From patchwork Tue Apr 26 12:46:32 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38905 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 4F12827BBEA; Tue, 26 Apr 2022 13:48:52 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 F3CDA27BBE9 for ; Tue, 26 Apr 2022 13:48:51 +0100 (BST) Received: from localhost ([::1]:50238 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKcd-0000N3-5j for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:48:51 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43896) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Bv-4G for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43665) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKaw-0007VV-Ei for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKaw-0004mX-Av for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 2/9] gnu: tabixpp: Use #:make-flags. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55125 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55125@debbugs.gnu.org Cc: Arun Isaac Received: via spool by 55125-submit@debbugs.gnu.org id=B55125.165097721617854 (code B ref 55125); Tue, 26 Apr 2022 12:47:06 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:56 +0000 Received: from localhost ([127.0.0.1]:37549 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKal-0004dd-Ih for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:55 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36278) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004UV-56 for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:48 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=LQptLdcOwdJ8Bx52Wn4ymRX9f/UG+82V6We2YMQd0sg=; b=cw+Fk/zI5Zimo321Ed/8NqC9Gf 5HoZpwMDOrEsiiMvkiBHpVspDU6qAeozksHYCTUPOsIK+125OCfAp+QTaF0ePA3JFluFtAMmhlyBT oT/53mn4cravtaBoxVjoEx4vPD5SeciQrYowE0eLn917A91qi5M+pv6tGVn3owgwrF4evWe6QIYgW AYjcESfqEJoJ5D3zzYaAFSBGMvGjL0EMT8go3wQABWw+LjTClVzz1ZQQbzoLQuJSyTy28lxn8/S6E YzwvRThzx4Sig1fGvuBlsS2d30YprNE9Z3s8UvQWzABxASN8BtvFuBmx8spjpCHJ8Dkp+tItfg9Vg OfwSnmfg==; Received: from [192.168.2.1] (port=53438 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1njKaZ-000HJN-Hj; Tue, 26 Apr 2022 18:16:43 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:32 +0530 Message-Id: <20220426124639.17159-2-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.35.1 In-Reply-To: <20220426124639.17159-1-arunisaac@systemreboot.net> References: <20220426124639.17159-1-arunisaac@systemreboot.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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the build phase. Move the required make arguments to #:make-flags. Add build-libraries phase. --- gnu/packages/bioinformatics.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 774da809d8..6c24c1c26f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14279,18 +14279,18 @@ (define-public tabixpp (inputs (list htslib zlib)) (arguments - (list #:tests? #f ; There are no tests to run. + (list #:make-flags #~(list "HTS_HEADERS=" + (string-append "HTS_LIB=" + (search-input-file %build-inputs + "/lib/libhts.a")) + "INCLUDES=") + #:tests? #f ; There are no tests to run. #:phases #~(modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - ;; The build phase needs overriding the location of htslib. - (replace 'build + ;; Build shared and static libraries. + (add-after 'build 'build-libraries (lambda* (#:key inputs #:allow-other-keys) - (invoke "make" - (string-append "HTS_LIB=" (search-input-file inputs "/lib/libhts.a")) - (string-append "INCLUDES= -I" (search-input-directory inputs "/include/htslib")) - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" (search-input-directory inputs "/include"))) (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))) (replace 'install