From owner-freebsd-python@FreeBSD.ORG Sun May 18 04:30:26 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 E7CC8684; Sun, 18 May 2014 04:30:25 +0000 (UTC) Received: from mail-ve0-x232.google.com (mail-ve0-x232.google.com [IPv6:2607:f8b0:400c:c01::232]) (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 877BD277E; Sun, 18 May 2014 04:30:25 +0000 (UTC) Received: by mail-ve0-f178.google.com with SMTP id sa20so4993245veb.37 for ; Sat, 17 May 2014 21:30:23 -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=6MCM8wpjFjYBJT1BgGkT+mMLQrYhxJmNhiEtNq7R9c4=; b=K9VXoixMqAZhVrqatK3Ns6rcLHqghVfuDde8K4Y6Vg4ChupGA1iZxZWMqqgl4usWtA LWNVo1xh0fGMIh7+k0sJLOX8GW6v2wsJpYDKWNHncxBTRAZc4MIjKZgUrpPhWEgbPQxk XluNcFkgB2JlXZUDubrma2VbNk0ltuDe6HXIbfLIhsOLlMeWthPKYP46P3s1VXXhMMBS n9D+iWODybI5AHzfPyUHN/5NQvTbqNan4Fn7VPJpbeRXu50KepgoHnkw3Yr2Jor4ntua a5rERHhg2iDhahwyYBsOLl1z5Eh4tmm2laZczZWXSopcGRZJopxTZz0v2f2SgMF8xjjb pbMQ== MIME-Version: 1.0 X-Received: by 10.52.137.174 with SMTP id qj14mr5343047vdb.32.1400387423724; Sat, 17 May 2014 21:30:23 -0700 (PDT) Received: by 10.58.168.199 with HTTP; Sat, 17 May 2014 21:30:23 -0700 (PDT) In-Reply-To: <53718C14.1040807@saltant.com> References: <536C40B0.2060705@saltant.com> <53718C14.1040807@saltant.com> Date: Sun, 18 May 2014 12:30:23 +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, 18 May 2014 04:30:26 -0000 John, Thank you for looking at this. Apologies for my late reply it's been crazy busy at work lately. Here's answers to your questions: 1. 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] 2. 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 3. cat /etc/make.conf # added by use.perl 2013-03-25 18:12:09 PERL_VERSION=5.12.4 #WITH_MPM=worker 4. I use portmaster exclusively, to install: portmaster --packages-build --delete-build-only port-name to upgrade: portmaster --dwv port-name Thanks, Irjohn On Tue, May 13, 2014 at 11:05 AM, John W. O'Brien wrote: > On 5/8/14 11:33 PM, Irjohn Junus wrote: > > Hi John, > > > > No worries and yes I'm still having the problem. > > > > I remember seeing this message: > > ===>>> pkg-message for gcc-4.7.3_1 > > To ensure binaries built with this toolchain find appropriate versions > > of the necessary run-time libraries, you may want to link using > > > > -Wl,-rpath=/usr/local/lib/gcc47 > > > > after upgrading gcc port a few days ago, which is described in your link > > [0]. Do I issue this command as root? Need advice here, thanks. > > > > Regards, > > Irjohn > > > > > > On Fri, May 9, 2014 at 10:42 AM, John W. O'Brien > > wrote: > > > > On 4/18/14 8:45 AM, Irjohn Junus wrote: > > > Dear All, > > > > > > I'm running 9.1-RELEASE and today just after freebsd-update to p11 > and > > > updating ports to the latest found out that pandas won't import > after > > > MySQLdb is imported first. Strangely, it will import no problem if > > > MySQLdb is imported after: > > > > Hi Irjohn, > > > > Sorry for the long delay. Are you still having this problem? > > > > >>>> import MySQLdb > > >>>> import pandas as pd > > > /lib/libgcc_s.so.1: version GCC_4.6.0 required by > > > /usr/local/lib/gcc47/libgfortran.so.3 not found > > [...] > > > Traceback (most recent call last): > > [...] > > > File > > "/usr/local/lib/python2.7/site-packages/numpy/linalg/linalg.py", > > > line 29, in > > > from numpy.linalg import lapack_lite, _umath_linalg > > > ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by > > > /usr/local/lib/gcc47/libgfortran.so.3 not found > > > > It looks like this thread [0], these commits [1] [2], and this PR [3] > > are related. > > > > [0] > > > https://lists.freebsd.org/pipermail/freebsd-toolchain/2014-April/001149.html > > > > [1] https://svnweb.freebsd.org/ports?view=revision&revision=351167 > > > > [2] https://svnweb.freebsd.org/ports?view=revision&revision=351159 > > > > [3] https://www.freebsd.org/cgi/query-pr.cgi?pr=185902 > > Irjohn, > > This is just a little out of my depth, so I'm going to talk through it > out loud while I investigate. Presumably somebody more knowledgeable > than I will step in to correct me if I get something wrong. > > First off, there are a few open PRs ([0], [1]) on math/py-numpy, both of > which seem to have been triggered when ports started using GCC 4.7 by > default [2]. > > What I know from reading gcc(1) is that "-Wl,