From patchwork Thu Feb 15 15:40:19 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 60363 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 3A47B27BBEA; Thu, 15 Feb 2024 15:42:03 +0000 (GMT) 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,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL, 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 DF0FB27BBE2 for ; Thu, 15 Feb 2024 15:41:57 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1radru-0000sb-Tb; Thu, 15 Feb 2024 10:41:48 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1radrs-0000sO-14 for guix-patches@gnu.org; Thu, 15 Feb 2024 10:41:44 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1radrr-0004CI-PN for guix-patches@gnu.org; Thu, 15 Feb 2024 10:41:43 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1radsA-0001Uq-Dv for guix-patches@gnu.org; Thu, 15 Feb 2024 10:42:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#69167] [PATCH] gnu: r-harmony: Update to 1.2.0. Resent-From: nafkhamdc Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 15 Feb 2024 15:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 69167 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69167@debbugs.gnu.org Cc: nafkhamdc X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.17080117105732 (code B ref -1); Thu, 15 Feb 2024 15:42:02 +0000 Received: (at submit) by debbugs.gnu.org; 15 Feb 2024 15:41:50 +0000 Received: from localhost ([127.0.0.1]:56790 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1radry-0001UN-D4 for submit@debbugs.gnu.org; Thu, 15 Feb 2024 10:41:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:59248) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1radrv-0001UF-FG for submit@debbugs.gnu.org; Thu, 15 Feb 2024 10:41:48 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1radrc-0000rf-9O for guix-patches@gnu.org; Thu, 15 Feb 2024 10:41:28 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1radrZ-00048j-Mf for guix-patches@gnu.org; Thu, 15 Feb 2024 10:41:28 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1708011679; x=1709826080; bh=HE7OqnW+PDP9RYi 13sI+4e35l9pEsQpoJFXRYtG5KT8=; b=avTKKwk4i4s1KVhwXee00oW2JVxnfDM AGqKInXao1coy2cprfDyhHnzKXVQ/jWQfVdbqSBNF82iYOIAjGMAOrhIJ/jD/7+s NZQWP2JmjscbO5IdEU6UwlIe2sM9m3lZB/9B0dtt3u2LJQw0bOJdokn6hKDRYya5 ItURhgLpF4TA= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id ECFD4300171 for ; Thu, 15 Feb 2024 16:41:18 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Thu, 15 Feb 2024 16:41:18 +0100 From: nafkhamdc Date: Thu, 15 Feb 2024 15:40:19 +0000 Message-ID: <88868cdb132cbdd5e0a39ef61d271e9cb9397be4.1708011619.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.1006-28194.000 X-TM-AS-Result: No-10--7.590400-5.000000 X-TMASE-MatchedRID: utTYmLJDm0f1zRJIGToPzjiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt10ieHN50/kHxi///JpaHQOXBPRemiwRNcIubEPSkNnJvmK TdxbGqLJ7MSP7SLpuGNis7QFIkrd7VoG8mkAKgzzjpxdo/JwVm5Slv/9klkDiD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58hYfw868k05Yzqx6DtfVZtvcUt5lc1lLgoGRyAacnhaa9qLIsDEbFbEc8k xf0jjzl4vLgMk1YiQdChu/YCvqht37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.590400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28194.000 X-TM-SNTS-SMTP: E966773B3F51D05C624BEC701EE31900299C44C6AF4576137BD6F0F8C115512F2000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-harmony): Update to 1.2.0. [propagated-inputs]: Remove r-irlba and r-tidyr; add r-rhpcblasctl. [native-inputs]: Remove autoconf; add r-knitr. Change-Id: I3c554bbb29ccc2b8a24d2d46e362b7d7cae56c1c --- gnu/packages/cran.scm | 52 +++++++++++++++++-------------------------- 1 file changed, 20 insertions(+), 32 deletions(-) base-commit: 2ba2875dbda4b080fcad4e6d672bb4104d59dd0c prerequisite-patch-id: 4e4ac5c149de95802186383997235d855b9d08de diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3b8ad2baac..fa28814827 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26934,44 +26934,32 @@ (define-public r-liger (define-public r-harmony (package (name "r-harmony") - (version "0.1") + (version "1.2.0") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/immunogenomics/harmony") - (commit version))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (cran-uri "harmony" version)) (sha256 - (base32 - "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9")) - (modules '((guix build utils))) - (snippet - '(begin - (for-each delete-file '("config.status" "configure")) - #t)))) + (base32 "1df7bb9ba3m0c44fhmh8cs4hlkh4fffjwm8rz7l87lf5pdy7sg56")))) + (properties `((upstream-name . "harmony"))) (build-system r-build-system) - (propagated-inputs - (list r-cowplot - r-dplyr - r-ggplot2 - r-irlba - r-matrix - r-rcpp - r-rcpparmadillo - r-rcppprogress - r-rlang - r-tibble - r-tidyr)) - (native-inputs - (list autoconf)) - (home-page "https://github.com/immunogenomics/harmony") + (propagated-inputs (list r-cowplot + r-dplyr + r-ggplot2 + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-rhpcblasctl + r-rlang + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/web/packages/harmony/index.html") (synopsis "Integration of single cell sequencing data") (description - "This package provides an implementation of the Harmony algorithm for -single cell integration, described in Korsunsky et al -@url{doi.org/10.1101/461954}. The package includes a standalone Harmony -function and interfaces to external frameworks.") + "Implementation of the Harmony algorithm for single cell integration. +This package includes a standalone Harmony function and interfaces to +external frameworks.") (license license:gpl3))) (define-public r-covr