From patchwork Fri Apr 21 00:03:57 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49338 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 90EFC27BBE9; Fri, 21 Apr 2023 01:05:28 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 7EAE027BBE2 for ; Fri, 21 Apr 2023 01:05:26 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ppeH3-0005uj-41; Thu, 20 Apr 2023 20:05:13 -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 1ppeGu-0005uM-Tf for guix-patches@gnu.org; Thu, 20 Apr 2023 20:05:05 -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 1ppeGt-0001ip-2E for guix-patches@gnu.org; Thu, 20 Apr 2023 20:05:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ppeGs-00014q-GW; Thu, 20 Apr 2023 20:05:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62980] [PATCH 1/2] gnu: bpp-popgen: Update to 2.4.1. References: <5f1d7d011e24483ba7785b38c3fadef3@mdc-berlin.de> In-Reply-To: <5f1d7d011e24483ba7785b38c3fadef3@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 21 Apr 2023 00:05:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62980 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62980@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 62980-submit@debbugs.gnu.org id=B62980.16820354674083 (code B ref 62980); Fri, 21 Apr 2023 00:05:02 +0000 Received: (at 62980) by debbugs.gnu.org; 21 Apr 2023 00:04:27 +0000 Received: from localhost ([127.0.0.1]:38902 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppeGJ-00013j-7v for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:27 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppeGF-00013S-SJ for 62980@debbugs.gnu.org; Thu, 20 Apr 2023 20:04:24 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1682035457; x=1683849858; bh=rGtaXtO3/AHM8SP J4rdmqcwwoxgjf3VfGhDy3f71HV0=; b=U4dpoenqz+QtglMf9CbY8Jwlpp4PcZf lgYjZ1YgumAyTbAwQyOhJqc1P4vsZuUHI5jfL0B2b+2cBEcDoGrUFrYj/fBhGvQf LqZNG6Fl24/IXpqJ7cWqb0k8fADbpCpC4Khq77iaM4wzWpv2vN5VxehGpFZCWZ0P j0Bnir+rHPfQ= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8007C160123 for <62980@debbugs.gnu.org>; Fri, 21 Apr 2023 02:04:17 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr 2023 02:04:15 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 21 Apr 2023 02:03:57 +0200 Message-ID: <20230421000358.11316-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--3.511100-5.000000 X-TMASE-MatchedRID: 8iOsdbjc4EnBP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4qAI7Mvq/sL54PN dYXFrfiyIVOe0TAdekipgf1jMun5ewV2NKF6aideEXjPIvKd74BMkOX0Uoduuc3wMjzgVvguChb 10lmaN/ZYzJcD0gVKSpzSLZJ1HkA9+YQ9ocFzl0vece0aRiX9Wn607foZgOWypjlkbDvDJ4dU82 kILwgVLQ1RxwBNHJ3Uh6Tqy0vOnV4qACWCM+Film9OepgphdNGEOS/art35UOXBXaJoB9JZ4MbH 85DUZXy3wtt/1c/bBwXvQkGi3tjz/cUt5lc1lLgKIzdZS3ou0XYe+4pAcUAuiLBJq0qUXetrOJy I5Skqs9/srIR4pXmuZiuxBoOVGvdYBkKFGzNFj71irJpp6s6FgR/Ol8WNETk2qgVOBb5vuxZKCa lsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.511100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 3FE7DB78EF4B509B71EADEA0BCA50F9F0669CE3648AEBC9BE910D0754D0200542002:F 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/bioinformatics.scm (bpp-popgen): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. --- gnu/packages/bioinformatics.scm | 49 +++++++++++++++------------------ 1 file changed, 22 insertions(+), 27 deletions(-) base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01 prerequisite-patch-id: 5853dbe5778b2160c2bf5dca3f01be75fcbb678c prerequisite-patch-id: 4af2ed7c595ec571d717d161aff1ef51a8dfc365 prerequisite-patch-id: e460dac992e961a5f13af1ed99bfad48d2f0ceb5 prerequisite-patch-id: 4241e6e34dc593a321a69e135db83293eaf011f7 prerequisite-patch-id: 78c7d0a29aee256ae2df1759863ef7e6dc34102f prerequisite-patch-id: 4dc46155f0d7730f6996403f20442c2892e08a7c diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4cea24632..3969e205b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2296,35 +2296,30 @@ (define-public bpp-phyl-omics (license license:cecill))) (define-public bpp-popgen - ;; The last release was in 2014 and the recommended way to install from source - ;; is to clone the git repository, so we do this. - ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page - (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) - (package - (name "bpp-popgen") - (version (string-append "2.2.0-1." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "http://biopp.univ-montp2.fr/git/bpp-popgen") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) - (build-system cmake-build-system) - (arguments - `(#:parallel-build? #f - #:tests? #f)) ; There are no tests. - (inputs - (list bpp-core bpp-seq)) - (home-page "http://biopp.univ-montp2.fr") - (synopsis "Bio++ population genetics library") - (description - "Bio++ is a set of C++ libraries for Bioinformatics, including sequence + (package + (name "bpp-popgen") + (version "2.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-popgen") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; There are no tests. + (inputs + (list bpp-core bpp-seq)) + (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/") + (synopsis "Bio++ population genetics library") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides population genetics-related modules.") - (license license:cecill-c)))) + (license license:cecill-c))) (define-public bpp-seq (package