What's the official state of Python module scipy in Cygwin?
My Name
mname989@gmail.com
Sun Jun 21 22:47:13 GMT 2020
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/
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>
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