[Biopython] Antwort: Re: installation as non-administrator

[Paul.Czodrowski at merck.de]

Dear Peter,

maybe as additonal question/issue:
numpy is not located in
"/usr/lib/python2.6/site-packages/numpy/core/include "
but in another, rather global, python-lib-directory.

As stated in my previous email,
python setup.py build gives
"gcc -pthread -fno-strict-aliasing -DNDEBUG -fomit-frame-pointer
-fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables -g -fPIC
-I/usr/lib/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-i686-2.6/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:31: fatal error: numpy/arrayobject.h: No such
file or directory"

and I would like to adapt the
"-I/usr/lib/python2.6/site-packages/numpy/core/includ" accordingly to the
directory where it is actually located.

Cheers & thanks,
Paul


> >
> > Dear folks,
> >
> > I'm struggling around with the biopython installation.
> > As non-administrator, the manual states the following:
> > http://biopython.org/DIST/docs/install/Installation.html#htoc30
> >
> > However, the setup.py (version 1.57) does not contain any entry "
> > include_dirs=["Bio/Cluster", "your_dir/include/python"]
> > ", but rather only "Bio" entries.
> >
> > (See attached file: setup.py)
>
> You didn't really need to attach a whole file, you could have
> linked to our repository or quoted the bit of interest.
>
> > Or do I oversee anything?
>
> What OS are you using? Some flavour of Linux?
>
> What version of NumPy do you have, and how was it installed?
>
> What command did you use to attempt the install, and what
> error message did you get.
>
> Have you tried the --prefix argument?
>
> e.g.
>
> python setup.py build
> python setup.py test
> python setup.py install --prefix=$HOME
>
> Peter


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