From patchwork Sun Jan 28 23:02:01 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59549 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 A7B2727BBE9; Sun, 28 Jan 2024 23:04:06 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable 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 C88C227BBE2 for ; Sun, 28 Jan 2024 23:04:05 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEBw-0006jF-OE; Sun, 28 Jan 2024 18:03:56 -0500 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 1rUEBv-0006eD-KG for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEBv-0005vz-Ad for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEC3-0004aM-6P for guix-patches@gnu.org; Sun, 28 Jan 2024 18:04:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648298817523 (code B ref 68790); Sun, 28 Jan 2024 23:04:03 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:03:08 +0000 Received: from localhost ([127.0.0.1]:58632 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEB9-0004YT-IQ for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:03:07 -0500 Received: from mout01.posteo.de ([185.67.36.65]:36857) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAw-0004WB-DZ for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id D66F9240027 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:40 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482960; bh=IVAn8t0f+MsY16zKNYINU4vs8CmZXSAUuF+WEc1DxYM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=pX4TLc8gWVOcSsjO2kaf7sbMsdEDp8sUmxCuKEBeTdlwfMn5sHpTYsoMGIgb55c8Q oc9Y0FARitTsm+GAmoBAOe7bJkC3svkUI+iS51qq5r1Z32XwoR4Ft8aqRdfsUzTpPN x5unZqrWzubAC/5fwJ9cgbb+2EQvST37xRAivjaM4a+olvppc4P2WRZUz6spJiEpt+ OexKsvIv1OctIvDT/IspvTl6gM0SqL/uF7vdVBJLSNHajz0xcjzrBGTj3+iK5kJ1Ju rW0rdjtGnAO0HqNU/m4REN1rVc83uDALfEKHJjdTQEIqy5Oamjfr/lBwbOVP3dUX+n j29+SHeYrz8JQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRm03KFZz6twm; Mon, 29 Jan 2024 00:02:40 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:02:01 +0000 Message-ID: <20240128230215.1389-8-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> MIME-Version: 1.0 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 | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5e19bdf182..98141737ac 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -708,7 +708,12 @@ (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. This was fixed upstream, remove once there is a + ;; new release. + "CFLAGS=-fno-builtin-malloc") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-libc++-linking