From patchwork Tue Apr 26 12:46:31 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38909 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 4F1B727BBEA; Tue, 26 Apr 2022 13:56:27 +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 BB7EC27BBE9 for ; Tue, 26 Apr 2022 13:56:26 +0100 (BST) Received: from localhost ([::1]:44082 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKjx-0006yg-Qt for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43890) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKav-0007B8-7l for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43661) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKat-0007VA-O3 for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKat-0004kY-LD for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 1/9] gnu: tabixpp: Use G-expressions. References: <20220426124426.16845-1-arunisaac@systemreboot.net> In-Reply-To: <20220426124426.16845-1-arunisaac@systemreboot.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:03 +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=B55125.165097720917484 (code B ref 55125); Tue, 26 Apr 2022 12:47:03 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:49 +0000 Received: from localhost ([127.0.0.1]:37539 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKae-0004XW-Vc for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:49 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36274) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004UR-4o for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:47 -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: 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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=fhX6aMVFl7JG7gS21iWUKApvWWjTppiI+ftfyQbJEOo=; b=dEBZo8Fq7HxOLPVve/gTNWfoPn 0unTFkyNm/mxoXDFT5XWeIsMKncVXUwSghik37vhIQHqV66VgxVT+IhNDXt94k0HCQOjApLk2WrmL zCrWzt6uUm2DOi0v+TZWkrV8dTd/D0y7VSsiVAOkfSw+fV7EGFszJVn2GPg+CXrLYjC8g0kBRIK8s wgNDY8ivTyEsr8xJpyz4kOGRAuqn/VcbQXtJf75/G3fMzcOo5Uw7DKEvvLxqWgKI7UIVT9/Jx0EFU v8W3yJYzQONV5dQEcQbLFTPQ/BmOcgbh+O/CZC/hYWSXO3vvMEWL3fEXb0pW8gENl3TKTuCqYWxS1 GClWnzMg==; 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-Bb; Tue, 26 Apr 2022 18:16:43 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:31 +0530 Message-Id: <20220426124639.17159-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.35.1 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)[source]: Reindent. [arguments]: Use search-input-file and search-input-directory. [source, arguments]: Rewrite using G-expressions. Do not return #t from snippets and custom phases. --- gnu/packages/bioinformatics.scm | 80 ++++++++++++++++----------------- 1 file changed, 39 insertions(+), 41 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40ccba247c..774da809d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14264,49 +14264,48 @@ (define-public tabixpp (name "tabixpp") (version "1.1.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) - (modules '((guix build utils))) - (snippet - `(begin - (delete-file-recursively "htslib") #t)))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd")) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "htslib"))))) (build-system gnu-build-system) (inputs (list htslib zlib)) (arguments - `(#: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 - (lambda* (#:key inputs #:allow-other-keys) - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "INCLUDES= -I" htslib-ref "/include/htslib") - "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include")) - (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (install-file "tabix++" bin) - (install-file "libtabixpp.so" lib) - (install-file "libtabixpp.a" lib) - (install-file "tabix.hpp" (string-append out "/include")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") - (lambda _ - (format #t "prefix=~a~@ + (list #: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 + (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 + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "tabix++" bin) + (install-file "libtabixpp.so" lib) + (install-file "libtabixpp.a" lib) + (install-file "tabix.hpp" (string-append out "/include")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14317,8 +14316,7 @@ (define-public tabixpp Description: C++ wrapper around tabix project~@ Libs: -L${libdir} -ltabixpp~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts 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 From patchwork Tue Apr 26 12:46:33 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38907 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 2844B27BBEA; Tue, 26 Apr 2022 13:53:28 +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=-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 E7C2A27BBE9 for ; Tue, 26 Apr 2022 13:53:27 +0100 (BST) Received: from localhost ([::1]:38168 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKh5-0002uB-3K for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:53:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43892) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKav-0007B9-7S for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43663) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKau-0007VE-QA for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKau-0004lS-OS for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 3/9] gnu: tabixpp: Use build tools specific to the target. