From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 6C838138689 for ; Fri, 25 Jan 2013 17:56:11 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A6DF8E05B4; Fri, 25 Jan 2013 17:56:08 +0000 (UTC) Received: from mx1.d.umn.edu (mx1.d.umn.edu [131.212.109.15]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id E8A20E05A1 for ; Fri, 25 Jan 2013 17:56:07 +0000 (UTC) Received: from mxr1.d.umn.edu (mxr1.d.umn.edu [131.212.109.92]) by mx1.d.umn.edu (8.13.8/8.13.8) with ESMTP id r0PHu6pa003231 for ; Fri, 25 Jan 2013 11:56:06 -0600 (CST) Received: from mxv4.d.umn.edu (mxv4.d.umn.edu [131.212.109.48]) by mxr1.d.umn.edu (8.13.8/8.13.8) with ESMTP id r0PHu6Kx027271 for ; Fri, 25 Jan 2013 11:56:06 -0600 (CST) Received: from mx9-g.d.umn.edu (mx9-g.d.umn.edu [131.212.109.175]) by mxv4.d.umn.edu (8.14.3/8.14.3/Debian-9.4) with ESMTP id r0PHu6uI028160 for ; Fri, 25 Jan 2013 11:56:06 -0600 Received: from mail-oa0-f69.google.com (mail-oa0-f69.google.com [209.85.219.69]) by mx9-g.d.umn.edu (8.13.8/8.13.8) with ESMTP id r0PHu56p027598 for ; Fri, 25 Jan 2013 11:56:06 -0600 (CST) Received: by mail-oa0-f69.google.com with SMTP id l10so4016710oag.0 for ; Fri, 25 Jan 2013 09:56:05 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=google.com; s=20120113; h=x-received:x-received:date:from:to:subject:message-id:x-mailer :mime-version:content-type:content-transfer-encoding :x-gm-message-state; bh=MZpxWWjXRnZ/bhMGSsuCx5+oXa+NT4s7rkj/5UX07DY=; b=cxzUzBtTiiX2Oq7/D/cD5keAayENmgqswQeJNaDaLB0NjbMgrn+Je7G3bTfEOYxZhY 9U1liq69cfXPEIwmm3W68Jb1LGZH2THQOMhVrXmFpDbSDZkFLt51WtaL0ZeirSPvxPNB RY1wRqcp6lS7/0php6SuHH/NWVTxFYNqddFFTT9sv/Ycib2smPSdfNGIAdQf3l7kI6c+ aEYQiGQDe5oUzkGDWDa0yj27aTyh/TjCA6FgzrH0zubgaPg83AQy/KP0otPsbL5Nhpug X6gdH2+JOz5Z2SRBYvq//mwERgYm0Tnnkm5zDD/67NgjR8JX0J73/CdwYMbjVkFRTjBp dq0A== X-Received: by 10.50.150.148 with SMTP id ui20mr4488751igb.68.1359136565644; Fri, 25 Jan 2013 09:56:05 -0800 (PST) X-Received: by 10.50.150.148 with SMTP id ui20mr4488749igb.68.1359136565577; Fri, 25 Jan 2013 09:56:05 -0800 (PST) Received: from ledaig.d.umn.edu (ledaig.d.umn.edu. [131.212.64.12]) by mx.google.com with ESMTPS id s3sm1217930igb.14.2013.01.25.09.56.04 (version=TLSv1.2 cipher=RC4-SHA bits=128/128); Fri, 25 Jan 2013 09:56:04 -0800 (PST) Date: Fri, 25 Jan 2013 11:55:59 -0600 From: Steven Trogdon To: "gentoo-science@lists.gentoo.org" Subject: [gentoo-science] gentoo-science and gentoo-prefix Message-ID: <20130125115559.0e85c17a@ledaig.d.umn.edu> X-Mailer: Claws Mail 3.9.0 (GTK+ 2.24.12; 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: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Gm-Message-State: ALoCoQnE24yvjc8xrsos4aH08cFDzeU1F/f8LHW6pFOikLs9ISg/W7T/7je46YMKwWZGvyCZgeC0Ptuzzf/l5QGB+5Z2ioWIwQsOUFPKEjupv6ptcSsn98YBCtScmNvZqGQ08k1eThZlO247kZ4wSUjwpcnatrPcUQF55+LA+b40+3kaPF9ATkA= X-Virus-Scanned: clamav-milter 0.97.5 at mxv4 X-Virus-Status: Clean X-Archives-Salt: 60bd171d-e1b8-402a-a0b6-468bfda5bc3d X-Archives-Hash: 07cb46c8489b1c5e63cdde448d7d8735 I'm trying to install the gentoo-science overlay on top of gentoo-prefix. I