From patchwork Wed Mar 30 09:23:09 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38214 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 1ADC127BBE9; Wed, 30 Mar 2022 10:24:53 +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 3218727BBEC for ; Wed, 30 Mar 2022 10:24:50 +0100 (BST) Received: from localhost ([::1]:57706 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZUZN-0007sU-Ae for patchwork@mira.cbaines.net; Wed, 30 Mar 2022 05:24:49 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56640) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0007pX-DI for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40609) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0000Ss-3o for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZUYc-00013n-0i for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH 1/5] gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux. References: <20220330091913.23206-1-arunisaac@systemreboot.net> In-Reply-To: <20220330091913.23206-1-arunisaac@systemreboot.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Mar 2022 09:24:01 +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: 54635@debbugs.gnu.org Cc: Arun Isaac , Efraim Flashner Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.16486322033990 (code B ref 54635); Wed, 30 Mar 2022 09:24:01 +0000 Received: (at 54635) by debbugs.gnu.org; 30 Mar 2022 09:23:23 +0000 Received: from localhost ([127.0.0.1]:34496 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXw-00011r-6X for submit@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:23 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51802) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXt-00011b-KQ for 54635@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:19 -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: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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=zMvabFjZY3Am0dZy4NS03MJ1hvRlema0+m2EfOMj0sI=; b=Lu0MTK2V9WI47prLhspTlH/iw4 KFUMhwyG07zhY8KFCIfaQ9Nk7eJY4U2CmmO4V3KIyT5hKc4Wirqz9cgxm3NSVYsjPMP5m11T/GVB4 nkNu7qQqp2Hrjn3bw9nj69FAZE8yAGPSsjYZCKQyun+WbvCk9SeG2ip0XAKhOITHh6sOwbxyFZPrz FRFhMaHSHKkXahoAdT1JOJDu+jYwG0MbkXM/HefRSncEYTzNDAfLTx/09yqcH+YCMkppTem0RAdmy kgm5WeCxRboXFFKnRGUT8EAQsGkQRUL+9+dItMtJcK9o/etefcfjxS2y4kbwFjp7nlk4di7pdeIx1 Al2KDaSw==; Received: from [192.168.2.1] (port=6582 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 1nZUXq-000T5d-KT; Wed, 30 Mar 2022 14:53:14 +0530 From: Arun Isaac Date: Wed, 30 Mar 2022 14:53:09 +0530 Message-Id: <20220330092313.23584-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 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 | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ecb85642ec..f01bf51580 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 +575,12 @@ (define-public gsl (string-append "exit (77);\n" all))))))) (else '())))))) + (native-inputs + (if (target-riscv64?) + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool)) + '())) (home-page "https://www.gnu.org/software/gsl/") (synopsis "Numerical library for C and C++") (description From patchwork Wed Mar 30 09:23:10 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38215 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 4733527BBE9; Wed, 30 Mar 2022 10:24:53 +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 1FE1F27BBEB for ; Wed, 30 Mar 2022 10:24:50 +0100 (BST) Received: from localhost ([::1]:57694 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZUZN-0007sB-8N for patchwork@mira.cbaines.net; Wed, 30 Mar 2022 05:24:49 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56638) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0007pK-7S for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40608) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZUYb-0000So-UD for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZUYb-00013f-LC for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH 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: Wed, 30 Mar 2022 09:24:01 +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: 54635@debbugs.gnu.org Cc: Arun Isaac , Efraim Flashner Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.16486322003962 (code B ref 54635); Wed, 30 Mar 2022 09:24:01 +0000 Received: (at 54635) by debbugs.gnu.org; 30 Mar 2022 09:23:20 +0000 Received: from localhost ([127.0.0.1]:34494 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXv-00011p-Tj for submit@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:20 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51800) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXt-00011a-KN for 54635@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:18 -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=e7L6oB/p82yrwnFkgBXe8iXkum