From patchwork Sun Jun 18 11:28:51 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 51044 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 3D9D327BBEA; Sun, 18 Jun 2023 12:31:05 +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=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, 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 69BAC27BBE2 for ; Sun, 18 Jun 2023 12:31:04 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qAqc6-0006NQ-L5; Sun, 18 Jun 2023 07:30:34 -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 1qAqbl-000647-93 for guix-patches@gnu.org; Sun, 18 Jun 2023 07:30:14 -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 1qAqbk-0003uw-Pn for guix-patches@gnu.org; Sun, 18 Jun 2023 07:30:13 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qAqbk-0004FP-Lx for guix-patches@gnu.org; Sun, 18 Jun 2023 07:30:12 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64150] [PATCH 24/24] gnu: bioruby: Update to 2.0.4. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 18 Jun 2023 11:30:12 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64150 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64150@debbugs.gnu.org Received: via spool by 64150-submit@debbugs.gnu.org id=B64150.168708776614100 (code B ref 64150); Sun, 18 Jun 2023 11:30:12 +0000 Received: (at 64150) by debbugs.gnu.org; 18 Jun 2023 11:29:26 +0000 Received: from localhost ([127.0.0.1]:53365 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qAqaz-0003fG-OH for submit@debbugs.gnu.org; Sun, 18 Jun 2023 07:29:26 -0400 Received: from mira.cbaines.net ([212.71.252.8]:42690) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qAqaX-0003Zi-7g for 64150@debbugs.gnu.org; Sun, 18 Jun 2023 07:29:01 -0400 Received: from localhost (unknown [217.155.61.229]) by mira.cbaines.net (Postfix) with ESMTPSA id 4E2AC27BBFD for <64150@debbugs.gnu.org>; Sun, 18 Jun 2023 12:28:55 +0100 (BST) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id 2bd769fc for <64150@debbugs.gnu.org>; Sun, 18 Jun 2023 11:28:54 +0000 (UTC) From: Christopher Baines Date: Sun, 18 Jun 2023 12:28:51 +0100 Message-Id: X-Mailer: git-send-email 2.40.1 In-Reply-To: <87leghko6e.fsf@cbaines.net> References: <87leghko6e.fsf@cbaines.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/bioinformatics.scm (bioruby): Update to 2.0.4. [arguments]: Update style. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e356cba5d..4edcc28d12 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10876,34 +10876,34 @@ (define-public bio-blastxmlparser (define-public bioruby (package (name "bioruby") - (version "1.5.2") + (version "2.0.4") (source (origin (method url-fetch) (uri (rubygems-uri "bio" version)) (sha256 (base32 - "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) + "08aknxk2ingwscwfqpw5vnax6jpk1sxfaialravladb63hcl8dx9")))) (build-system ruby-build-system) (propagated-inputs (list ruby-libxml)) (native-inputs (list which)) ; required for test phase (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'patch-test-command - (lambda _ - (substitute* '("test/functional/bio/test_command.rb") - (("/bin/sh") (which "sh"))) - (substitute* '("test/functional/bio/test_command.rb") - (("/bin/ls") (which "ls"))) - (substitute* '("test/functional/bio/test_command.rb") - (("which") (which "which"))) - (substitute* '("test/functional/bio/test_command.rb", - "test/data/command/echoarg2.sh") - (("/bin/echo") (which "echo"))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'patch-test-command + (lambda _ + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/sh") (which "sh"))) + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/ls") (which "ls"))) + (substitute* '("test/functional/bio/test_command.rb") + (("which") (which "which"))) + (substitute* '("test/functional/bio/test_command.rb" + "test/data/command/echoarg2.sh") + (("/bin/echo") (which "echo")))))))) (synopsis "Ruby library, shell and utilities for bioinformatics") (description "BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has