12:40 PM Eliot Moss <moss@cs.umass.edu> wrote: > You need to install openblas (and lapack, if openblas does not install it). > > You also need gcc, g++, and gfortran for building various components, and > the suitable python-devel and python-pip packages. I further have the > suitable python tkinter, six, and wheel packages installed from cygwin. > > I am finding that building scipy takes quite a while (a lot of long > C and Fortran optimizing compilations). > > Above, when I say "suitable", I mean python37 (or whatever). scipy > built for me under 3.7 just now, and I am starting a 3.8 build, which > will require a local build of numpy, I believe, tediously longer :-) ... > > Regards - Eliot Moss > -- > 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 > ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: What's the official state of Python module scipy in Cygwin? 2020-06-21 23:16 ` My Name @ 2020-06-22 2:38 ` My Name 0 siblings, 0 replies; 11+ messages in thread From: My Name @ 2020-06-22 2:38 UTC (permalink / raw) To: moss; +Cc: The Cygwin Mailing List E.M., Your recipe has worked for me. I've successfully installed scipy per your instructions. Thanks for your time and patience. I have wanted to use scipy in Cygwin for three or four years, but had not asked here until yesterday. Please don't apologize for abbreviating the package names at first. I imagine everyone else reading knew exactly which packages you meant; but despite relying on Cygwin for some basic things, my Cygwin expertise is just novice. I work on my own development projects full-time, but haven't been at a university or worked in a development team for thirty years; haven't used gcc for three years and don't remember its details. My Cygwin Setup which allowed me to install scipy was this: ========================= setup-x86_64.exe -P libopenblas,openblas-doc,liblapack-devel,liblapack-doc,gcc-core,gcc-g++,gcc-fortran,libgfortran4,libgfortran5,python27,python37,python37-devel,python37-pip,python37-tkinter,python37-six,python37-wheel,python37-numpy,bzr,emacs-w32,aspell,aspell-en,octave ========================= I surely did some overkill with the three fortran packages, not knowing which was meant by "gfortran", but it didn't hurt anything. > Maybe I missed it, but I don't see anything indicating that you have installed openblas or lapack Before trying your relatively complex recipe, I tried MA and BI's simpler recipes. First I tried MA's recipe, so I installed lapack but not libopenblas. Next I tried BI's recipe, so I installed them both, but still could not install scipy. Then, while preparing my batch file for your recipe, I noticed I'd been installing python37 but not python37-devel previously while trying MA and BI's recipes. That omission was accidental not deliberate, and for all I know now, their solutions might have worked if I'd installed python37-devel at the time. I'm plenty satisfied with python3.7, but good luck with python3.8 / scipy. Considering the power of scipy and (I'm guessing) its popularity, and considering that the solution required nothing more than installing the necessary packages via Cygwin Setup and then pip scipy, I respectfully propose that the solution be included somewhere in the Cygwin documentation or FAQ, even without scipy as an official Cygwin package. Thanks to everyone in this thread for helping me. Best regards On Sun, Jun 21, 2020 at 4:16 PM My Name <mname989@gmail.com> wrote: > E.M., > > Can you please clarify several points you make? > > - In the Cygwin installer, I find no "lapack", but searching the installer > for that term does return "liblapack". Would that Cygwin package suffice? > If not, how would you suggest I install it? > > - In the Cygwin installer, I find no "openblas", but searching the > installer for that term does return "libopenblas" (and the Cygwin installer > tells me I already have v 0.3.9-1 installed). Does that suffice? > > - In the Cygwin installer, I find no "gcc", "g++", or "gfortran", but > searching the installer for those terms does return "gcc-core", "gcc-g++", > "libgfortran4", and "libgfortran5". Can you please tell me the exact > spellings of the packages that worked for you? I lack the background to > interpret your informal descriptions. > > - In the Cygwin installer, I find Packages with names of the form > "python37-" followed respectively by "tkinter", "six", and "wheel", and I'm > pretty confident that the long names I've found are what you're describing. > Are you saying that these three are necessary for installing scipy, or that > they're possibly necessary, and you're not sure? > > Since you had recent success installing scipy, I'd like to try your > recipe, but could use exact spellings if you have time. Thank you. > > > On Sun, Jun 21, 2020 at 12:40 PM Eliot Moss <moss@cs.umass.edu> wrote: > >> You need to install openblas (and lapack, if openblas does not install >> it). >> >> You also need gcc, g++, and gfortran for building various components, and >> the suitable python-devel and python-pip packages. I further have the >> suitable python tkinter, six, and wheel packages installed from cygwin. >> >> I am finding that building scipy takes quite a while (a lot of long >> C and Fortran optimizing compilations). >> >> Above, when I say "suitable", I mean python37 (or whatever). scipy >> built for me under 3.7 just now, and I am starting a 3.8 build, which >> will require a local build of numpy, I believe, tediously longer :-) ... >> >> Regards - Eliot Moss >> -- >> 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 >> > ^ permalink raw reply [flat|nested] 11+ messages in thread
end of thread, other threads:[~2020-06-22 2:39 UTC | newest] Thread overview: 11+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2020-06-21 13:03 What's the official state of Python module scipy in Cygwin? My Name 2020-06-21 17:51 ` Marco Atzeri 2020-06-21 18:31 ` My Name 2020-06-21 19:36 ` Brian Inglis 2020-06-21 19:47 ` Marco Atzeri 2020-06-21 22:47 ` My Name 2020-06-21 23:28 ` My Name 2020-06-21 19:40 ` Eliot Moss 2020-06-21 21:09 ` Marco Atzeri 2020-06-21 23:16 ` My Name 2020-06-22 2:38 ` My Name
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