[Numpy-discussion] Installing numpy under cygwin

Olivia Cheronet cheronetolivia@yahoo....
Wed Nov 18 03:08:47 CST 2009


Hello.

I am currently trying to install the latest version of NumPy for my cygwin Python, and I am having problems...

I have downloaded the source, and unzipped and untarred it in my home directory.
Subsequently, I included the following in the site.cfg file:
>[DEFAULT]
>library_dirs = /cygdrive/c/cygwin/lib
>include_dirs = /cygdrive/c/cygwin/usr/local/include
>[blas_opt]
>libraries = f77blas, cblas, atlas
>[lapack_opt]
>libraries = lapack, f77blas, cblas, atlas

In the Cygwin bash shell, after going to my home directory, I have executed:
python setup.py config --compiler=mingw32 build --compiler=mingw32 install
as instructed in the "Installing SciPy/Windows" page.

The result is the following:

error: Command "gcc -mno-cygwin -mdll -O -Wall -Inumpy/core/include -Ibuild/src.
cygwin-1.5.25-i686-2.5/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/in
clude -I/usr/include/python2.5 -c build/src.cygwin-1.5.25-i686-2.5/numpy/core/sr
c/npy_math.c -o build/temp.cygwin-1.5.25-i686-2.5/build/src.cygwin-1.5.25-i686-2
.5/numpy/core/src/npy_math.o" failed with exit status 1

I have included below the complete output (and error) I get.

What could be the problem?

Thank you,

Olivia
==================================================================================

  libraries lapack_atlas not found in /cygdrive/c/cygwin/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /cygdrive/c/cygwin/lib
  libraries lapack_atlas not found in /cygdrive/c/cygwin/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/system_info.py:1290:
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.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/cygdrive/c/cygwin/lib']
    language = f77

  FOUND:
    libraries = ['lapack', 'blas']
    library_dirs = ['/cygdrive/c/cygwin/lib']
    define_macros = [('NO_ATLAS_INFO', 1)]
    language = f77

running config
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler opti
ons
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler opt
ions
running build_src
building py_modules sources
building library "npymath" sources
building extension "numpy.core._sort" sources
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h' to
 sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/numpyconfig.
h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__multiarray
_api.h' to sources.
numpy.core - nothing done with h_files = ['build/src.cygwin-1.5.25-i686-2.5/nump
y/core/include/numpy/config.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/inc
lude/numpy/numpyconfig.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/
numpy/__multiarray_api.h']
building extension "numpy.core.multiarray" sources
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h' to
 sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/numpyconfig.
h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__multiarray
_api.h' to sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files = ['build/src.cygwin-1.5.25-i686-2.5/nump
y/core/src/scalartypes.inc', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/ar
raytypes.inc', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config
.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/numpyconfig.h',
'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__multiarray_api.h']
building extension "numpy.core.umath" sources
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h' to
 sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/numpyconfig.
h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__ufunc_api.
h' to sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files = ['build/src.cygwin-1.5.25-i686-2.5/nump
y/core/src/scalartypes.inc', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/ar
raytypes.inc', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/umath_funcs.inc'
, 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/umath_loops.inc', 'build/src.
cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h', 'build/src.cygwin-1.5
.25-i686-2.5/numpy/core/include/numpy/numpyconfig.h', 'build/src.cygwin-1.5.25-i
686-2.5/numpy/core/include/numpy/__ufunc_api.h']
building extension "numpy.core.scalarmath" sources
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h' to
 sources.
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/numpyconfig.
h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__multiarray
_api.h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
  adding 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/__ufunc_api.
h' to sources.
numpy.core - nothing done with h_files = ['build/src.cygwin-1.5.25-i686-2.5/nump
y/core/include/numpy/config.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/inc
lude/numpy/numpyconfig.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/
numpy/__multiarray_api.h', 'build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/
numpy/__ufunc_api.h']
building extension "numpy.core._dotblas" sources
building extension "numpy.core.umath_tests" sources
building extension "numpy.lib._compiled_base" sources
building extension "numpy.numarray._capi" sources
building extension "numpy.fft.fftpack_lite" sources
building extension "numpy.linalg.lapack_lite" sources
  adding 'numpy/linalg/lapack_litemodule.c' to sources.
  adding 'numpy/linalg/python_xerbla.c' to sources.
building extension "numpy.random.mtrand" sources
/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/config.py:39:
 DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of try_run is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++

