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 1Saedd-0000K5-Di for garchives@archives.gentoo.org; Sat, 02 Jun 2012 03:04:25 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C765CE0743 for ; Sat, 2 Jun 2012 03:04:24 +0000 (UTC) Received: from mxi2.callplus.net.nz (mx194.callplus.net.nz [202.180.66.194]) by pigeon.gentoo.org (Postfix) with ESMTP id 036C1E06B1 for ; Sat, 2 Jun 2012 02:05:43 +0000 (UTC) X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AuQcANhzyU/KtHWD/2dsb2JhbABFh3uoeIInBIElgQiCGAEBBTocGBsLGAkVEA8BKR6II7gEiw9OhUIDpQ6CdQ X-IronPort-AV: E=Sophos;i="4.75,701,1330858800"; d="scan'208";a="269493379" Received: from 202-180-117-131.callplus.net.nz (HELO vrooom-vrooom.localnet) ([202.180.117.131]) by ismtp2.tranzpeer.net with ESMTP/TLS/DHE-RSA-AES256-SHA; 02 Jun 2012 14:05:46 +1200 From: Francois Bissey To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] World updates with sage installed - portage bug? Date: Sat, 02 Jun 2012 14:05:33 +1200 Message-ID: <3944886.XjHiqvjW53@vrooom-vrooom> User-Agent: KMail/4.8.3 (Linux/3.0.0-sabayon; KDE/4.8.3; i686; ; ) In-Reply-To: <20120601211358.GK22017@schlaumatte.ethz.ch> References: <20120601095224.GI22017@schlaumatte.ethz.ch> <2406647.QNWjxfJBFB@vrooom-vrooom> <20120601211358.GK22017@schlaumatte.ethz.ch> 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-Transfer-Encoding: 7Bit Content-Type: text/plain; charset="us-ascii" X-Archives-Salt: fc2651c1-c4d5-41f5-8091-be847dc25f9e X-Archives-Hash: fe4b8dcc073bc67b06222bac1116b89c On Fri, 01 Jun 2012 23:13:58 Thomas Kahle wrote: > On 07:26 Sat 02 Jun 2012, Francois Bissey wrote: > > On Fri, 01 Jun 2012 11:52:24 Thomas Kahle wrote: > > > Hi, > > > > > > now that I have sage-on-gentoo installed I can't do world updates with > > > the -D option anymore. Looks like a portage quirk to me. > > > > > > There seem to be at least two problems: > > > > > > I have sci-mathematics/singular in my world file and the -D option > > > forces portage to think that I insist on the latest version. Therefore > > > it collides with sage-on-gentoo insisting on 3.1.3: > > > > > > sci-mathematics/singular:0 > > > > > > (sci-mathematics/singular-3.1.3.3::gentoo, installed) pulled in by > > > > > > ~sci-mathematics/singular-3.1.3.3 required by > > > > > > (sci-mathematics/sage-5.0-r1::sage-on-gentoo, installed) > > > > > > (sci-mathematics/singular-3.1.4-r1::gentoo, ebuild scheduled for > > > merge) > > > > > > pulled in by (no parents that aren't satisfied by other packages in this > > > slot) > > > > > > > > > There also is an eselect issue. I don't know why, but eselect-blas and > > > eselect-lapack are pulled in, although blocked by the new gsl: > > > > > > [blocks B ] app-admin/eselect-blas ("app-admin/eselect-blas" is > > > blocking sci-libs/gsl-1.15-r2, sci-libs/cblas-reference-20110218) > > > [blocks B > > > > > > ] app-admin/eselect-lapack ("app-admin/eselect-lapack" is blocking > > > > > > sci-libs/gsl-1.15-r2, sci-libs/cblas-reference-20110218) > > > > > > However, without the -D option I just get a warning: > > > > > > WARNING: One or more updates have been skipped due to a dependency > > > conflict: > > > > > > sci-mathematics/singular:0 > > > > > > (sci-mathematics/singular-3.1.4-r1::gentoo, ebuild scheduled for > > > merge) > > > > > > conflicts with ~sci-mathematics/singular-3.1.3.3 required by > > > (sci-mathematics/sage-5.0-r1::sage-on-gentoo, installed) > > > > > > > > > Any ideas? Shall I carry this to the portage mailing list? > > > Cheers, > > > > We need to know what pulls these eselect modules. What is the portage > > output when you add the "t" option. It should show what wants what. > > Goes back to dev-lang/R and sci-libs/superlu. My setup has superlu > stable, but R keyworded ~amd64 the entire slot. > > [ebuild U ~] sci-mathematics/singular-3.1.4-r1 [3.1.3.3] USE="boost doc > emacs python%* readline -examples -test" 0 kB [nomerge ] > dev-lang/R-2.15.0 USE="X bash-completion cairo doc java jpeg lapack nls > openmp perl png readline tiff tk -icu -minimal -profile -static-libs" > [nomerge ] virtual/lapack-3.1 > [nomerge ] sci-libs/lapack-reference-3.1.1-r1 USE="-doc" > [ebuild N ] app-admin/eselect-lapack-0.1 0 kB > [nomerge ] sci-mathematics/sage-5.0-r1::sage-on-gentoo USE="latex > -testsuite" [nomerge ] sci-libs/scipy-0.9.0-r1 USE="-doc -umfpack" > [nomerge ] sci-libs/superlu-4.1-r1 USE="-doc -examples -static-libs > -test" [nomerge ] virtual/blas-1.0 > [nomerge ] sci-libs/blas-reference-20070226 USE="-doc" > [ebuild N ] app-admin/eselect-blas-0.1 0 kB > [nomerge ] sci-mathematics/sage-5.0-r1::sage-on-gentoo USE="latex > -testsuite" [nomerge ] dev-python/sympy-0.7.1 USE="gtk latex opengl > pdf png -doc -examples -imaging -ipython -mathml -pyglet -test -texmacs" > [ebuild U ] dev-python/pexpect-2.4::gentoo [2.0-r1::sage-on-gentoo] > USE="-doc% -examples%" 0 kB [blocks B ] app-admin/eselect-lapack > ("app-admin/eselect-lapack" is blocking sci-libs/gsl-1.15-r2, > sci-libs/cblas-reference-20110218) [blocks B ] app-admin/eselect-blas > ("app-admin/eselect-blas" is blocking sci-libs/gsl-1.15-r2, > sci-libs/cblas-reference-20110218) > You have the virtual/{blas,lapack} from the main tree not from the science overlay! Now I am not sure why eselect-blas blocks gsl which gives you cblas. Anyway keyword virtual/{blas,cblas,lapack} and upgrade them. Then let's see if you still have troubles. Francois