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

[Peter Cock]

On Tue, May 3, 2011 at 3:38 PM,  <Paul.Czodrowski at merck.de> wrote:
> 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.

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)

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


>> 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

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.

Peter