From patchwork Mon Jul 10 18:06:11 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 51665 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 549BB27BBEA; Mon, 10 Jul 2023 19:07:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9C4EB27BBE9 for ; Mon, 10 Jul 2023 19:07:10 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qIvHs-0003zh-Pt; Mon, 10 Jul 2023 14:07:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qIvHr-0003zY-9I for guix-patches@gnu.org; Mon, 10 Jul 2023 14:07:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qIvHr-0005W1-1Y for guix-patches@gnu.org; Mon, 10 Jul 2023 14:07:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qIvHp-00021E-QY; Mon, 10 Jul 2023 14:07:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net, guix-patches@gnu.org Resent-Date: Mon, 10 Jul 2023 18:07:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 64559 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64559@debbugs.gnu.org Cc: David Elsing , andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Received: via spool by submit@debbugs.gnu.org id=B.16890124167747 (code B ref -1); Mon, 10 Jul 2023 18:07:01 +0000 Received: (at submit) by debbugs.gnu.org; 10 Jul 2023 18:06:56 +0000 Received: from localhost ([127.0.0.1]:49087 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qIvHg-00020o-5j for submit@debbugs.gnu.org; Mon, 10 Jul 2023 14:06:56 -0400 Received: from lists.gnu.org ([209.51.188.17]:46806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qIvHP-00020Q-Bl for submit@debbugs.gnu.org; Mon, 10 Jul 2023 14:06:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qIvHO-0003wo-R5 for guix-patches@gnu.org; Mon, 10 Jul 2023 14:06:35 -0400 Received: from mout02.posteo.de ([185.67.36.66]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qIvHM-0005MT-Tl for guix-patches@gnu.org; Mon, 10 Jul 2023 14:06:34 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 27CC1240101 for ; Mon, 10 Jul 2023 20:06:28 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1689012388; bh=QT7d2Qgjc2dKBs2x+0e/Cy5kfLpdTLtU/q3JTkMlii0=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=nuTmGfuAycF6PXRhN4VP0nVsS089b0FwiKyabw9Qx8Kw0rfElpM5wZ/ca2mBMrttg Ej5MTuzTW/456cPRnEyBkHhUdXo/nxuvRlD8Ery4H33bGHzke6VcKf6XULVzqtR7zv ue5hZU0TZ0Gw201F9tqLIPyzH4Y4XvQn8va5k8ANq8+Bx46fs2lD04l0YoZpdOQM4t 9SqdL5Tq4wX7SbDUU9tmZeVPF+YFFZzVvxrqCgBW05UbyjvAY7twrQw6gWToI32diO brYSZrzRJvi5MBZqMtwVu4fIwLvhjdnHi4D4VAXVTM2dLljyRGiYNknMItrPllFSq7 bdGKA8U6ZS+sA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4R0BlR4pyRz6txG; Mon, 10 Jul 2023 20:06:27 +0200 (CEST) From: David Elsing Date: Mon, 10 Jul 2023 18:06:11 +0000 Message-Id: MIME-Version: 1.0 Received-SPF: pass client-ip=185.67.36.66; envelope-from=david.elsing@posteo.net; helo=mout02.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (freesasa)[arguments]: Add "CFLAGS=-fno-builtin-malloc" to #:configure-flags. --- gnu/packages/chemistry.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index cddccf8aea..431b845989 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -703,7 +703,11 @@ (define-public freesasa #~(list "--enable-check" "--enable-parser-generator" "CXXFLAGS=-std=c++17" - "--enable-doxygen") + "--enable-doxygen" + ;; Some tests rely on replacing malloc with a wrapper which + ;; fails in a controlled way, but this does not work if the call + ;; is replaced. + "CFLAGS=-fno-builtin-malloc") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-libc++-linking