From patchwork Thu Mar 31 07:28:45 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38240 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 CE51227BBEA; Thu, 31 Mar 2022 08:30:22 +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 62A8227BBE9 for ; Thu, 31 Mar 2022 08:30:22 +0100 (BST) Received: from localhost ([::1]:54356 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpG9-0006kQ-D7 for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:30:21 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46782) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFq-0006jU-KR for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43747) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFq-00068g-Bc for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFq-0004T5-7j for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 1/5] gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871174817037 (code B ref 54635); Thu, 31 Mar 2022 07:30:02 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:08 +0000 Received: from localhost ([127.0.0.1]:37632 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEv-0004Qc-1d for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:08 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51816) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEs-0004QQ-Pp for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender :Reply-To: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=89RmlLIFLrDguICsp52XrOOutjN3JQ9crwx+mZjeVKo=; b=qRKNGNQyjGhl6z4MZAvFJY7INH QvsJOtO7D0x8SnS4hMb3yiJcQ4p5k14lCI80uy5q8rNRhGkAXSfaN6Jsj0rxLySMqfhAvLp18iiSB tQGYPuMa/K84BRlOXWt7PQrnnd/zFdgPg/Pz1hJmO1vqNpSlmkR9nQGdBpMJs3o6Z1tiK3qTGdZKH YNJKO4HGaItjhNCrZptkhfRmcojSmicsUBCNvbmWC9Cwto4K11wovi+G1WGNjMKNzZcIAVCxFHUX/ HZjDJ1BNgZd64z2HNmh0DtKVbihSKcPfU8mf/8EJtX7rN1Thd34v88fjDMgLAj8j1y/Dc/so4vL67 9K/jcaeA==; Received: from [192.168.2.1] (port=47376 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 1nZpEh-000V88-E4; Thu, 31 Mar 2022 12:58:51 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:45 +0530 Message-Id: <20220331072849.22417-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: References: 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/maths.scm (gsl)[arguments]: Force autotools bootstrap when cross-compiling to riscv64-linux. [native-inputs]: Add autoconf, automake and libtool when cross-compiling to riscv64-linux. --- gnu/packages/maths.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ecb85642ec..a05f89cb4e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2017 Nikita ;;; Copyright © 2017 Ben Woodcroft ;;; Copyright © 2017 Theodoros Foradis -;;; Copyright © 2017, 2019 Arun Isaac +;;; Copyright © 2017, 2019, 2022 Arun Isaac ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice ;;; Copyright © 2017 Dave Love ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen @@ -533,6 +533,13 @@ (define-public gsl #:phases (modify-phases %standard-phases ,@(cond + ((target-riscv64?) + '((add-after 'unpack 'force-bootstrap + (lambda _ + ;; gsl ships with an old configure script that does not + ;; support riscv64. Regenerate it. + (delete-file "configure"))))) + ((or (string-prefix? "aarch64" system) (string-prefix? "powerpc" system)) ;; Some sparse matrix tests are failing on AArch64 and PowerPC: @@ -568,6 +575,10 @@ (define-public gsl (string-append "exit (77);\n" all))))))) (else '())))))) + (native-inputs + (if (target-riscv64?) + (list autoconf automake libtool) + '())) (home-page "https://www.gnu.org/software/gsl/") (synopsis "Numerical library for C and C++") (description From patchwork Thu Mar 31 07:28:46 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38242 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 EF23A27BBEB; Thu, 31 Mar 2022 08:31:07 +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 A602427BBE9 for ; Thu, 31 Mar 2022 08:31:07 +0100 (BST) Received: from localhost ([::1]:55008 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpGs-0007G5-N6 for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:31:06 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46788) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFs-0006kO-8D for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43750) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFr-00069B-UI for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFr-0004TU-Qz for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 2/5] gnu: htslib: Add bzip2 and xz to inputs. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871175317086 (code B ref 54635); Thu, 31 Mar 2022 07:30:03 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:13 +0000 Received: from localhost ([127.0.0.1]:37642 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpF3-0004RQ-5x for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:13 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51820) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEw-0004Qe-DI for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender :Reply-To: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=7vNXv7lUJiAVR/n2OTfZzpM62iwa6YV6yQWykxxu3s4=; b=CbNvm1aWNQdexYMnf68JxgaUe4 zYW36IPVW+gvP/ysd005pGK7HtrCro6oqbwo7OGcHqUIoRjHm8X0XqCEHS0AvnqYUTgPVK51Qi86W cFrLmdSAlMtenJCSAIO5aQjHEWUWTdav7c4IruhQdd8i3QvtqnTkOLD11f8Os6e//xG2us0Ygxi9L I4tgx9M8QTWmTymdO387Re/EKEfYDN/vhWqwn0ADtJqlS3k6rlQBuRfVb4VWsjMGxg9kSo8PRPjV1 jC5sHdCJ5hcWZrgcmcFkhJO7WsRX6THI2xNOUoBsyiVrrg3a6oJv2LCQsyhrlcGU7YamdX3s8THrA Dih0G6Zw==; Received: from [192.168.2.1] (port=47376 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 1nZpEh-000V88-Nt; Thu, 31 Mar 2022 12:58:51 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:46 +0530 Message-Id: <20220331072849.22417-2-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: References: 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 htslib 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 (htslib)[inputs]: Add bzip2 and xz. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4e1028b3ce..2f6f3efb66 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020, 2022 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice -;;; Copyright © 2017, 2021 Arun Isaac +;;; Copyright © 2017, 2021, 2022 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu @@ -4788,7 +4788,7 @@ (define-public htslib "--enable-libcurl" "--enable-s3"))) (inputs - (list curl openssl)) + (list bzip2 curl openssl xz)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs (list zlib)) From patchwork Thu Mar 31 07:28:47 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38239 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 B51E327BBEB; Thu, 31 Mar 2022 08:30:22 +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 6EC0A27BBEA for ; Thu, 31 Mar 2022 08:30:22 +0100 (BST) Received: from localhost ([::1]:54374 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpG9-0006le-Ct for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:30:21 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46784) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFr-0006jb-46 for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43748) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFq-00068l-Qp for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFq-0004TD-NM for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 3/5] gnu: atomic-queue: Run tests correctly. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871174917062 (code B ref 54635); Thu, 31 Mar 2022 07:30:02 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:09 +0000 Received: from localhost ([127.0.0.1]:37637 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEz-0004R3-FA for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:09 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51824) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEx-0004Qg-2k for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:08 -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=zCzIPrvcABlLLfgBuYEpTJo55fiBaLAVkuvkcQrTmFE=; b=E6L0KOHHXS4mwD3V+LY0OuRf+s Uep6SyCLyIb4zM7dzRWuz3s8BEoCGW5V7eICzHjrGtzhXTN7vwUuOXSD5+KfQDAwEbaU2M1m1GXcp eeS+VjYtM+rqnHS5VrTpTl38WIRHWStrrcj8es/w0qTgF/lZ9TAf9ohxd11nDDcK+BdOf/6k3GynK iJfRqmD0T8ZNzI6xASAit96rV0opb8CFdmvX8kmwOUm2VHOms16y4OXmpoFCVIWVClv78SfJfWcx9 +ZcQ8L/PmgO026OzvBbPG7QeWMk83OecuJ3LyxPc/IDFH1czu1IRs6ds1xydkry0AzRauVrkWoy6O MWl2HW0g==; Received: from [192.168.2.1] (port=47376 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 1nZpEi-000V88-13; Thu, 31 Mar 2022 12:58:52 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:47 +0530 Message-Id: <20220331072849.22417-3-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: References: 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/cpp.scm (atomic-queue)[arguments]: In the check phase, run tests instead of returning a function to run them. --- gnu/packages/cpp.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index bb7f5ab95a..eb48902034 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -1297,8 +1297,7 @@ (define-public atomic-queue (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (lambda _ - (invoke "make" "run_tests"))))) + (invoke "./tests")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (copy-recursively "../source/include/atomic_queue" From patchwork Thu Mar 31 07:28:48 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38241 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 AF7B327BBEA; Thu, 31 Mar 2022 08:30:28 +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 78D2D27BBE9 for ; Thu, 31 Mar 2022 08:30:28 +0100 (BST) Received: from localhost ([::1]:54414 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpGF-0006nR-BO for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:30:27 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46790) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFs-0006l0-PV for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43751) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFs-0006A0-GL for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFs-0004Tb-9w for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 4/5] gnu: atomic-queue: Do not look for boost when cross-compiling. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871175917098 (code B ref 54635); Thu, 31 Mar 2022 07:30:04 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:19 +0000 Received: from localhost ([127.0.0.1]:37644 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpF8-0004Rh-Id for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:18 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51826) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpF2-0004RH-AW for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:12 -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=urVEWQh6U0Sizl7naOjWCvAZ/L4J1AfvavArtLdRRRU=; b=c8auhFRRP6d14xqDDnSsZK5E/a z6QZHoNzfSybM0wb/gKv2QgXsT9GvGMO1XbbOEuWi9OQjqwkiTETYN11fq8uReUe3XIhOI4IvlZAU OFr9fhiUFqktd32T8eIWFsPsDJZu4wjTuH9PZU0m/wznK7Y+xURi7ogzUw0HgyFZLc6pNZT3i/KJR 4aTmRQPT4EhsruotkFggvlikao6z+nY6glh5ArfvfL1KEL8LwuX/i0xXQmy4jkht4xTfaNj74GZmO dKaKRoAkV50tyl9bC96z1i/Xl0D6p9dl4w1R1PsRyCinb2OSgFy0hG5D9NLbEqRfq1JlmvYwmqKf2 DRRON7rQ==; Received: from [192.168.2.1] (port=47376 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 1nZpEi-000V88-Al; Thu, 31 Mar 2022 12:58:52 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:48 +0530 Message-Id: <20220331072849.22417-4-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: References: 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/cpp.scm (atomic-queue)[arguments]: When cross-compiling, add a do-not-check-for-boost phase. --- gnu/packages/cpp.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index eb48902034..b0d4fdeb3e 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -1294,6 +1294,15 @@ (define-public atomic-queue `(#:configure-flags '("-Dbenchmarks=false") #:phases (modify-phases %standard-phases + ,@(if (%current-target-system) + `(;; boost is a test dependency. We don't run tests when + ;; cross-compiling. Disable all targets that depend on it. + (add-after 'unpack 'do-not-check-for-boost + (lambda _ + (substitute* "meson.build" + (("unit_test_framework = [^\n]*" all) + "unit_test_framework = disabler()"))))) + '()) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From patchwork Thu Mar 31 07:28:49 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38243 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 2A07927BBE9; Thu, 31 Mar 2022 08:31:08 +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 BFE6827BBEA for ; Thu, 31 Mar 2022 08:31:07 +0100 (BST) Received: from localhost ([::1]:55002 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpGs-0007Fg-Ja for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:31:06 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46786) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFs-0006kF-0S for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43749) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFr-000694-Mr for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFr-0004TM-AN for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 5/5] gnu: Add wfmash. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871175317079 (code B ref 54635); Thu, 31 Mar 2022 07:30:03 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:13 +0000 Received: from localhost ([127.0.0.1]:37640 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpF2-0004RK-S8 for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:13 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51822) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEx-0004Qf-2W for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:08 -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=qdxbq1pvz3OvQqxf4iO+hoUkerdg5PrwZlSuFuVyO6I=; b=W6imaFCsxxe6fqOSS8UoOY0lIj 5paIlTeGF0GLeKVoB13rj91PBYH+VxpZTtC6QlI4XdLPfy7CgxecxolLZoiu2hyGQpkR66nhvERET 9H9tbAZAlvJXifTnW65TSmKITcw8LvjOaCWZScJYUjTfXsEuaJEeMoTTnH+0ITyZPtHKGauAltPtz gDKRUgJVQ79xITQhLt3HpN/LTmjeLE3+QBinMNTiNizSbzSmJCqytMXLUaDEPNmaYE2vKzeNPogDT jzij9+j2Y1t8jhhthQsblwzIWadsNju+YPpT+5XP4kcHD+YTNm3mfiyUMJLLa9MLQrXpL4g4J3DyI wTyptS3g==; Received: from [192.168.2.1] (port=47376 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 1nZpEi-000V88-Lq; Thu, 31 Mar 2022 12:58:52 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:49 +0530 Message-Id: <20220331072849.22417-5-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: References: 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 (wfmash): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2f6f3efb66..500ba4ac60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16107,3 +16107,54 @@ (define-public ccwl @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "")))))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; Remove compiler flags and checks specific to x86 when not + ;; targeting it. + ,@(if (target-x86-64?) + '() + '((add-after 'unpack 'remove-x86-specific-compile-flags + (lambda _ + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16") "") + (("-march=native") "")) + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0"))))))))) + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +alignment algorithm. It completes MashMap with a high-performance alignment +module capable of computing base-level alignments for very large sequences.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat)))