From patchwork Sun Jan 28 23:01:56 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59545 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 4F35427BBEA; Sun, 28 Jan 2024 23:03:14 +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=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 AC62727BBE2 for ; Sun, 28 Jan 2024 23:03:13 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEB7-00064F-4y; Sun, 28 Jan 2024 18:03:05 -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 1rUEAy-00062H-Ca for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:58 -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 1rUEAx-0005py-45 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:56 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB4-0004Xh-VB for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:02 +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=B68790.170648297517413 (code B ref 68790); Sun, 28 Jan 2024 23:03:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:55 +0000 Received: from localhost ([127.0.0.1]:58613 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAv-0004WT-J2 for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from mout02.posteo.de ([185.67.36.66]:38237) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAp-0004Vb-KR for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:48 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 14670240106 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:34 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482954; bh=C1YIyT0st2coxHazmijrHjh84MsNqtSQQFTSHEjtLNw=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=NVVotSbvnOX1CudYyhMqdf8p/J9zIY1bEgDH07oHHAarJNoGCQM1X+pL3WHuGpbPl eADh5o5IhbhHo+GKi66GyUdMNz9v0aYOQQB1fwCaTFWaxtNXFRLBxMUELcH3WZcmcb FI109W8V499Xyz3CDmy+KNVldjKpNL4Dyqixb9h2Q/AvaaBmBRj8CsxLNDplIZWFUT /DsrZGeA30OMe/5NUNUqZbHErJ2tGmmSu42FsrVNTtohlGIboR+4nCq5ObmvV/uPFm Mcy2iVLHMHh709zP6c5yyQUKxKhCMbyw7F/USCgCfKvXRF0QKB1S0j1nTP1od+B+mA P14gcP8kbKoSA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRls5DFPz6tsb; Mon, 29 Jan 2024 00:02:33 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:56 +0000 Message-ID: <20240128230215.1389-3-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 (gemmi): Update to 0.6.4. [arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp. (freesasa)[arguments]: Link to gemmi_cpp explicitly. --- gnu/packages/chemistry.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index df96a2f5c1..5129470e1e 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -589,7 +589,7 @@ (define-public python-pymol (define-public gemmi (package (name "gemmi") - (version "0.5.7") + (version "0.6.4") (source (origin (method git-fetch) (uri (git-reference @@ -598,7 +598,7 @@ (define-public gemmi (file-name (git-file-name name version)) (sha256 (base32 - "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) + "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y")) (patches (search-patches "gemmi-fix-sajson-types.patch" "gemmi-fix-pegtl-usage.patch")) @@ -625,7 +625,7 @@ (define-public gemmi #~(modify-phases %standard-phases (add-after 'unpack 'patch-includes (lambda _ - (substitute* (list "include/gemmi/sprintf.hpp" + (substitute* (list "src/sprintf.cpp" "include/gemmi/dirwalk.hpp" "include/gemmi/cif.hpp" "include/gemmi/json.hpp" @@ -722,7 +722,7 @@ (define-public freesasa (("libfreesasa\\.a") "libfreesasa.la") (("freesasa_LDADD \\+= libfreesasa\\.la" prev) (string-append prev "\nlibfreesasa_la_LIBADD" - " = -ljson-c ${libxml2_LIBS}\n")) + " = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n")) (("_a_SOURCES") "_la_SOURCES")) (substitute* "configure.ac" (("AC_PROG_INSTALL" inst)