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

[Paul.Czodrowski at merck.de]

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!



>
> > Or do I oversee anything?
>
> What OS are you using? Some flavour of Linux?
OpenSuse 11.3

>
> 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.

>
> 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
"

>
> Have you tried the --prefix argument?
>
> e.g.
>
> python setup.py build
> python setup.py test
> python setup.py install --prefix=$HOME
>
> Peter

python setup.py --test
==> ERROR MESSAGE
"
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_AlignIO ... ok
test_AlignIO_convert ... ok
test_BioSQL ... /xyz: UserWarning: order location operators are not fully
supported
  % feature.location_operator)
ok
test_BioSQL_SeqIO ... ERROR
test_CAPS ... ok
test_Clustalw ... ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want
to use Bio.Clustalw.
test_Cluster ... skipping. If you want to use Bio.Cluster, install NumPy
first and then reinstall Biopython
test_CodonTable ... ok
test_CodonUsage ... ok
test_Compass ... ok
test_Crystal ... ok
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the
Bio.Align.Applications wrapper.
test_DocSQL ... ok
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew'
if you want to use the Bio.Emboss.Applications wrappers for phylogenetic
tools.
test_EmbossPrimer ... ok
test_Entrez ... Segmentation fault (core dumped)
"

python setup.py install --prefix=$HOME
==> the same ERROR MESSAGE as from "python setup.py build"


Cheers & thanks in advance,

Paul

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