From owner-freebsd-ports-bugs@freebsd.org Mon Feb 4 16:33:57 2019 Return-Path: Delivered-To: freebsd-ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 6D24614D4C11 for ; Mon, 4 Feb 2019 16:33:57 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 054C68DC0C for ; Mon, 4 Feb 2019 16:33:57 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: by mailman.ysv.freebsd.org (Postfix) id B4CB514D4C0C; Mon, 4 Feb 2019 16:33:56 +0000 (UTC) Delivered-To: ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 8D1B614D4C0B for ; Mon, 4 Feb 2019 16:33:56 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mxrelay.ysv.freebsd.org (mxrelay.ysv.freebsd.org [IPv6:2001:1900:2254:206a::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.ysv.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 236C48DC09 for ; Mon, 4 Feb 2019 16:33:56 +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 mxrelay.ysv.freebsd.org (Postfix) with ESMTPS id 50AC141DC for ; Mon, 4 Feb 2019 16:33:55 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id x14GXtNj012699 for ; Mon, 4 Feb 2019 16:33:55 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id x14GXtfZ012698 for ports-bugs@FreeBSD.org; Mon, 4 Feb 2019 16:33:55 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 235499] science/py-abipy Date: Mon, 04 Feb 2019 16:33:54 +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: rmason@mun.ca X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: yuri@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-ports-bugs@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 04 Feb 2019 16:33:57 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D235499 Bug ID: 235499 Summary: science/py-abipy Product: Ports & Packages Version: Latest Hardware: i386 OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: yuri@freebsd.org Reporter: rmason@mun.ca Flags: maintainer-feedback?(yuri@freebsd.org) Assignee: yuri@freebsd.org Running abiview as per the abinit RF2 tutorial produces an error: abiview.py-3.6 ddb trf2_3_DDB -sns=3Dtalk Traceback (most recent call last): File "/usr/local/bin/abiview.py-3.6", line 15, in from abipy import abilab File "/usr/local/lib/python3.6/site-packages/abipy/abilab.py", line 43, in from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter, ElectronDos, ElectronDosPlotter, File "/usr/local/lib/python3.6/site-packages/abipy/electrons/__init__.py", line 3, in from .gsr import * File "/usr/local/lib/python3.6/site-packages/abipy/electrons/gsr.py", line 20, in from abipy.tools.tensors import Stress File "/usr/local/lib/python3.6/site-packages/abipy/tools/tensors.py", line 10, in from pymatgen.analysis.elasticity.tensors import Tensor, SquareTensor File "/usr/local/lib/python3.6/site-packages/pymatgen/analysis/elasticity/__init= __.py", line 5, in from .elastic import * File "/usr/local/lib/python3.6/site-packages/pymatgen/analysis/elasticity/elasti= c.py", line 14, in from scipy.integrate import quad File "/usr/local/lib/python3.6/site-packages/scipy/integrate/__init__.py", line 93, in from ._bvp import solve_bvp File "/usr/local/lib/python3.6/site-packages/scipy/integrate/_bvp.py", li= ne 11, in from scipy.optimize import OptimizeResult File "/usr/local/lib/python3.6/site-packages/scipy/optimize/__init__.py", line 271, in from ._minimize import * File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_minimize.py", line 32, in from ._trustregion_constr import _minimize_trustregion_constr File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/= __init__.py", line 4, in from .minimize_trustregion_constr import _minimize_trustregion_constr File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/= minimize_trustregion_constr.py", line 10, in from .equality_constrained_sqp import equality_constrained_sqp File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/= equality_constrained_sqp.py", line 5, in from .projections import projections File "/usr/local/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/= projections.py", line 9, in from sksparse.cholmod import cholesky_AAt File "sksparse/cholmod.pyx", line 240, in init sksparse.cholmod AssertionError The same error can be triggered thus: Python 3.6.8 (default, Jan 3 2019, 20:20:29)=20 [GCC 4.2.1 Compatible FreeBSD Clang 6.0.0 (tags/RELEASE_600/final 326565)] = on freebsd11 Type "help", "copyright", "credits" or "license" for more information. >>> import spglib >>> import pymatgen >>> from abipy import abilab I have tested py27-abinit with the same result. I have tested abipy instal= led from both the FreeBSD repository and from my own poudriere repository. In = each case the same error occurs. This is my first FreeBSD bug report: please accept my apology if it is incomplete in some way. Thanks, Roger --=20 You are receiving this mail because: You are the assignee for the bug.=