  DeprecationWarning)
No module named cygwinccompiler in numpy.distutils; trying from distutils
customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
C compiler: gcc -mno-cygwin -mdll -O -Wall

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5
 -c'
gcc -mno-cygwin -mdll -O -Wall -Inumpy/core/src -Inumpy/core/include -I/usr/incl
ude/python2.5 -c _configtest.c -o _configtest.o
gcc -mno-cygwin -s _configtest.o -o _configtest.exe
_configtest.exe
success!
removing: _configtest.c _configtest.o _configtest.exe
building data_files sources
running build_py
copying numpy/version.py -> build/lib.cygwin-1.5.25-i686-2.5/numpy
copying build/src.cygwin-1.5.25-i686-2.5/numpy/__config__.py -> build/lib.cygwin
-1.5.25-i686-2.5/numpy
copying build/src.cygwin-1.5.25-i686-2.5/numpy/distutils/__config__.py -> build/
lib.cygwin-1.5.25-i686-2.5/numpy/distutils
running build_clib
No module named cygwinccompiler in numpy.distutils; trying from distutils
customize Mingw32CCompiler
customize Mingw32CCompiler using build_clib
building 'npymath' library
compiling C sources
C compiler: gcc -mno-cygwin -mdll -O -Wall

compile options: '-Inumpy/core/include -Ibuild/src.cygwin-1.5.25-i686-2.5/numpy/
core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.
5 -c'
gcc -mno-cygwin -mdll -O -Wall -Inumpy/core/include -Ibuild/src.cygwin-1.5.25-i6
86-2.5/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/usr/inc
lude/python2.5 -c build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/npy_math.c -o
build/temp.cygwin-1.5.25-i686-2.5/build/src.cygwin-1.5.25-i686-2.5/numpy/core/sr
c/npy_math.o
In file included from /usr/include/python2.5/Python.h:57,
                 from numpy/core/src/npy_math.c.src:45:
/usr/include/python2.5/pyport.h:257:24: sys/select.h: No such file or directory
numpy/core/src/npy_math.c.src:187: warning: static declaration of 'log2' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sinl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'cosl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'tanl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sinhl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'coshl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'tanhl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'fabsl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'floorl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'ceill' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'rintl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'truncl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sqrtl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log10l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'logl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'expl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'expm1l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'asinl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'acosl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'atanl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'asinhl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'acoshl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'atanhl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log1pl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'exp2l' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log2l' follow
s non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'atan2l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'hypotl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'powl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'fmodl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:278: warning: static declaration of 'modfl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log2f' follow
s non-static declaration
In file included from /usr/include/python2.5/Python.h:57,
                 from numpy/core/src/npy_math.c.src:45:
/usr/include/python2.5/pyport.h:257:24: sys/select.h: No such file or directory
numpy/core/src/npy_math.c.src:187: warning: static declaration of 'log2' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sinl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'cosl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'tanl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sinhl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'coshl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'tanhl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'fabsl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'floorl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'ceill' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'rintl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'truncl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'sqrtl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log10l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'logl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'expl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'expm1l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'asinl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'acosl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'atanl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'asinhl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'acoshl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'atanhl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log1pl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'exp2l' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log2l' follow
s non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'atan2l' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'hypotl' follo
ws non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'powl' follows
 non-static declaration
numpy/core/src/npy_math.c.src:267: warning: static declaration of 'fmodl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:278: warning: static declaration of 'modfl' follow
s non-static declaration
numpy/core/src/npy_math.c.src:251: warning: static declaration of 'log2f' follow
s non-static declaration
error: Command "gcc -mno-cygwin -mdll -O -Wall -Inumpy/core/include -Ibuild/src.
cygwin-1.5.25-i686-2.5/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/in
clude -I/usr/include/python2.5 -c build/src.cygwin-1.5.25-i686-2.5/numpy/core/sr
c/npy_math.c -o build/temp.cygwin-1.5.25-i686-2.5/build/src.cygwin-1.5.25-i686-2
.5/numpy/core/src/npy_math.o" failed with exit status 1


      


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