From owner-freebsd-python@FreeBSD.ORG Wed May 28 11:58:25 2014 Return-Path: Delivered-To: python@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 74053B73; Wed, 28 May 2014 11:58:25 +0000 (UTC) Received: from homiemail-a74.g.dreamhost.com (sub4.mail.dreamhost.com [69.163.253.135]) by mx1.freebsd.org (Postfix) with ESMTP id 4AFAB2DAD; Wed, 28 May 2014 11:58:24 +0000 (UTC) Received: from homiemail-a74.g.dreamhost.com (localhost [127.0.0.1]) by homiemail-a74.g.dreamhost.com (Postfix) with ESMTP id 372D467C06E; Wed, 28 May 2014 04:58:18 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=saltant.com; h=message-id :date:from:mime-version:to:cc:subject:references:in-reply-to: content-type; s=saltant.com; bh=2ZAqD5qiEFdu1nVrR+5HbwLB7Mc=; b= IWFlhKzQv5UWcq5rEAo8PyAZKaGwwbflgOgWUltx8W5Q3vHREnVK6EPS4BQkYU9r e0W37cWW9UBdTFP0NI4GWfseepXPh7dfaiqUX/hhkPpxaQox6g9JhtZ4zZtMLYLB u8cd79IOWu+C+zaOUA9+12x5IGnLRWEMvysM++XMBiU= Received: from dreck.saltant.net (dreck.saltant.net [72.78.188.150]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) (Authenticated sender: john@saltant.com) by homiemail-a74.g.dreamhost.com (Postfix) with ESMTPSA id D4D2A67C06B; Wed, 28 May 2014 04:58:17 -0700 (PDT) Message-ID: <5385CF53.10608@saltant.com> Date: Wed, 28 May 2014 07:58:11 -0400 From: "John W. O'Brien" Organization: Saltant Solutions User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:24.0) Gecko/20100101 Thunderbird/24.5.0 MIME-Version: 1.0 To: Irjohn Junus Subject: Re: math/py-numpy cannot satisfy libgfortran dependency on libgcc_s/GCC_4.6.0 [WAS: Re: py27-pandas-0.13.1_1 conflict with py27-MySQLdb-1.2.3_4] References: <536C40B0.2060705@saltant.com> <53718C14.1040807@saltant.com> In-Reply-To: X-Enigmail-Version: 1.6 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="QLPrh6JwJHKsEpdsil8auDjr0ExSmxXob" Cc: python@freebsd.org, Jimmy Olgeni X-BeenThere: freebsd-python@freebsd.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: FreeBSD-specific Python issues List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 28 May 2014 11:58:25 -0000 This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --QLPrh6JwJHKsEpdsil8auDjr0ExSmxXob Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On 5/18/14 12:30 AM, Irjohn Junus wrote: > Thank you for looking at this. Apologies for my late reply it's been > crazy busy at work lately. I completely understand. As you can probably tell, my situation is simila= r. > Here's answers to your questions: >> 1. What is the rpath stored in your copy of those numpy files? >> That is, what is the output from >> >> cd /usr/local/lib/python2.7/site-packages/numpy/linalg >> readelf -d _umath_linalg.so | grep RPATH >> readelf -d lapack_lite.so | grep RPATH >> >> ? > readelf -d _umath_linalg.so | grep RPATH > 0x000000000000000f (RPATH) Library rpath: > [/usr/local/lib/gcc47] > readelf -d lapack_lite.so | grep RPATH > 0x000000000000000f (RPATH) Library rpath: > [/usr/local/lib/gcc47] That looks correct to me. >> 2. What is the contents of >> /usr/local/lib/python2.7/site-packages/numpy/distutils/site.cfg on = your >> machine? > cat /usr/local/lib/python2.7/site-packages/numpy/distutils/site.cfg > [DEFAULT] > lapack_type=3Datlas > library_dirs =3D > /usr/lib:/usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd= 9.1/4.7.3/../../../ > include_dirs =3D > /usr/include:/usr/local/include:/usr/local/include/suitesparse > src_dirs =3D /usr/local/src > # search static libraries (.a) in preference to shared ones (.so) > search_static_first =3D 0 > [atlas] > library_dirs =3D > /usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd9.1/4.7.3= /../../../ > atlas_libs =3D lapack, blas Just like mine. >> 2. What is the contents of /etc/make.conf on your machine? > cat /etc/make.conf > # added by use.perl 2013-03-25 18:12:09 > PERL_VERSION=3D5.12.4 > #WITH_MPM=3Dworker Totally innocuous. >> 4. How to you install and upgrade your ports? Build from source >> by hand? Build from source with the help of portmaster, >> poudriere, etc? >> Install binary packages with pkg_* or ports-mgmt/pkg (pkgng)? > 4. > I use portmaster exclusively, to install: > portmaster --packages-build --delete-build-only port-name > to upgrade: > portmaster --dwv port-name I'm taking a stab in the dark here. Based on the '-w' option, might there be any stale libs hanging around in /usr/local/lib/compat/pkg? I haven't been able to reproduce this, so I'm not sure which tree to bark up next. -John --QLPrh6JwJHKsEpdsil8auDjr0ExSmxXob Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) iQEcBAEBCgAGBQJThc9XAAoJEORay8JGGICYjwoIAJoMRU8woJaMx6S4lM4y1XUm KwNyW4wltLRnPijz5tInWOapd6ZtM2Nd+INpFmxCfgFs6mrUmaW79bPEINl761XI Oh3KgYaKhULEXFsOBXqWpABxDl9vJuY7ogf6rYemXedmZ0CO15CKT9sFEhUKLpjW 7xBqi10nGI7CFzpAmkOiFxwfQqox+enQDcA3DqcYDRhp+jeLWwDRW8JTFRZcx+Q9 FZYJiscgH5v4idISJS+rG/rjixgwfxjMDqslPu1iTvmz14NlgegVffrObELLsIiS qmjdxg+DFvL2eLezzISnCdsyTrePHWHf2BWu9J7G6VQ1TbB4LXlGZJ+a385d61k= =x50t -----END PGP SIGNATURE----- --QLPrh6JwJHKsEpdsil8auDjr0ExSmxXob--