From owner-freebsd-python@FreeBSD.ORG Sun Jun 15 02:24:18 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 4F2796C0; Sun, 15 Jun 2014 02:24:18 +0000 (UTC) Received: from mail-ve0-x233.google.com (mail-ve0-x233.google.com [IPv6:2607:f8b0:400c:c01::233]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (Client CN "smtp.gmail.com", Issuer "Google Internet Authority G2" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id EC3BC2477; Sun, 15 Jun 2014 02:24:17 +0000 (UTC) Received: by mail-ve0-f179.google.com with SMTP id sa20so2894489veb.38 for ; Sat, 14 Jun 2014 19:24:16 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :cc:content-type; bh=kiUd6Q2Ec1lMYee/7LvQN2rW/fCorSz+bEWkWPOrpwA=; b=PoJOFvh6PJ5QYNpR0oRbGwK9drZdrNE6J5ZAxBXZGsDFSvJrw8qS4IN7fJRzHc5Utv 5BXDSUNCwEEJCqIYR/xPHNGfr9CQpIYDtmsxQdzFBhtVWoFaQ85wTAiMCuQ9J9h9lPi+ gP6xmWr6l+EOcPpVEj14nz9KnFSuB1Gc1PdTMHASZsNJon5Q1UGLNDQWun3OG2yTSD2G Z3Lc3XBJD6+DbyzJSgn8FZAFGnh40UPXRAL/hTh2QWrCYdZ2d2imEuqXHlYX8g0TmkdX q8XwK6wxf0XLMYIsXPdOEpoLgK/Yza8qk9ObkVN3Utp2ZH0tyvsBOAyynCML+v5c7IHf O83A== MIME-Version: 1.0 X-Received: by 10.52.248.146 with SMTP id ym18mr2028283vdc.8.1402799056649; Sat, 14 Jun 2014 19:24:16 -0700 (PDT) Received: by 10.58.80.38 with HTTP; Sat, 14 Jun 2014 19:24:16 -0700 (PDT) In-Reply-To: <5385CF53.10608@saltant.com> References: <536C40B0.2060705@saltant.com> <53718C14.1040807@saltant.com> <5385CF53.10608@saltant.com> Date: Sun, 15 Jun 2014 10:24:16 +0800 Message-ID: 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] From: Irjohn Junus To: "John W. O'Brien" Content-Type: text/plain; charset=UTF-8 X-Content-Filtered-By: Mailman/MimeDel 2.1.18 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: Sun, 15 Jun 2014 02:24:18 -0000 John, Here's my /usr/local/lib/compat/pkg: [ijunus@mars /]$ ls /usr/local/lib/compat/pkg libXau.so.0 libgd.so.4 libxcb-sync.so.0 libaprutil-1.so.3 libpcre.so.1 libxcb-xkb.so.0 libatalk.so.3 libpcre16.so.0 libxcb.so.2 libffi.so.5 libpixman-1.so.30 lxml-3.1.0-py2.7.egg-info libfreetype.so.9 libsvn_ra_neon-1.so.0 libgcrypt.so.18 libxcb-randr.so.1 Thanks, Irjohn On Wed, May 28, 2014 at 7:58 PM, John W. O'Brien wrote: > 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 similar. > > > 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=atlas > > library_dirs = > > > /usr/lib:/usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd9.1/4.7.3/../../../ > > include_dirs = > > /usr/include:/usr/local/include:/usr/local/include/suitesparse > > src_dirs = /usr/local/src > > # search static libraries (.a) in preference to shared ones (.so) > > search_static_first = 0 > > [atlas] > > library_dirs = > > > /usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd9.1/4.7.3/../../../ > > atlas_libs = 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=5.12.4 > > #WITH_MPM=worker > > 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 > >