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:04 +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=B55125.165097721517819 (code B ref 55125); Tue, 26 Apr 2022 12:47:04 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:55 +0000 Received: from localhost ([127.0.0.1]:37545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKak-0004cz-Un for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:55 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36276) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004UU-4r 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=/OUzdve/5HL9X23RaxaqmcffQxA0zHZXvNefqSAy2to=; b=fxfK4RtmUnurjf3IfXF4eVjFhe 5zhw1edM9036240fKT8RJBVbq0Jyigr6ljvNW+kYONkT1a4sft+5D0zv7lvrkJlineKB815mJR6HG kssTtJohg75qkyXygnqpZHR0Up3dN9hsUjqOSKDAHc9gr8ApuwuSn1TQ6lA1jGqAdLZlwauxARhl9 Ru0Qo9cBhV6VZ+Cq4fPOGuA37rTjIYy5razTpbZZ1djrSb3aHGaa2RMxNzXXMqg18k/fHBPIeH9Po EYU9eZQ16EBvIUCPtFUm+v0UPa47mb7pdSMI5XYR2CALrTkz6qmO8QYgRGRi64zyG5aorlL0fs7Cz ZE90ZucA==; 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-MB; Tue, 26 Apr 2022 18:16:43 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:33 +0530 Message-Id: <20220426124639.17159-3-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]: Set CC and CXX in #:make-flags. In the build-libraries phase, use cxx-for-target instead of g++ and ar-for-target instead of ar. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c24c1c26f..e745fa9353 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14279,7 +14279,9 @@ (define-public tabixpp (inputs (list htslib zlib)) (arguments - (list #:make-flags #~(list "HTS_HEADERS=" + (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "CXX=" #$(cxx-for-target)) + "HTS_HEADERS=" (string-append "HTS_LIB=" (search-input-file %build-inputs "/lib/libhts.a")) @@ -14291,8 +14293,9 @@ (define-public tabixpp ;; Build shared and static libraries. (add-after 'build 'build-libraries (lambda* (#:key inputs #:allow-other-keys) - (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") - (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))) + (invoke #$(cxx-for-target) + "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke #$(ar-for-target) "rcs" "libtabixpp.a" "tabix.o"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) From patchwork Tue Apr 26 12:46:34 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38908 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 D9EE827BBEA; Tue, 26 Apr 2022 13:56:14 +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 AF09C27BBE9 for ; Tue, 26 Apr 2022 13:56:14 +0100 (BST) Received: from localhost ([::1]:43308 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKjl-0006So-Sf for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43888) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKat-0007Ab-BY for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43660) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKat-0007V5-29 for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKas-0004k3-Se for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 4/9] gnu: tabixpp: Add bzip2 and xz to inputs. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:02 +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=B55125.165097720917459 (code B ref 55125); Tue, 26 Apr 2022 12:47:02 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:49 +0000 Received: from localhost ([127.0.0.1]:37537 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKae-0004X4-7R for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:48 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36280) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004Uj-4g for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:46 -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=Ywpi9SvgHJECd+hI05JBFlaf22w/73tp3iMgY72hgKU=; b=e9p1CdmgBJQ3kKCpkF2xeSD4qo HGCrM86iXxK5QPddB7S+IWdN8QrD82fie6VB06KrR/3cyy/vcwIWNg4Ua7Phfot77Qfw/QiLz/72+ Es6ib67vZIYOMHM2aQvP2wb2+3Vkpk4wRn0W3h7ULy8kebSZDImp7yEQwAaghqyP+gYl2RJjS31SN LFZzoCdygci7yvHJz+IZmS1W+pGmZJxDuHkkN6MC+qEItMXFBzlxA5+msRW2JRDtrT8eJ9jp7YruN /nLmImbpsmj9ygmv73GJ7tJjJSRB2zH/tpVoQFDKgGAEC1C9XT5QbyO/qpwXLQVcScq4vsCduKpzV wWXt9k3w==; 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-QN; Tue, 26 Apr 2022 18:16:43 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:34 +0530 Message-Id: <20220426124639.17159-4-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 tabixpp links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (tabixpp)[inputs]: Add bzip2 and xz. