[SciPy-User] scikits.sparse

[Nils Wagner]

On Sat, 20 Feb 2010 10:07:25 -0800
  Nathaniel Smith <njs at pobox.com> wrote:
> On Sat, Feb 20, 2010 at 2:31 AM, Nils Wagner
> <nwagner at iam.uni-stuttgart.de> wrote:
>> I am using
>>
>> cython --version
>> Cython version 0.10.3
>>
>> That version is shipped with Open SuSe 11.2 which is 
>>quite
>> new.
>>
>> What is needed by scikits.sparse ?
> 
> Unfortunately, Cython moves fast (but it's no harder to 
>install than
> any other Python package).
> 
> I don't know the minimum version required, but I'm using 
>0.12 and it
> works for me. I'd just upgrade to 0.12.1, the latest 
>stable release.
> 
> -- Nathaniel
> ___________

Hi Nathanial,

I followed your advice and installed 0.12.1

Now

python setup.py install --prefix=$HOME/local

fails with

/home/nwagner/local/lib64/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/setuptools/command/sdist.py:4: 
UserWarning: Module pkg_resources was already imported 
from 
/home/nwagner/local/lib64/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/pkg_resources.py, 
but 
/home/nwagner/local/lib64/python2.6/site-packages/distribute-0.6.4-py2.6.egg 
is being added to sys.path
/home/nwagner/local/lib64/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/setuptools/command/sdist.py:4: 
UserWarning: Module setuptools was already imported from 
/home/nwagner/local/lib64/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/setuptools/__init__.py, 
but 
/home/nwagner/local/lib64/python2.6/site-packages/distribute-0.6.4-py2.6.egg 
is being added to sys.path
/home/nwagner/local/lib64/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/setuptools/command/sdist.py:4: 
UserWarning: Module site was already imported from 
/usr/lib64/python2.6/site.pyc, but 
/home/nwagner/local/lib64/python2.6/site-packages/distribute-0.6.4-py2.6.egg 
is being added to sys.path
/home/nwagner/local/lib64/python2.6/site-packages/Pyrex/Compiler/Errors.py:17: 
DeprecationWarning: BaseException.message has been 
deprecated as of Python 2.6
   self.message = message
running install
running bdist_egg
running egg_info
writing requirements to 
scikits.sparse.egg-info/requires.txt
writing scikits.sparse.egg-info/PKG-INFO
writing namespace_packages to 
scikits.sparse.egg-info/namespace_packages.txt
writing top-level names to 
scikits.sparse.egg-info/top_level.txt
writing dependency_links to 
scikits.sparse.egg-info/dependency_links.txt
writing requirements to 
scikits.sparse.egg-info/requires.txt
writing scikits.sparse.egg-info/PKG-INFO
writing namespace_packages to 
scikits.sparse.egg-info/namespace_packages.txt
writing top-level names to 
scikits.sparse.egg-info/top_level.txt
writing dependency_links to 
scikits.sparse.egg-info/dependency_links.txt
reading manifest file 
'scikits.sparse.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*~' found 
anywhere in distribution
warning: no previously-included files matching '*.so' 
found anywhere in distribution
warning: no previously-included files matching '*.pyc' 
found anywhere in distribution
writing manifest file 
'scikits.sparse.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
creating build/lib.linux-x86_64-2.6/scikits
copying scikits/__init__.py -> 
build/lib.linux-x86_64-2.6/scikits
creating build/lib.linux-x86_64-2.6/scikits/sparse
copying scikits/sparse/__init__.py -> 
build/lib.linux-x86_64-2.6/scikits/sparse
copying scikits/sparse/test_cholmod.py -> 
build/lib.linux-x86_64-2.6/scikits/sparse
running build_ext
cythoning scikits/sparse/cholmod.pyx to 
scikits/sparse/cholmod.c
building 'scikits.sparse.cholmod' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/scikits
creating build/temp.linux-x86_64-2.6/scikits/sparse
/usr/bin/gcc -fno-strict-aliasing -DNDEBUG 
-fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 
-fstack-protector -funwind-tables 
-fasynchronous-unwind-tables -g -fwrapv -fPIC 
-I/usr/include/python2.6 -c scikits/sparse/cholmod.c -o 
build/temp.linux-x86_64-2.6/scikits/sparse/cholmod.o
scikits/sparse/cholmod.c:158:31: error: 
numpy/arrayobject.h: Datei oder Verzeichnis nicht gefunden
scikits/sparse/cholmod.c:159:31: error: 
numpy/ufuncobject.h: Datei oder Verzeichnis nicht gefunden
  

"Datei oder Verzeichnis nicht gefunden" means "No such 
file or directory "

However

locate arrayobject.h

/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h
/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h
/home/nwagner/src/ScientificPython-2.9.0/Include/Scientific/arrayobject.h
/home/nwagner/svn/ironclad-read-only/stub/Include/.svn/text-base/bytearrayobject.h.svn-base
/home/nwagner/svn/ironclad-read-only/stub/Include/bytearrayobject.h
/home/nwagner/svn/numpy/numpy/core/include/numpy/.svn/prop-base/arrayobject.h.svn-base
/home/nwagner/svn/numpy/numpy/core/include/numpy/.svn/text-base/arrayobject.h.svn-base
/home/nwagner/svn/numpy/numpy/core/include/numpy/.svn/text-base/ndarrayobject.h.svn-base
/home/nwagner/svn/numpy/numpy/core/include/numpy/arrayobject.h
/home/nwagner/svn/numpy/numpy/core/include/numpy/ndarrayobject.h
/home/nwagner/svn/numpy/numpy/core/src/multiarray/.svn/text-base/arrayobject.h.svn-base
/home/nwagner/svn/numpy/numpy/core/src/multiarray/arrayobject.h
/usr/include/python2.6/bytearrayobject.h
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h

How can I fix the problem ?

  Nils