From owner-freebsd-python@freebsd.org Mon Mar 20 20:24:27 2017 Return-Path: Delivered-To: freebsd-python@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 14CFFD14664 for ; Mon, 20 Mar 2017 20:24:27 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mailman.ysv.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id ED679C1E for ; Mon, 20 Mar 2017 20:24:26 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: by mailman.ysv.freebsd.org (Postfix) id ECC88D14663; Mon, 20 Mar 2017 20:24:26 +0000 (UTC) Delivered-To: python@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id EC7A1D14662 for ; Mon, 20 Mar 2017 20:24:26 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2001:1900:2254:206a::16:76]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id C3DA3C1D for ; Mon, 20 Mar 2017 20:24:26 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from bugs.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id v2KKOQfE002475 for ; Mon, 20 Mar 2017 20:24:26 GMT (envelope-from bugzilla-noreply@freebsd.org) From: bugzilla-noreply@freebsd.org To: python@FreeBSD.org Subject: [Bug 217968] math/py-numpy: Possible regression with fortran linkage Date: Mon, 20 Mar 2017 20:24:26 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Only Me X-Bugzilla-Who: bacon4000@gmail.com X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: python@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter flagtypes.name Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated MIME-Version: 1.0 X-BeenThere: freebsd-python@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: FreeBSD-specific Python issues List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 20 Mar 2017 20:24:27 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D217968 Bug ID: 217968 Summary: math/py-numpy: Possible regression with fortran linkage Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: python@FreeBSD.org Reporter: bacon4000@gmail.com Assignee: python@FreeBSD.org Flags: maintainer-feedback?(python@FreeBSD.org) The following error started appearing since running pkg upgrade this mornin= g.=20 The qiime-test script had been working for the past couple weeks and there = have been no major changes to the qiime port lately. I can still build and run fortran programs using -Wl,-rpath,/usr/local/lib/gcc49. This looks to me like a numpy link error, maybe failing to use rpath to load the correct libgcc? Thanks, Jason FreeBSD unixdev.ceas bacon ~ 403: ./qiime-test qiime-tests/ Traceback (most recent call last): File "./all_tests.py", line 10, in from qiime.util import (parse_command_line_parameters, get_options_look= up, File "/usr/local/lib/python2.7/site-packages/qiime/util.py", line 35, in from numpy import (array, zeros, shape, vstack, ndarray, asarray, File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 142= , in from . import add_newdocs File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line = 13, in from numpy.lib import add_newdoc File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line= 8, in from .type_check import * File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", li= ne 11, in import numpy.core.numeric as _nx File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 14, in from . import multiarray ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by /usr/local/lib/gcc49/libgfortran.so.3 not found --=20 You are receiving this mail because: You are the assignee for the bug.=