ohElwS/tpMjHo9veEEx6B3Exzi26vY4P8rJT8Vhml/Uj8cpVh9z5S0ErXH9mTSKuzShDX6kKSDmcH TfXMcn4qqIssWvkPUILAYTl+KtBYC/FCaz7oaSR9HIoj+rLG4TYQtqrzs7Y1Op68/eq7Ft0IoYuL4 wq8/hapf4iiY3EIbAhDuQuBs5YPMX9WdpGFJtJDcb5zQ/l9FNrO7CyjbofZc/zU4pOfMGIR9XMim5 gIP15CA/98VX2gljjajgNlHBC3Q9DAg+E76FqShGlqr7RyuR6hZc93+xluJF/XHiJI6tFOoi9FW4X NvSlAohQ==; Received: from [192.168.2.1] (port=6582 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 1nZUXq-000T5d-QQ; Wed, 30 Mar 2022 14:53:14 +0530 From: Arun Isaac Date: Wed, 30 Mar 2022 14:53:10 +0530 Message-Id: <20220330092313.23584-2-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220330092313.23584-1-arunisaac@systemreboot.net> References: <20220330092313.23584-1-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 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 Wed Mar 30 09:23:11 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38217 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 E8F3E27BBEA; Wed, 30 Mar 2022 10:25:16 +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 6ADDB27BBE9 for ; Wed, 30 Mar 2022 10:25:16 +0100 (BST) Received: from localhost ([::1]:58818 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZUZn-0000JI-II for patchwork@mira.cbaines.net; Wed, 30 Mar 2022 05:25:15 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56646) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZUYd-0007qn-AP for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40611) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0000T7-TS for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZUYc-000141-Pw for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH 3/5] gnu: atomic-queue: Run tests correctly. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Mar 2022 09:24:02 +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: 54635@debbugs.gnu.org Cc: Arun Isaac , Efraim Flashner Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.16486322074013 (code B ref 54635); Wed, 30 Mar 2022 09:24:02 +0000 Received: (at 54635) by debbugs.gnu.org; 30 Mar 2022 09:23:27 +0000 Received: from localhost ([127.0.0.1]:34503 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUY2-00012Y-Vk for submit@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:27 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXy-000121-4q for 54635@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:23 -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=Zuluk4aI5QTGGswuXmaOdqa1nu 9Sz0Oqg5j4AEWMrLpzvJ9d79/BPG2UBjuOfroBljkLTQoLsBKPEHZYuV59VNI+21COkb0eFOfOVEF WmBiEf/YpRLKKLHdxgjtLPb9/17/sBupEbfWDaIQtaCGixnsDyyNDAxG3blY5AFzTMwZFX21hvQFh Q79tz7Es/7Pg7RuZ7RAtRblS78GlQrzHplvJ1ao9QyXEoUwndhrE4//dMV9QAxawVRAcI6ljZRnzI +IYiLGjb6u8Vaa4tg7+So6alMWYv3gpzBfQurqXz5eh+y/BTbq5KzZuqhpchSp3HXlIUkr36MVHns dchHzBPA==; Received: from [192.168.2.1] (port=6582 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 1nZUXq-000T5d-Vv; Wed, 30 Mar 2022 14:53:15 +0530 From: Arun Isaac Date: Wed, 30 Mar 2022 14:53:11 +0530 Message-Id: <20220330092313.23584-3-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220330092313.23584-1-arunisaac@systemreboot.net> References: <20220330092313.23584-1-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/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 Wed Mar 30 09:23:12 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38218 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 DA85327BBEB; Wed, 30 Mar 2022 10:34:47 +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=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3A55B27BBEA for ; Wed, 30 Mar 2022 10:34:47 +0100 (BST) Received: from localhost ([::1]:36812 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZUj0-0005GZ-5t for patchwork@mira.cbaines.net; Wed, 30 Mar 2022 05:34:46 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56644) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0007qD-Q8 for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40610) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZUYc-0000Sz-HF for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZUYc-00013u-DW for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH 4/5] gnu: atomic-queue: Do not depend on boost when cross-compiling. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Mar 2022 09:24:02 +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: 54635@debbugs.gnu.org Cc: Arun Isaac , Efraim Flashner Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.16486322074005 (code B ref 54635); Wed, 30 Mar 2022 09:24:02 +0000 Received: (at 54635) by debbugs.gnu.org; 30 Mar 2022 09:23:27 +0000 Received: from localhost ([127.0.0.1]:34501 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUY2-00012W-JZ for submit@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:26 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51804) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXy-000120-4d for 54635@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:22 -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=QAb4L9OYpYrSl1DkACShXuhE+fa1vIvTrjUidSNk7go=; b=VmIVvCNbQrAE1NyuMvf2/DogE3 TQELBt/MKnOva4m+0o/hlYsU2d/cUF/W66a8W3O9VSWqiPitfDYe/o1bSP3dIxloH7T8s9Mnde/lK 64OCKkacDNkqIVmjb3zQOwU+7HuDUFBCNPf3/sVh0sByn2A3CBentPSNcuEx688B1ByJoVvj43fjC zkqBiUUzVsyaQ0rtIs9nMyrZO9oNMjnnYKHzWt0Wj8BWSQ1bRsQmZsAzVhPeIpR1LWbu6fKIYhGa0 DSoubdIaQ+e6/k/6TZRr81xUpFcffyL/+pJpdGAFPOGTh/DvgjraOLddbHCBb9nVWhGB7qHBbUDm+ bpYSRZGQ==; Received: from [192.168.2.1] (port=6582 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 1nZUXr-000T5d-4h; Wed, 30 Mar 2022 14:53:15 +0530 From: Arun Isaac Date: Wed, 30 Mar 2022 14:53:12 +0530 Message-Id: <20220330092313.23584-4-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220330092313.23584-1-arunisaac@systemreboot.net> References: <20220330092313.23584-1-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/cpp.scm (atomic-queue)[arguments]: When cross-compiling, add do-not-check-for-boost phase and delete the build phase. [native-inputs]: Do not include boost when cross-compiling. --- gnu/packages/cpp.scm | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index eb48902034..649a57b0d5 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -1294,6 +1294,21 @@ (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. So, do not check for it. + (add-after 'unpack 'do-not-check-for-boost + (lambda _ + (substitute* "meson.build" + (("unit_test_framework =" all) + (string-append "# " all)) + ((", unit_test_framework") "")))) + ;; atomic-queue is a header-only library. Excepting the + ;; tests, no building is required. And since we don't run + ;; tests when cross-compiling, delete the build phase + ;; entirely. + (delete 'build)) + '()) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -1303,9 +1318,11 @@ (define-public atomic-queue (copy-recursively "../source/include/atomic_queue" (string-append (assoc-ref outputs "out") "/include/atomic_queue"))))))) - (native-inputs - (list boost - pkg-config)) + (native-inputs + (cons pkg-config + (if (%current-target-system) + '() + (list boost)))) (home-page "https://github.com/max0x7ba/atomic_queue") (synopsis "C++ lockless queue") (description From patchwork Wed Mar 30 09:23:13 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38216 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 C077927BBEA; Wed, 30 Mar 2022 10:25:06 +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 4695D27BBE9 for ; Wed, 30 Mar 2022 10:25:06 +0100 (BST) Received: from localhost ([::1]:58330 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZUZd-0008Nt-Cf for patchwork@mira.cbaines.net; Wed, 30 Mar 2022 05:25:05 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56652) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZUYd-0007rI-Mh for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40612) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZUYd-0000TE-9T for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZUYd-000149-64 for guix-patches@gnu.org; Wed, 30 Mar 2022 05:24:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH 5/5] gnu: Add wfmash. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Mar 2022 09:24:03 +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: 54635@debbugs.gnu.org Cc: Arun Isaac , Efraim Flashner Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.16486322074019 (code B ref 54635); Wed, 30 Mar 2022 09:24:03 +0000 Received: (at 54635) by debbugs.gnu.org; 30 Mar 2022 09:23:27 +0000 Received: from localhost ([127.0.0.1]:34505 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUY3-00012g-BG for submit@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:27 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51808) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZUXy-000123-AB for 54635@debbugs.gnu.org; Wed, 30 Mar 2022 05:23:23 -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=BZHEFGwQhF9qZQPw1YqYyARooR JQtuQroLniIhU3fzX1QA8IHnvxn3QccxjoAi1yQScYKxUgdy9V99DULIbgTaAF2NX3W21bNOFemHe Nz44NlMtPxTKTrbqmSuagJ50/9oQkjp+6w07dFpxx38UHLBWPudkQwhzep9i39RPe/5wHr4++D9jC yTteT+meZBftyVBMh7BNub7v+V7pFfar9+veLFYM+loVeXHyvWax0qIO5/0lVXxGmp+XHHjgF26cC TZ+/WSudNXgw6BrxbEExNyClIRBER4bHyVCF7iMyKBkODRxmWeoC3ZjevBHJWbL0wZcWZvYywW7Tz m3o+1/Ow==; Received: from [192.168.2.1] (port=6582 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 1nZUXr-000T5d-9p; Wed, 30 Mar 2022 14:53:15 +0530 From: Arun Isaac Date: Wed, 30 Mar 2022 14:53:13 +0530 Message-Id: <20220330092313.23584-5-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220330092313.23584-1-arunisaac@systemreboot.net> References: <20220330092313.23584-1-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 (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)))