[SciPy-User] scikits.sparse
Nils Wagner
nwagner at iam.uni-stuttgart.de
Sun Feb 21 14:32:51 EST 2010
On Sun, 21 Feb 2010 11:26:34 -0800
Nathaniel Smith <njs at pobox.com> wrote:
> On Sun, Feb 21, 2010 at 2:00 AM, Nils Wagner
> <nwagner at 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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