[SciPy-User] scikits.sparse

Nils Wagner nwagner@iam.uni-stuttgart...
Sun Feb 21 13:32:51 CST 2010


On Sun, 21 Feb 2010 11:26:34 -0800
  Nathaniel Smith <njs@pobox.com> wrote:
> On Sun, Feb 21, 2010 at 2:00 AM, Nils Wagner
> <nwagner@iam.uni-stuttgart.de> wrote:
>> 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
> 
> Oops, this is indeed a scikits.sparse bug. Thanks for 
>the reminder,
> actually -- it came up before, but I forgot to commit 
>the fix for the
> next release...
> 
> Anyway, the solution is to edit setup.py:
> 1) near the top, add the line:
>  from numpy.distutils.misc_util import 
>get_numpy_include_dirs
> 
> 2) near the bottom, where it says:
>              Extension("scikits.sparse.cholmod",
>                        ["scikits/sparse/cholmod.pyx"],
>                        libraries=["cholmod"],
>                        ),
> add an include_dirs line, like:
>              Extension("scikits.sparse.cholmod",
>                        ["scikits/sparse/cholmod.pyx"],
>                        libraries=["cholmod"],
>                        include_dirs=get_numpy_include_dirs(),
>                        ),
> 
> This will be in the next release, of course.
> 
> -- Nathaniel

O.k.
here comes another issue

python setup.py install --prefix=$HOME/local
/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
building 'scikits.sparse.cholmod' extension
C compiler: /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

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
compile options: 
'-I/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include 
-I/usr/include/python2.6 -c'
gcc: scikits/sparse/cholmod.c
scikits/sparse/cholmod.c:160:33: error: 
suitesparse/cholmod.h: Datei oder Verzeichnis nicht 
gefunden


  locate cholmod.h
/home/nwagner/hg/scikits.sparse/doc/_build/html/cholmod.html
/home/nwagner/src/CHOLMOD/Include/cholmod.h
/home/nwagner/src/cvxopt-1.1/src/C/SuiteSparse/CHOLMOD/Include/cholmod.h
/home/nwagner/src/SuiteSparse/CHOLMOD/Include/cholmod.h
/home/nwagner/src/SuiteSparse/KLU/User/klu_cholmod.h
/home/nwagner/src/trilinos-9.0.2/packages/amesos/src/SuiteSparse/CHOLMOD/Include/amesos_cholmod.h

Any idea ?

  Cheers,
                        Nils



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