From unknown Sun Jun 22 00:16:34 2025 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 Content-Transfer-Encoding: 8bit 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-Spam-Score: 1.0 (+) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * 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 -- 2.40.1 From unknown Sun Jun 22 00:16:34 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests. Resent-From: Bruno Victal Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Jul 2023 02:34:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64559 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: David Elsing Cc: andreas@enge.fr, efraim@flashner.co.il, 64559@debbugs.gnu.org, bavier@posteo.net Received: via spool by 64559-submit@debbugs.gnu.org id=B64559.16893019905046 (code B ref 64559); Fri, 14 Jul 2023 02:34:01 +0000 Received: (at 64559) by debbugs.gnu.org; 14 Jul 2023 02:33:10 +0000 Received: from localhost ([127.0.0.1]:41116 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qK8cI-0001JK-2n for submit@debbugs.gnu.org; Thu, 13 Jul 2023 22:33:10 -0400 Received: from smtpmciv4.myservices.hosting ([185.26.107.240]:36090) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qK8cE-0001J9-HB for 64559@debbugs.gnu.org; Thu, 13 Jul 2023 22:33:09 -0400 Received: from mail1.netim.hosting (unknown [185.26.106.173]) by smtpmciv4.myservices.hosting (Postfix) with ESMTP id 4D60F20781; Fri, 14 Jul 2023 04:33:03 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by mail1.netim.hosting (Postfix) with ESMTP id 9121180097; Fri, 14 Jul 2023 04:33:03 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at mail1.netim.hosting Received: from mail1.netim.hosting ([127.0.0.1]) by localhost (mail1-2.netim.hosting [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id 26NuG2z0fhKX; Fri, 14 Jul 2023 04:33:03 +0200 (CEST) Received: from [192.168.1.116] (unknown [10.192.1.83]) (Authenticated sender: lumen@makinata.eu) by mail1.netim.hosting (Postfix) with ESMTPSA id 0137580060; Fri, 14 Jul 2023 04:33:02 +0200 (CEST) Message-ID: <8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu> Date: Fri, 14 Jul 2023 03:33:02 +0100 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:102.0) Gecko/20100101 Thunderbird/102.12.0 Content-Language: en-US References: From: Bruno Victal In-Reply-To: Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit X-Spam-Score: -0.1 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.1 (-) Hi David, On 2023-07-10 19:06, David Elsing wrote: > + ;; 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") Have you filed an issue with upstream regarding this? It looks to me that this is something that should be figured out by the build system or the unit tests. -- Furthermore, I consider that nonfree software must be eradicated. Cheers, Bruno. From unknown Sun Jun 22 00:16:34 2025 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: guix-patches@gnu.org Resent-Date: Fri, 14 Jul 2023 23:02:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64559 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Bruno Victal Cc: andreas@enge.fr, efraim@flashner.co.il, 64559@debbugs.gnu.org, bavier@posteo.net Received: via spool by 64559-submit@debbugs.gnu.org id=B64559.1689375718693 (code B ref 64559); Fri, 14 Jul 2023 23:02:02 +0000 Received: (at 64559) by debbugs.gnu.org; 14 Jul 2023 23:01:58 +0000 Received: from localhost ([127.0.0.1]:43627 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qKRnS-0000B7-D7 for submit@debbugs.gnu.org; Fri, 14 Jul 2023 19:01:58 -0400 Received: from mout01.posteo.de ([185.67.36.65]:60293) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qKRnP-0000Ar-9D for 64559@debbugs.gnu.org; Fri, 14 Jul 2023 19:01:57 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id DC46D240027 for <64559@debbugs.gnu.org>; Sat, 15 Jul 2023 01:01:48 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1689375708; bh=+XbBFk9ZCtvvcNc3o2xfep/2QHxcc0oiXXhGzp33Kl4=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:From; b=eLTXBH6RRwKqgm99I1zBQtKJNsi3FVTmCxR745sub0Zb8PVt2zU2a4WxTPfYHkM0l Ve+gLFxC5lfasvQo84FvByj8Bj//3fn3OTocc0MR7yFSYgc16HbCb2FiWtZHpw1KPR QElcW2Ix0eHoba4anaqxLWjxCrObHaADaR84xl0wStxdLEM9mbdoyB6ka0G6cDEJyX jufHAvafnlRuBIhSfwvdo97FooO4l+nmOzNvADw+tuj6oz4WtOgUbUOTTjPv0DPRug uq+x2SLj3EKeQ/I0+mhJtW6w+Px4EZgpTtxySaKtJYeLPuWqMbmRGV4+OQtQdjPX5g k/qOT2fugmPvw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4R2n6M2srwz6tvh; Sat, 15 Jul 2023 01:01:47 +0200 (CEST) From: David Elsing In-Reply-To: <8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu> References: <8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu> Date: Fri, 14 Jul 2023 23:01:46 +0000 Message-ID: <861qhajdwl.