[SciPy-user] SciPy-user Digest, Vol 57, Issue 44

Wed May 28 22:52:49 EDT 2008

> Thanks Robert, you're right: numpy was busted. Unfortunately it's  
> still busted. I installed the ActivePython 2.5 and made sure that  
> it's the python that it's getting used, then
tried to compile numpy again but I get this error message (seem to be  
with the gcc compilation options). Unfortunately I don't know enough  
to fix it. I'm attaching below the output of the "python setup.py  
build". Really appreciate your help.

python setup.py build
Running from numpy source directory.
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2_5234
blas_opt_info:
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/ 
vecLib.framework/Headers']

lapack_opt_info:
   FOUND:
     extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
     define_macros = [('NO_ATLAS_INFO', 3)]
     extra_compile_args = ['-faltivec']

running build
running scons
customize UnixCCompiler
Found executable /usr/bin/gcc
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Found executable /usr/local/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 UnixCCompiler
customize UnixCCompiler using scons
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
creating build/src.macosx-10.3-ppc-2.5
creating build/src.macosx-10.3-ppc-2.5/numpy
creating build/src.macosx-10.3-ppc-2.5/numpy/distutils
building extension "numpy.core.multiarray" sources
creating build/src.macosx-10.3-ppc-2.5/numpy/core
Generating build/src.macosx-10.3-ppc-2.5/numpy/core/config.h
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
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 -arch ppc -arch i386 -isysroot /Developer/SDKs/ 
MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp  
-mno-fused-madd -fPIC -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 - 
Wall -Wstrict-prototypes

compile options: '-I/Library/Frameworks/Python.framework/Versions/2.5/ 
include/python2.5 -Inumpy/core/src -Inumpy/core/include -I/Library/ 
Frameworks/Python.framework/Versions/2.5/include/python2.5 -I/Library/ 
Frameworks/Python.framework/Versions/2.5/include/python2.5 -c'
gcc: _configtest.c
gcc: cannot specify -o with -c or -S and multiple compilations
gcc: cannot specify -o with -c or -S and multiple compilations
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
   File "setup.py", line 96, in <module>
     setup_package()
   File "setup.py", line 89, in setup_package
     configuration=configuration )
   File "/Users/mlsichit/temp/numpy/numpy/distutils/core.py", line  
184, in setup
     return old_setup(**new_attr)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/core.py", line 151, in setup
     dist.run_commands()
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/dist.py", line 974, in run_commands
     self.run_command(cmd)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/dist.py", line 994, in run_command
     cmd_obj.run()
   File "/Users/mlsichit/temp/numpy/numpy/distutils/command/ 
build.py", line 40, in run
     old_build.run(self)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/command/build.py", line 112, in run
     self.run_command(cmd_name)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/cmd.py", line 333, in run_command
     self.distribution.run_command(command)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/distutils/dist.py", line 994, in run_command
     cmd_obj.run()
   File "/Users/mlsichit/temp/numpy/numpy/distutils/command/ 
build_src.py", line 130, in run
     self.build_sources()
   File "/Users/mlsichit/temp/numpy/numpy/distutils/command/ 
build_src.py", line 147, in build_sources
     self.build_extension_sources(ext)
   File "/Users/mlsichit/temp/numpy/numpy/distutils/command/ 
build_src.py", line 250, in build_extension_sources
     sources = self.generate_sources(sources, ext)
   File "/Users/mlsichit/temp/numpy/numpy/distutils/command/ 
build_src.py", line 307, in generate_sources
     source = func(extension, build_dir)
   File "numpy/core/setup.py", line 83, in generate_config_h
     raise SystemError,"Failed to test configuration. "\
SystemError: Failed to test configuration. See previous error  
messages for more information.

--------------------------------

Thanks for the help,
Mihai


> ------------------------------
>
> Message: 3
> Date: Sat, 24 May 2008 21:32:32 -0500
> From: "Robert Kern" <robert.kern at gmail.com>
> Subject: Re: [SciPy-user] Help with installing scypy
> To: "SciPy Users List" <scipy-user at scipy.org>
> Message-ID:
> 	<3d375d730805241932i2c2cc9bau40e8a33c308c1985 at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Sat, May 24, 2008 at 9:19 PM, Mihail Sichitiu <junky at nc.rr.com>  
> wrote:
>> I tried to follow the instructions here:
>> http://www.scipy.org/Installing_SciPy/Mac_OS_X#head- 
>> cfc918ee2c334f8cf364c08fff51e210e7913062
>> for installing numpy and scipy on a Mac OS X (10.4.11), but no luck.
>> According to the advice there here are my software versions:
>> Legolas:~/temp/scipy root# gcc --version
>> gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1819)
>> Copyright (C) 2002 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.   
>> There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR  
>> PURPOSE.
>> Legolas:~/temp/scipy root# gfortran --version
>> GNU Fortran (GCC) 4.2.1
>> Legolas:~/temp/scipy root# g77 --version
>> GNU Fortran (GCC) 3.4.6
>> Legolas:~/temp/scipy root#
>>
>> Also, the message error when trying to make scipy (after building and
>> installing numpy):
>> Legolas:~/temp/scipy root# python setup.py build_src build_clib
>> --fcompiler=gnu build_ext --fcompiler=gnu build
>> Traceback (most recent call last):
>>   File "setup.py", line 92, in ?
>>     setup_package()
>>   File "setup.py", line 63, in setup_package
>>     from numpy.distutils.core import setup
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/numpy/__init__.py",
>> line 93, in ?
>>     import add_newdocs
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/numpy/add_newdocs.py",
>> line 9, in ?
>>     from lib import add_newdoc
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/numpy/lib/__init__.py",
>> line 18, in ?
>>     from io import *
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/numpy/lib/io.py",
>> line 16, in ?
>>     from _compiled_base import packbits, unpackbits
>> ImportError: cannot import name packbits
>> Any ideas what's going wrong?
>
> Your numpy install is busted somehow. What version of numpy did you
> try to install? Did you have a previous version sitting there?
>
> Also, the instructions recommend (and I strongly concur) that you
> install the official binaries from python.org instead of using the
> system-installed Python. That's probably not your problem, but it's
> worth doing.
>
> -- 
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless
> enigma that is made terrible by our own mad attempt to interpret it as
> though it had an underlying truth."
>  -- Umberto Eco
>