From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QRnfl-0000fx-0z for garchives@archives.gentoo.org; Wed, 01 Jun 2011 15:49:30 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9E18A1C0E5; Wed, 1 Jun 2011 15:48:52 +0000 (UTC) Received: from homiemail-a6.g.dreamhost.com (mailbigip.dreamhost.com [208.97.132.5]) by pigeon.gentoo.org (Postfix) with ESMTP id 55CA11C0E5 for ; Wed, 1 Jun 2011 15:48:52 +0000 (UTC) Received: from homiemail-a6.g.dreamhost.com (localhost [127.0.0.1]) by homiemail-a6.g.dreamhost.com (Postfix) with ESMTP id 633A1598070 for ; Wed, 1 Jun 2011 08:48:51 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; c=nofws; d=velodius.com; h=date:from:to :subject:message-id:in-reply-to:references:mime-version: content-type; q=dns; s=velodius.com; b=z4IOOhPfUW/esxU4t0ipCDHXg GLDPBda0ZJnGruCPZs5DH03h6qE72HM4lH+Oy7vDuLg/xwVK5dDj/dVWKsQuJL9D L1A/FKQaxwkoLXonAoqUdR4t3dgzzOMq+++crRiZOGYTHWp8Qkl0tqZH7IydMEKe 78yfN6qLlrpBiuJPQk= DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=velodius.com; h=date:from :to:subject:message-id:in-reply-to:references:mime-version: content-type; s=velodius.com; bh=srwcMeCA/qWDNE2DoDj416j7Zp8=; b=VSCyUEuqHwwFD7IlHUpIgGB+LaH3xRUsO87H7MllWbkFZ7bDDe3vsUn11E1BY bgSJjqb0B64AUP0cExtUBiv+GlFaNuq2aSQ4l4TadBQE/uTUwqdwT5lInRL2gSjs caIj8Eo+v48FGxE6mtG69oQWHdP/D5rWJkZ0sB9hoJd36o= Received: from pcbox-marc (113.Red-95-120-66.dynamicIP.rima-tde.net [95.120.66.113]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) (Authenticated sender: timer@velodius.com) by homiemail-a6.g.dreamhost.com (Postfix) with ESMTPSA id 55CF8598077 for ; Wed, 1 Jun 2011 08:48:50 -0700 (PDT) Date: Wed, 1 Jun 2011 17:48:46 +0200 From: Marc Vinyals To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv Message-ID: <20110601174846.5687d413@pcbox-marc> In-Reply-To: <201106010657.03824.fbissey@slingshot.co.nz> References: <20110531154403.0d6f08fd@pcbox-marc> <201106010657.03824.fbissey@slingshot.co.nz> X-Mailer: Claws Mail 3.7.9 (GTK+ 2.24.3; x86_64-pc-linux-gnu) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org Mime-Version: 1.0 Content-Type: multipart/signed; micalg=PGP-SHA1; boundary="Sig_/tMeu=VpWFMoQUv1I62W8Arz"; protocol="application/pgp-signature" X-Archives-Salt: X-Archives-Hash: d8abf5f9c929b675c8a6a29341992f20 --Sig_/tMeu=VpWFMoQUv1I62W8Arz Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable EL Wed, 1 Jun 2011 06:57:03 +1200 Francois Bissey escrigu=C3=A9: > > Hi, > >=20 > > 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 > >=20 > > import scipy.optimize > >=20 > > fails with > >=20 > > [...] > > from scipy.linalg import clapack > > ImportError: /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so: > > undefined symbol: clapack_sgesv > >=20 > > 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. > >=20 > > Then I tried rebuilding numpy and scipy with lapack, blas and cblas > > provided (eselect) by atlas and scipy worked flawlessly. > >=20 > > Should scipy depend on a specific lapack provider instead of a > > virtual? Enable it at compile time? Is it an unfortunate > > combination what fails? > >=20 > > I can provide build logs if you need them. > >=20 > Hi Marc, >=20 > 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.=20 >=20 > 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? >=20 > Francois >=20 Hi Francois, I tried rebuilding arpack and superlu without luck. Since you mentioned that eselect fixed your problems, I also tried installing cblas-reference and using it instead of gsl, also without luck. I'm using the main tree implementation. Best, Marc. --Sig_/tMeu=VpWFMoQUv1I62W8Arz Content-Type: application/pgp-signature; name=signature.asc Content-Disposition: attachment; filename=signature.asc -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) iEYEARECAAYFAk3mX14ACgkQu4rFT+k3kmSj7wCfaLXE3kHHdyQ7/vSVpBpORjex XnQAoMC4j744rt9hE8w3PuC04pJ6FHd/ =kJCU -----END PGP SIGNATURE----- --Sig_/tMeu=VpWFMoQUv1I62W8Arz--