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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 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Spam-Score: 3.65 X-Migadu-Queue-Id: 38B7943867 X-Spam-Score: 3.65 X-Migadu-Scanner: mx11.migadu.com X-TUID: 8+Z8o6UKK/Cz * 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 -- 2.41.0