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e745fa9353..7cdbb748ef 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14277,7 +14277,7 @@ (define-public tabixpp (delete-file-recursively "htslib"))))) (build-system gnu-build-system) (inputs - (list htslib zlib)) + (list bzip2 htslib xz zlib)) (arguments (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) (string-append "CXX=" #$(cxx-for-target)) From patchwork Tue Apr 26 12:46:35 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38904 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 72F9F27BBEA; Tue, 26 Apr 2022 13:48:38 +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 F3F7C27BBE9 for ; Tue, 26 Apr 2022 13:48:37 +0100 (BST) Received: from localhost ([::1]:49262 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKcP-00087Z-4S for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:48:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43894) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKav-0007BA-7A for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43662) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKau-0007VD-BA for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKau-0004l5-7t for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 5/9] gnu: fastahack: Use G-expressions. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:04 +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=B55125.165097721517797 (code B ref 55125); Tue, 26 Apr 2022 12:47:04 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:55 +0000 Received: from localhost ([127.0.0.1]:37543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKak-0004cc-Ie for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:54 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36282) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004V4-4h for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:47 -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=0FkPZ8GPnrHAKpDs0RM7Bkd07hRZN1tm6anGmR2R9Ow=; b=TKpgJK3FtVqfTua+U3IEykZ+xW AxFvsnmRm80xRrjkvdJPl+FQJ7ydB427P2KQXpHyBzh7eAY3DZhKGsu5C/KcdPhBghauEIFEkjSnh PT6KTlwXiqUr+hHBMWPGQQ4gtiINV4G9m6Xr4V4O+MKW7EBdXePSsAVZE47HGr+CwNppyG1BM5obM n00SawMeBwaerf4EhtCct0BirUBAEnbKqACxbpSucIQ1dUjlWR0pQA99Qi6CUJWYpCX/6Tx0/0rnI LB6VF64Cwr4bbZHRK2XFBU93/TDclBqX3Q7Zp+wjZGI1FaNIBu9oOhLHaU50aPiDbcFxnElKvFv71 w2STqDyA==; 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 1njKaa-000HJN-0P; Tue, 26 Apr 2022 18:16:44 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:35 +0530 Message-Id: <20220426124639.17159-5-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 (fastahack)[arguments]: Rewrite using G-expressions. Do not return #t from custom phases. --- gnu/packages/bioinformatics.scm | 60 ++++++++++++++++----------------- 1 file changed, 29 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7cdbb748ef..699a4eaf47 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14483,36 +14483,35 @@ (define-public fastahack (base32 "0rp1blskhzxf7vbh253ibpxbgl9wwgyzf1wbkxndi08d3j4vcss9")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 - #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "Makefile" - (("-c ") "-c -fPIC ")) - #t)) - (add-after 'build 'build-dynamic - (lambda _ - (invoke "g++" - "-shared" "-o" "libfastahack.so" - "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib (string-append out "/lib")) - (bin (string-append out "/bin"))) - (mkdir-p (string-append out "/include/fastahack")) - (for-each - (lambda (file) - (install-file file (string-append out "/include/fastahack"))) - (find-files "." "\\.h$")) - (install-file "fastahack" bin) - (install-file "libfastahack.so" lib) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (list #:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source (lambda _ - (format #t "prefix=~a~@ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")))) + (add-after 'build 'build-dynamic + (lambda _ + (invoke "g++" + "-shared" "-o" "libfastahack.so" + "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (mkdir-p (string-append out "/include/fastahack")) + (for-each + (lambda (file) + (install-file file (string-append out "/include/fastahack"))) + (find-files "." "\\.h$")) + (install-file "fastahack" bin) + (install-file "libfastahack.so" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include/fastahack~@ @@ -14523,8 +14522,7 @@ (define-public fastahack Description: Indexing and sequence extraction from FASTA files~@ Libs: -L${libdir} -lfastahack~@ Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + out #$version))))))))) (home-page "https://github.com/ekg/fastahack") (synopsis "Indexing and sequence extraction from FASTA files") (description "Fastahack is a small application for indexing and From patchwork Tue Apr 26 12:46:36 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38912 