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Numpy 1.12.1 setup issue (targetting Python 3.6.1) from Cygwin 2.8.0




Not possible to setup Numpy 1.12.1 from Cygwin:

pip3 install numpy

Collecting numpy
Using cached numpy-1.12.1.zip
Building wheels for collected packages: numpy
Running setup.py bdist_wheel for numpy ... error
Complete output from command /usr/bin/python3 -u -c "import setuptools,
tokenize;file='/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/setup.py';f=getattr(tokenize,
'open', open)(file);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d
/.gfmwk_tmp_120417204610_19564/spectools/tmpdbmu4l3rpip-wheel- --python-tag
cp36:
Running from numpy source directory.
blas_opt_info:
blas_mkl_info:
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

/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/system_info.py:572:
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:
libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE

/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/system_info.py:572:
UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE

/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/system_info.py:572:
UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE

non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
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

atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/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/
libraries lapack_atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE

atlas_3_10_info:
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/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/
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
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/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/
libraries lapack_atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE

atlas_info:
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/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/
libraries lapack_atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE

lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE

/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/system_info.py:572:
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()
lapack_src_info:
NOT AVAILABLE

/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/system_info.py:572:
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()
NOT AVAILABLE

/usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution
option: 'define_macros'
warnings.warn(msg)
running bdist_wheel
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-2.8.0-x86_64-3.6
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/distutils
building library "npymath" sources
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 /cygdrive/d/GFMWK_NEXT/base/cygwin/bin/DF
customize IntelItaniumVisualFCompiler
Could not locate executable efl
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize G95FCompiler
Could not locate executable g95
don't know how to compile Fortran code on platform 'posix'
C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1
-ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1

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/python3.6m -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 -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1
-ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1

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/python3.6m -c'
gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function 'exp'
int exp (void);
^
gcc _configtest.o -o _configtest.exe
success!
removing: _configtest.c _configtest.o _configtest.exe
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/core
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npymath
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npymath/npy_math.c
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npymath/ieee754.c
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npymath/npy_math_complex.c
building library "npysort" sources
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort/quicksort.c
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort/mergesort.c
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort/heapsort.c
creating build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private/npy_partition.h
adding 'build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private' to
include_dirs.
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort/selection.c
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private/npy_binsearch.h
conv_template:>
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/npysort/binsearch.c
None - nothing done with h_files =
['build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private/npy_partition.h',
'build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/src/private/npy_binsearch.h']
building extension "numpy.core._dummy" sources
Generating
build/src.cygwin-2.8.0-x86_64-3.6/numpy/core/include/numpy/config.h
C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1
-ggdb -O2 -pipe -Wimplicit-function-declaration
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/build=/usr/src/debug/python3-3.6.1-1
-fdebug-prefix-map=/usr/src/ports/python3/python3-3.6.1-1.x86_64/src/Python-3.6.1=/usr/src/debug/python3-3.6.1-1

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/python3.6m -c'
gcc: _configtest.c
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "", line 1, in
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/setup.py",
line 391, in
setup_package()
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/setup.py",
line 383, in setup_package
setup(**metadata)
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/core.py",
line 169, in setup
return old_setup(**new_attr)
File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/lib/python3.6/site-packages/wheel/bdist_wheel.py", line 199, in
run
self.run_command('build')
File "/usr/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/command/build.py",
line 47, in run
old_build.run(self)
File "/usr/lib/python3.6/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/command/build_src.py",
line 148, in run
self.build_sources()
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/command/build_src.py",
line 165, in build_sources
self.build_extension_sources(ext)
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/command/build_src.py",
line 324, in build_extension_sources
sources = self.generate_sources(sources, ext)
File
"/.gfmwk_tmp_120417204610_19564/spectools/pip-build-zu8uhs4m/numpy/numpy/distutils/command/build_src.py",
line 377, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 416, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 40, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 275, in check_types
"install {0}-dev|{0}-devel.".format(python))
SystemError: Cannot compile 'Python.h'. Perhaps you need to install
python-dev|python-devel.

Current configuration:
Cygwin 2.8.0
Python: 3.6.1

As I have understand that Numpy requirements are automatically selected also
for install, could you clarified which package have to be available on
Cygwin in order to proceed Numpy setup.

I have identified that Openblas, Atlas (or math-atlas), lapack packages have
to be installed but could you
clarify which cygwin packages exactly. 

It concerns, I guess most of Sci-Py Python modules.

I would add that python3-numpy package was added when I have selected cygwin
package for setup.
But when, I am doing:
import numpy
from my script
-> it's failing with meassage below:
$ python3 numpy_sample.py
Traceback (most recent call last):
File "numpy_sample.py", line 3, in
a = np.array([1,2,3,4])
AttributeError: module 'numpy' has no attribute 'array'

Thanks in advance for your help,




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