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Bruno Victal writes: Hello Bruno, > Have you filed an issue with upstream regarding this? > It looks to me that this is something that should be figured out by the > build system or the unit tests. that's true, I just filed an issue: https://github.com/mittinatten/freesasa/issues/94. Cheers, David From unknown Sun Jun 22 00:16:34 2025 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: guix-patches@gnu.org Resent-Date: Wed, 14 Feb 2024 19:21:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64559 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64559@debbugs.gnu.org Cc: Bruno Victal , 64559-done@debbugs.gnu.org Received: via spool by 64559-submit@debbugs.gnu.org id=B64559.17079384483475 (code B ref 64559); Wed, 14 Feb 2024 19:21:02 +0000 Received: (at 64559) by debbugs.gnu.org; 14 Feb 2024 19:20:48 +0000 Received: from localhost ([127.0.0.1]:53122 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raKoK-0000ty-6A for submit@debbugs.gnu.org; Wed, 14 Feb 2024 14:20:48 -0500 Received: from mout01.posteo.de ([185.67.36.65]:37657) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raKoH-0000tf-Ee for 64559@debbugs.gnu.org; Wed, 14 Feb 2024 14:20:46 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 22C5E240028 for <64559@debbugs.gnu.org>; Wed, 14 Feb 2024 20:20:20 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1707938421; bh=zQBynIQQ4HrzXzA4bqRMgq2p4jkvdY/N1Qy9uqTqNas=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=P/iQZBhG6DObxcp6RYpC8HhrrxEW9JsOQL2Xo2pU3U46vkoCaD5U0L1nTZunFGvUm b45JKM6LJrWOv1ZfW15IW2UduYSIPOa/6nKBiLIYQuEc49efg8AYwR/rfy+t6ty/p3 yQuLvuzI9qM9LmG70EpAxupRdBXZLl3StCHvyA9Tm8ENiubWQwv2k7NDZh3gZ8Erdu orvIVnRUTu3kuMC8VPL3tWdaYSfqa+EhzKQJCb7w9/VknI7nEM+M76q8QW4r+8XguO 8vYPqvB+f/PjreYwcG55hlvEqFdHmV9NjKK/8Dy1KX/hQlHiW5wTCTMyGM59N8quB5 7eOhMHZZXmM9g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TZp1c1tsvz9rxS; Wed, 14 Feb 2024 20:20:20 +0100 (CET) From: David Elsing In-Reply-To: <861qhajdwl.fsf@posteo.net> References: <8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu> <861qhajdwl.fsf@posteo.net> Date: Wed, 14 Feb 2024 19:20:19 +0000 Message-ID: <86a5o2n98s.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -4.2 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.2 (-----) David Elsing writes: > that's true, I just filed an issue: https://github.com/mittinatten/freesasa/issues/94. I included this patch in another patch series for rdkit, which was now applied in commit cc772e7f3172a8014e32c7ea3f6626963d4e9e16. The issue was also fixed upstream. From unknown Sun Jun 22 00:16:34 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: David Elsing Subject: bug#64559: closed (Re: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests.) Message-ID: References: <86a5o2n98s.fsf@posteo.net> X-Gnu-PR-Message: they-closed 64559 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 64559@debbugs.gnu.org Date: Wed, 14 Feb 2024 19:21:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1707938462-3520-1" This is a multi-part message in MIME format... ------------=_1707938462-3520-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #64559: [PATCH] gnu: freesasa: Fix memerr tests. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 64559@debbugs.gnu.org. --=20 64559: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D64559 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1707938462-3520-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 64559-done) by debbugs.gnu.org; 14 Feb 2024 19:20:48 +0000 Received: from localhost ([127.0.0.1]:53124 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raKoK-0000u0-GK for submit@debbugs.gnu.org; Wed, 14 Feb 2024 14:20:48 -0500 Received: from mout02.posteo.de ([185.67.36.66]:53239) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raKoH-0000td-62 for 64559-done@debbugs.gnu.org; Wed, 14 Feb 2024 14:20:46 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id E9DCD240103 for <64559-done@debbugs.gnu.org>; Wed, 14 Feb 2024 20:20:20 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1707938420; bh=zQBynIQQ4HrzXzA4bqRMgq2p4jkvdY/N1Qy9uqTqNas=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=m4JOpk4Puzpmy7+T1fqoaNhfXZotqCutpSsc7hJybXQDt395LL8dvo+GipkK2Nj2b pIX2TEfxEkI0HDV8cI4cxnB7QM0XJ4JWNd7CmFmsnln+DHFo0qwmgk18TVLxxqYjMk 7+50y729m2nNG8wuPYFkQw1TYEnJCS+qlI19ky+ZhSNXPzXHgB1FHAiFkEJKfqaO0I 87xgCTncuopphzmCVHrX4ezBEd8A7sIwKhmiXI4lXuGNmbdvvkoYjoRU6ekqBlNl4m jSIQRyqbrgsrPA76Sx2SI4lZxgWGzMnp2Uj1jTg1OGZPsDS9EUtWVmco6NYRw5T6EI 7jS+bv73JGACw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TZp1c1tsvz9rxS; Wed, 14 Feb 2024 20:20:20 +0100 (CET) From: David Elsing To: 64559@debbugs.gnu.org Subject: Re: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests. In-Reply-To: <861qhajdwl.fsf@posteo.net> References: <8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu> <861qhajdwl.fsf@posteo.net> Date: Wed, 14 Feb 2024 19:20:19 +0000 Message-ID: <86a5o2n98s.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -4.2 (----) X-Debbugs-Envelope-To: 64559-done Cc: Bruno Victal , 64559-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.2 (-----) David Elsing writes: > that's true, I just filed an issue: https://github.com/mittinatten/freesasa/issues/94. I included this patch in another patch series for rdkit, which was now applied in commit cc772e7f3172a8014e32c7ea3f6626963d4e9e16. The issue was also fixed upstream. ------------=_1707938462-3520-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 To: guix-patches@gnu.org Subject: [PATCH] gnu: freesasa: Fix memerr tests. Date: Mon, 10 Jul 2023 18:06:11 +0000 Message-Id: MIME-Version: 1.0 X-Debbugs-Cc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Content-Transfer-Encoding: 8bit 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-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * 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 -- 2.40.1 ------------=_1707938462-3520-1--