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 C086427BBEA; Tue, 26 Apr 2022 13:57:10 +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 8E6CB27BBE9 for ; Tue, 26 Apr 2022 13:57:10 +0100 (BST) Received: from localhost ([::1]:47182 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKkf-0000bd-OC for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:57:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43898) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKax-0007CE-5f for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43664) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKav-0007VU-KE 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 1njKav-0004m3-Hr for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 6/9] gnu: fastahack: Use compiler specific to the build target. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:05 +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=B55125.165097721517835 (code B ref 55125); Tue, 26 Apr 2022 12:47:05 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:55 +0000 Received: from localhost ([127.0.0.1]:37547 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKal-0004dK-9R for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:55 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36284) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004VD-5u 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=+bfeDCBoFBJ/hZ48qfjsfkJhW5W9+F7doDHmMxdqIBI=; b=layh5BFiCQHnVLP5NqhlLalNOc hpVG2Me01WFrxZeeUL2Sp5iB30JhF2xtH7JD6ATn2re/SnAkCZCoqx7W4LkfLFdnpJ1DYpHPHm1FU Y/Ecp7RBPjo0b4xEY4FWnnsdCoK9ZN3JcW5pjrvZc3QpKyJzcHNzyhn5lZAnc24AdFYdwDs6df7tJ 8u34EewFoSnadtWrz0Nw/7T5lADTpVQhPK8nIPwaOLgHf0Gq0wZTXXUXqM+CmPh3ArjLLddvcCRW1 zbyGK8cxHUYrfgep0/34mpdGmc/o4ty9hyYT5c4OI2fX353u1YYqxEGVISdyyrt33sjx/jA2Uf8yg h2JKTIkg==; 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 1njKaa-000HJN-96; Tue, 26 Apr 2022 18:16:44 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:36 +0530 Message-Id: <20220426124639.17159-6-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 (fastahack)[arguments]: Set CXX in #:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 699a4eaf47..ad69ca59cf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14483,7 +14483,8 @@ (define-public fastahack (base32 "0rp1blskhzxf7vbh253ibpxbgl9wwgyzf1wbkxndi08d3j4vcss9")))) (build-system gnu-build-system) (arguments - (list #:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 + (list #:make-flags #~(list (string-append "CXX=" #$(cxx-for-target))) + #:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 #:phases #~(modify-phases %standard-phases (delete 'configure) ; There is no configure phase. @@ -14493,7 +14494,7 @@ (define-public fastahack (("-c ") "-c -fPIC ")))) (add-after 'build 'build-dynamic (lambda _ - (invoke "g++" + (invoke #$(cxx-for-target) "-shared" "-o" "libfastahack.so" "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) (replace 'install From patchwork Tue Apr 26 12:46:37 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38910 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 920DC27BBEA; Tue, 26 Apr 2022 13:56:37 +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 08DDB27BBE9 for ; Tue, 26 Apr 2022 13:56:37 +0100 (BST) Received: from localhost ([::1]:44888 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKk8-0007WK-4s for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43900) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Ca-9U for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43666) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Vd-0J for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKaw-0004n0-Sf for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 7/9] gnu: vcflib: Use G-expressions. 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=B55125.165097721617886 (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]:37551 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKal-0004dt-Ri for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:56 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36286) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKac-0004VS-DO 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=1Mk35J4+8LbnUr5pc/Ygl355xCPWdPfUFUgXBpduoac=; b=mMPplOCd9k4WMuhBt500I4vdoF Uz52UKDzt3603iWTx00wPjKMvRX2QH+FigGxdEMElBBkQVCGsWSMBwfUxKM+3eujbqP1/myW2wmz1 rlUeZ2BfFlCxM/187nwPx2r8gdWUh2gQYa9q8gUT4HptYfgrkD2ieSNZoc9UvjdMMMLtzKQLsdGYp 3rho7RUizUNm+IlPCNE9QR+yN3CBmqEexUrScWd8QDWJ2l8/Av2wwv6/6oqq4XLWr5narawFM7VuU oDc2s5HOAM0KTaJUSyGuxap/wIhrBQK8LJBzUED8b35nAWliGeNocHXnhfyiTbYIGEAXxY6vatsns JBx+LifQ==; 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 1njKaa-000HJN-Gw; Tue, 26 Apr 2022 18:16:44 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:37 +0530 Message-Id: <20220426124639.17159-7-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 (vcflib)[source, arguments]: Rewrite using G-expressions. [arguments]: Do not return #t from custom phases. --- gnu/packages/bioinformatics.scm | 103 ++++++++++++++++---------------- 1 file changed, 51 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad69ca59cf..d74b8a0eb6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14548,27 +14548,27 @@ (define-public vcflib (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) (modules '((guix build utils))) (snippet - '(begin - (substitute* "CMakeLists.txt" - ((".