assume this can be done. However in building the three packages sci-libs/gsl-1.15-r3, sci-libs/blas-reference-20120925 and sci-libs/lapack-reference-3.4.2 I get postinst errors of the type: --- * ERROR: sci-libs/gsl-1.15-r3 failed (postinst phase): * skel.eclass could not be found by inherit() * * Call stack: * ebuild.sh, line 93: Called call-ebuildshell 'pkg_postinst' * environment, line 981: Called pkg_postinst * environment, line 3106: Called alternatives-2_pkg_postinst * environment, line 567: Called cleanup_old_alternatives_module 'cblas' * environment, line 1026: Called source '/storage/strogdon/gentoo//usr/share/eselect/modules/cblas.eselect' * cblas.eselect, line 5: Called inherit 'skel' * ebuild.sh, line 261: Called die * The specific snippet of code: * [ ! -e "$location" ] && die "${1}.eclass could not be found by inherit()" * --- Is this a bug or am I doing something stupid? The packages do install but there is the error. And lastly to update packages I need to "emerge @preserved-rebuild" because of --- !!! existing preserved libs: >>> package: sci-libs/blas-reference-20120925 * - /storage/strogdon/gentoo/usr/lib/blas/reference/libblas.so.0 * - /storage/strogdon/gentoo/usr/lib/blas/reference/libblas.so.0.0.0 * used by /storage/strogdon/gentoo/usr/bin/dnsimp (sci-libs/arpack-3.1.2) * used by /storage/strogdon/gentoo/usr/lib/libarpack.so.2.0.0 (sci-libs/arpack-3.1.2) * used by /storage/strogdon/gentoo/usr/lib/libsuperlu.so.4.0.2 (sci-libs/superlu-4.3) * used by /storage/strogdon/gentoo/usr/lib/libumfpack.so.0.0.0 (sci-libs/umfpack-5.6.1-r1) --- But upon doing the emerge I get failures in the configure step of superlu - the first to be re-emerged: --- >>> Failed to emerge sci-libs/superlu-4.3, Log file: >>> '/storage/strogdon/gentoo/var/tmp/portage/sci-libs/superlu-4.3/temp/build.log' * Messages for package sci-libs/superlu-4.3: * ERROR: sci-libs/superlu-4.3 failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 93: Called call-ebuildshell 'src_configure' * environment, line 971: Called src_configure * environment, line 3327: Called autotools-utils_src_configure * environment, line 721: Called econf '--docdir=/storage/strogdon/gentoo/usr/share/doc/superlu-4.3' '--enable-shared' '--disable-static' '--with-blas=' * phase-helpers.sh, line 511: Called die * The specific snippet of code: * die "econf failed" * * If you need support, post the output of `emerge --info '=sci-libs/superlu-4.3'`, * the complete build log and the output of `emerge -pqv '=sci-libs/superlu-4.3'`. * The complete build log is located at '/storage/strogdon/gentoo/var/tmp/portage/sci-libs/superlu-4.3/temp/build.log'. * The ebuild environment file is located at '/storage/strogdon/gentoo/var/tmp/portage/sci-libs/superlu-4.3/temp/environment'. * Working directory: '/storage/strogdon/gentoo/var/tmp/portage/sci-libs/superlu-4.3/work/SuperLU_4.3' * S: '/storage/strogdon/gentoo/var/tmp/portage/sci-libs/superlu-4.3/work/SuperLU_4.3' --- The apparent reason for the failure: configure: error: Cannot find blas libraries Thanks guys, Steve