[Numpy-discussion] Installing numpy under cygwin

Olivia Cheronet cheronetolivia@yahoo....
Wed Nov 25 01:40:47 CST 2009


Hello David,

Below is the full log.

Thanks very much for the help.

Olivia


Running from numpy source directory.
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib
NOT AVAILABLE

/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/system_info.py:1383: 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__)
blas_info:
  libraries blas not found in /usr/local/lib
  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib']
    language = f77

  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib']
    define_macros = [('NO_ATLAS_INFO', 1)]
    language = f77

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  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
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
numpy.distutils.system_info.atlas_info


/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:
  libraries lapack not found in /usr/local/lib
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/lib']
    language = f77

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

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
building py_modules sources
building library "npymath" sources
building extension "numpy.core._sort" sources
Generating build/src.cygwin-1.5.25-i686-2.5/numpy/core/include/numpy/config.h
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 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
success!
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes


compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prot
otypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
_configtest.c: In function `main':
_configtest.c:5: error: size of array `test_array' is negative
_configtest.c:4: warning: function declaration isn't a prototype
_configtest.c: In function `main':
_configtest.c:5: error: size of array `test_array' is negative
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5
 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
_configtest.c: In function `main':
_configtest.c:5: error: size of array `test_array' is negative
_configtest.c:4: warning: function declaration isn't a prototype
_configtest.c: In function `main':
_configtest.c:5: error: size of array `test_array' is negative
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:6: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:6: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:5: warning: function declaration isn't a prototype
success!
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:6: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:6: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:4: warning: function declaration isn't a prototype
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes


compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c:5: warning: function declaration isn't a prototype
success!
removing: _configtest.c _configtest.o
/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)
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc _configtest.o -llibm.a -o _configtest.exe
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc _configtest.o -o _configtest.exe
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc _configtest.o -lm -o _configtest.exe
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc _configtest.o -lcpml -o _configtest.exe
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: crt0.o: No such file: No such file or directory
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
  File "setup.py", line 172, in <module>
    setup_package()
  File "setup.py", line 165, in setup_package
    configuration=configuration )
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/usr/lib/python2.5/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib/python2.5/distutils/dist.py", line 974, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
    cmd_obj.run()
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/install.py", line 49, in run
    r = old_install.run(self)
  File "/usr/lib/python2.5/distutils/command/install.py", line 506, in run
    self.run_command('build')
  File "/usr/lib/python2.5/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
    cmd_obj.run()
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/usr/lib/python2.5/distutils/command/build.py", line 112, in run
    self.run_command(cmd_name)
  File "/usr/lib/python2.5/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
    cmd_obj.run()
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/build_src.py", line 130, in run
    self.build_sources()
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/build_src.py", line 147, in build_sources
    self.build_extension_sources(ext)
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/build_src.py", line 250, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/cygdrive/c/cygwin/home/Global/numpy-1.3.0/numpy/distutils/command/build_src.py", line 307, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 289, in generate_config_h
    mathlibs = check_mathlib(config_cmd)
  File "numpy/core/setup.py", line 253, in check_mathlib
    raise EnvironmentError("math library missing; rerun "
EnvironmentError: math library missing; rerun setup.py after setting the MATHLIB env variable

----- Original Message ----
> Hi Olivia,
> 
> On Mon, Nov 23, 2009 at 6:51 AM, Olivia Cheronet
> wrote:
> > Hello,
> >
> >  I attempted to install Numpy for my Cygwin python again, by simply executing:
> >  >python setup.py install
> >
> >  However, I now get the following:
> >  >File "numpy/core/setup.py", line 253, in check_mathlib
> >  >  raise EnvironmentError("math library missing; rerun "
> >  >EnvironmentError: math library missing; rerun setup.py after setting the
> >  MATHLIB
> >  >env variable
> >
> >
> >  I have a math library from cygwin (libm.a), but I have not managed to set it.
> 
> The message is misleading (the message is hopefully improved with the
> last trunk), and it is almost always caused by a broken toolchain
> (that is you are missing gcc, or g++, etc...).
> 
> It would be helpful to have the full build log to help you better,
> 
> David



      


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