[Biopython] Install problems (Numpy problem ?)

[João Rodrigues]

Hi Andrew,

My experience with numpy is that even though you install it and import
correctly, sometimes, it's still not proper. Try importing something within
numpy, like ndarray, and see if you can do it.

import numpy
na = numpy.ndarray(shape=(2,2), dtype=float, order='F')

I would debug this first and then move on to a biopython issue.

Cheers,

João


2014-04-11 10:28 GMT+02:00 Andrew Mather <mathera at gmail.com>:

> Hi,
>
> I'm attempting to install 1.63 from a git cloned directory into Python 2.7.
>
> Numpy 1.8.0 appears to have installed correctly and can be imported at
> the prompt.
>
> However the BioPython build fails with the message below:
>
> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes -fPIC
> -I/usr/local/lib/python2.7/site-packages/numpy/core/include
> -I/usr/local/include/python2.7 -c Bio/Cluster/clustermodule.c -o
> build/temp.linux-x86_64-2.7/Bio/Cluster/clustermodule.o
> In file included from
>
> /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
>                  from
>
> /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
>                  from
>
> /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from Bio/Cluster/clustermodule.c:3:
>
> /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:114:10:
> error: #error Unsupported size for type off_t
> error: command 'gcc' failed with exit status 1
>
> Any advice would be gratefully received, as we're in the middle of
> racing to commission a new system and running out of time.
>
> Thanks,
> Andrew
>
>
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