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

[Paul.Czodrowski at merck.de]

Dear Peter,



> > Dear Peter,
> >
> >
> >> >
> >> > 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.
> >
> > I'm sorry for this!
>
> Don't worry too much, its a fairly small file otherwise I wouldn't
> have let it though the moderation queue.
>
> >> > Or do I oversee anything?
> >>
> >> What OS are you using? Some flavour of Linux?
> >
> > OpenSuse 11.3
>
> Should be fine.
>
> >>
> >> What version of NumPy do you have, and how was it installed?
> >
> > NumPy version 1.3.0, installed locally by the built-in python routines.
> >
>
> Any reason for installing such an old version? I'm just curious.

No logical reason... :)


>
> Does NumPy work properly? At the very least, if you run python
> does "import numpy" work or give an error? What happens if you
> try and do this:
>
> $ python
> >>> import numpy
> >>> numpy.get_include()
> '/usr/local/lib/python2.6/site-packages/numpy/core/include'
>
> (That's the output on one of our Linux machines)

We have the same output:
>>>
>>>
>>> numpy.get_include()
'/usr/lib/python2.6/site-packages/numpy/core/include'


>
> If that doesn't work, perhaps your PYTHONPATH needs setting.
> How/where did you install NumPy? e.g. python setup.py --prefix=$HOME

The /usr/lib python is installed via the yast OpenSuse.
But it seems to me that this installation did not work properly, since
there are only 2 files in the directory
" /usr/lib/python2.6/site-packages/numpy/core/include/numpy/":
- ufunc_api.txt
- multiarray_api.txt

However, we have another installation of NumPy which is located here:
"/SW/python/lib/python2.6/site-packages/lib/python2.6/site-packages/numpy"

And yes, there is a mix-up of the directories... :)


> >> What command did you use to attempt the install, and what
> >> error message did you get.
> > python setup.py --build
> > ==> ERROR MESSAGE
> > "
> > running build
> > running build_py
> > running build_ext
> > building 'Bio.Cluster.cluster' extension
> > 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
> > compilation terminated.
> > error: command 'gcc' failed with exit status 1
> > "
>
> OK, it isn't finding the numpy header files. I'd guess from your
> next email the
> file is /usr/lib/python2.6/site-
> packages/numpy/core/include/numpy/arrayobject.h

You are wrong about this.
The header file is locate here:

"/SW/python/lib/python2.6/site-packages/lib/python2.6/site-packages/numpy/core/include/numpy/"


By appropiately setting the PYTHONPATH, it works properly.


>
> The hack suggested in the installation document is to edit our setup.py
> file to point to the path explicitly. There is probably a more elegant
way,
> right now my guess is that NumPy is not on the python path (see above).
>
> ---
>
> >From the test results,
>
> > python setup.py test
> > running test
> > Python version: 2.6.5 (r265:79063, Oct 28 2010, 20:56:56)
> > [GCC 4.5.0 20100604 [gcc-4_5-branch revision 160292]]
> > Operating system: posix linux2
> > test_Ace ... ok
> > ...
> > test_Entrez ... Segmentation fault (core dumped)
>
> Oh, nasty! That should *not* happen, and is probably a separate
> issue to the NumPy header install issue.


python setup.py install --prefix=$HOME works fine now.

Should the segmentation fault still be considered?

Cheers & thanks,
Paul

>
> Peter


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