*fastahack.*") "") - ((".*smithwaterman.*") "") - (("(pkg_check_modules\\(TABIXPP)" text) - (string-append + #~(begin + (substitute* "CMakeLists.txt" + ((".*fastahack.*") "") + ((".*smithwaterman.*") "") + (("(pkg_check_modules\\(TABIXPP)" text) + (string-append "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" text)) - (("\\$\\{TABIXPP_LIBRARIES\\}" text) - (string-append "${FASTAHACK_LIBRARIES} " - "${SMITHWATERMAN_LIBRARIES} " - text))) - (substitute* (find-files "." "\\.(h|c)(pp)?$") - (("\"SmithWatermanGotoh.h\"") "") - (("\"convert.h\"") "") - (("\"disorder.h\"") "") - (("Fasta.h") "fastahack/Fasta.h")) - (for-each delete-file-recursively - '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")))))) + (("\\$\\{TABIXPP_LIBRARIES\\}" text) + (string-append "${FASTAHACK_LIBRARIES} " + "${SMITHWATERMAN_LIBRARIES} " + text))) + (substitute* (find-files "." "\\.(h|c)(pp)?$") + (("\"SmithWatermanGotoh.h\"") "") + (("\"convert.h\"") "") + (("\"disorder.h\"") "") + (("Fasta.h") "fastahack/Fasta.h")) + (for-each delete-file-recursively + '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" + "libVCFH" "multichoose" "smithwaterman")))))) (build-system cmake-build-system) (inputs (list bzip2 @@ -14589,39 +14589,39 @@ (define-public vcflib ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'build-shared-library - (lambda _ - (substitute* "CMakeLists.txt" - (("vcflib STATIC") "vcflib SHARED")) - (substitute* "test/Makefile" - (("libvcflib.a") "libvcflib.so")))) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (mkdir target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) - ;; This pkg-config file is provided by other distributions. - (add-after 'install 'install-pkg-config-file - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (pkgconfig (string-append out "/lib/pkgconfig"))) - (mkdir-p pkgconfig) - (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (list #:tests? #f ; no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'build-shared-library (lambda _ - (format #t "prefix=~a~@ + (substitute* "CMakeLists.txt" + (("vcflib STATIC") "vcflib SHARED")) + (substitute* "test/Makefile" + (("libvcflib.a") "libvcflib.so")))) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (mkdir target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "intervaltree-src" "intervaltree") + (unpack "multichoose-src" "multichoose"))))) + ;; This pkg-config file is provided by other distributions. + (add-after 'install 'install-pkg-config-file + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pkgconfig (string-append out "/lib/pkgconfig"))) + (mkdir-p pkgconfig) + (with-output-to-file (string-append pkgconfig "/vcflib.pc") + (lambda _ + (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ @@ -14632,8 +14632,7 @@ (define-public vcflib Description: C++ library for parsing and manipulating VCF files~@ Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" - out ,version))) - #t)))))) + out #$version))))))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret From patchwork Tue Apr 26 12:46:38 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38911 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 542EC27BBEA; Tue, 26 Apr 2022 13:56:49 +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 2317927BBE9 for ; Tue, 26 Apr 2022 13:56:49 +0100 (BST) Received: from localhost ([::1]:45676 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKkK-000833-8g for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:56:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43902) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKax-0007De-Us for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43667) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKax-0007Vq-ML for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKax-0004nS-JQ for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 8/9] gnu: vcflib: Find submodule sources in native-inputs during cross-compilation. