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To: gentoo-science@g.o
From: Francois Bissey <fbissey@...>
Subject: Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Wed, 1 Jun 2011 06:57:03 +1200
> Hi,
> 
> While updating sage and python to 4.7 and 2.7, I hit a variation of an
> old bug (see http://bugs.gentoo.org/195619): scipy compiles with
> lapack-reference but is unusable. Running in python
> 
> import scipy.optimize
> 
> fails with
> 
> [...]
>     from scipy.linalg import clapack
> ImportError: /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so:
> undefined symbol: clapack_sgesv
> 
> I tried rebuilding numpy and scipy with lapack provided (eselect) by
> lapack-reference, blas provided by blas-reference, cblas provided by
> gsl and with/without clapack with the same result.
> 
> Then I tried rebuilding numpy and scipy with lapack, blas and cblas
> provided (eselect) by atlas and scipy worked flawlessly.
> 
> Should scipy depend on a specific lapack provider instead of a virtual?
> Enable it at compile time? Is it an unfortunate combination what fails?
> 
> I can provide build logs if you need them.
> 
Hi Marc,

Just one thing that I can think of on the top of my head. We recently made
scipy depend on arpack and superlu. They also have dependencies on blas/lapack
if you didn't rebuild them as well they may cause trouble. 

I had a similar problem recently but eselecting everything properly worked for
me. A last piece of info you could provide: are you using the main tree 
implementation or bicatali's overlay implementation?

Francois


Replies:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Marc Vinyals
References:
sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Marc Vinyals
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Updated Jul 05, 2012

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