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:07 +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=B55125.165097721617910 (code B ref 55125); Tue, 26 Apr 2022 12:47:07 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:56 +0000 Received: from localhost ([127.0.0.1]:37553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKam-0004eQ-A9 for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:56 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36288) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKah-0004ZF-KH for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:52 -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=znplA+xDzJbWw2etPp8FbD5B6HfABIe/ZHX4GlC2UwE=; b=FSHOPYDiiO09rSi85Vq3v7nC8o PIBrCikPt92GLo+SA2z+bMXgbZXQYY5gWOd9H5a6p4FsCV6avNGUPEGkjgvC8PoR21CThEHGORlkq 1F68ZMYpPuTLjQsz3uYOjEQavewMaDOdX27/y4xrgC4kDTo+KM4MXLoSW/aWqbLxul1kLI4IVy1in dOfDEgu5+lPXhE8BavHSlad+upDwGiMRamfgkuyE3CyW600Bud0yZU9FKd2kPsgoIn7F7ymn6nIKX fy1g0EUMLEtcW7M5SIsge2qBBJLzpKa7SPuV+RVM8imkReoGRWCvgeuJkHCuwznuBQR38RZczcO2a NuBMq8dQ==; 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 1njKaa-000HJN-Ok; Tue, 26 Apr 2022 18:16:44 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:38 +0530 Message-Id: <20220426124639.17159-8-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 (vcflib)[arguments]: In the unpack-submodule-sources phase, look for submodule sources in both inputs and native-inputs. --- gnu/packages/bioinformatics.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d74b8a0eb6..b4d809b4db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14599,15 +14599,17 @@ (define-public vcflib (substitute* "test/Makefile" (("libvcflib.a") "libvcflib.so")))) (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) + (lambda* (#:key inputs native-inputs #:allow-other-keys) (let ((unpack (lambda (source target) (mkdir target) (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) + (let ((source (or (assoc-ref inputs source) + (assoc-ref native-inputs source)))) + (if (file-is-directory? source) + (copy-recursively source ".") + (invoke "tar" "xvf" + source + "--strip-components=1"))))))) (and (unpack "filevercmp-src" "filevercmp") (unpack "fsom-src" "fsom") From patchwork Tue Apr 26 12:46:39 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38906 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 0DA1D27BBEA; Tue, 26 Apr 2022 13:49:05 +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=-2.7 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 D602C27BBE9 for ; Tue, 26 Apr 2022 13:49:04 +0100 (BST) Received: from localhost ([::1]:51084 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1njKcp-0000wN-Vz for patchwork@mira.cbaines.net; Tue, 26 Apr 2022 08:49:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43904) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njKay-0007EM-W9 for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:10 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43668) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1njKay-0007Vv-Ej for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1njKay-0004nx-C3 for guix-patches@gnu.org; Tue, 26 Apr 2022 08:47:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55125] [PATCH 9/9] gnu: vcflib: Set absolute path to pkg-config. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Apr 2022 12:47:08 +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=B55125.165097721717929 (code B ref 55125); Tue, 26 Apr 2022 12:47:08 +0000 Received: (at 55125) by debbugs.gnu.org; 26 Apr 2022 12:46:57 +0000 Received: from localhost ([127.0.0.1]:37555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKam-0004eo-Lx for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:56 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36290) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKah-0004ZY-Si for 55125@debbugs.gnu.org; Tue, 26 Apr 2022 08:46:52 -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=EfmrN9/an8n+Kt2wZSBWNXSrx89D+PoklMuC3uk+iic=; b=TRgDnDAagcqiFZd03zT2skCGxg v89TkeU3VsekE3+qRhSkNduStG1JE6u2llfISZVkhjyVzZ8vNO81cxZ6/BdjIAypjY7ya/QrO5bN1 9LkaPSBl/SV1IV6wJghDOD5w91bfUVUq4JPJxbqs5mBzomhteLAMJ3SyUBOhHq0DJB/TIUeD2HRgh jzVm5m8xj3VguAznN7Cqlq/XiRxBumYB+dmpMn1KvuNDCHV4UQWwmOd0YLZuOBVaYJT0A+iNR2YQY Dt2HoSTx3JORaqz6kako/OES4Jo0h1luWKnrJSiaqictfWksJxgy1wnmWoRRt/KswDAMVMWgjggeI GQpQnIKw==; 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 1njKaa-000HJN-Vq; Tue, 26 Apr 2022 18:16:45 +0530 From: Arun Isaac Date: Tue, 26 Apr 2022 18:16:39 +0530 Message-Id: <20220426124639.17159-9-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 Setting the absolute path to pkg-config is required to support cross-compilation. * gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set PKG_CONFIG_EXECUTABLE in #:configure-flags. --- gnu/packages/bioinformatics.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b4d809b4db..7f374873ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14589,7 +14589,13 @@ (define-public vcflib ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments - (list #:tests? #f ; no tests + (list #:configure-flags + #~(list (string-append + "-DPKG_CONFIG_EXECUTABLE=" + (search-input-file + %build-inputs (string-append + "/bin/" #$(pkg-config-for-target))))) + #:tests? #f ; no tests #:phases #~(modify-phases %standard-phases (add-after 'unpack 'build-shared-library