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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 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -4.2 (----) X-Debbugs-Envelope-To: submit Cc: nafkhamdc X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.2 (-----) * 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(-) 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 base-commit: 2ba2875dbda4b080fcad4e6d672bb4104d59dd0c prerequisite-patch-id: 4e4ac5c149de95802186383997235d855b9d08de -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Mon May 06 07:05:54 2024 Received: (at 69167-done) by debbugs.gnu.org; 6 May 2024 11:05:54 +0000 Received: from localhost ([127.0.0.1]:37312 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3wAM-0008FM-0j for submit@debbugs.gnu.org; Mon, 06 May 2024 07:05:54 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21176) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3wAK-0008FG-Au for 69167-done@debbugs.gnu.org; Mon, 06 May 2024 07:05:52 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1714993526; cv=none; d=zohomail.com; s=zohoarc; b=XBQ2LFoSV/FEHxDbCPNuccuKRuRhoe+QtjIw0wVouNM9bQ13pnq7c8qSy7K8YRkPBF/Qzboq4HPz7AZtcJRGLmhvvrGv/CqSOzkPXBj3GHnnn303EIgb+DPoQJ8NwXII+2x7i5nybo04cEZevDVm/9jgD6N1EEzmOBkaxA6uOl0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1714993526; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=pcjQsOhum5l7N25sZ75Qav/1a6vcUEOWTbPJsEZerxo=; b=BX6N7iloTjwjF350Ly7GmVuWENEYHtVSzbhK5XEWu812wdrLCRFJlkJtezt6m+tZ+vYmZN6IfAJHDqUg8VhTVIl8aM7jYgDxX8hkgKf8JAqv96oZRy4Nc9TSwFiZqd+cKnkaunvSM1/Q5gsLXvrKrvmEvxE+zaQhjwMpmSKHf7I= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1714993526; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=pcjQsOhum5l7N25sZ75Qav/1a6vcUEOWTbPJsEZerxo=; b=QDcZGvwFr6Hz6g9PP00f+l20gEPUlVmEJFKoowPqDIIpNVI9oGQehXbEm1Wrv+QM EYgAeBXc4luMHEsgG+CpXg9DDJ/Ho0Nvulymgx10vJIue4fTe4ctcR08+PAhPNnvP39 xySAw5+kP/pp1Gy6ZXvamaw6eBxANJrSuo49cUXI= Received: by mx.zohomail.com with SMTPS id 1714993523981799.5945297593457; Mon, 6 May 2024 04:05:23 -0700 (PDT) From: Ricardo Wurmus To: 69167-done@debbugs.gnu.org Subject: [PATCH] gnu: r-harmony: Update to 1.2.0. User-Agent: mu4e 1.12.4; emacs 29.3 Date: Mon, 06 May 2024 13:05:20 +0200 Message-ID: <87le4njj4f.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 69167-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks for the patch! This was applied with commit e3586aa61d58fd8992abb594edc2168d5bf5a6da on February 15, but we forgot to close this issue. -- Ricardo From unknown Mon Jun 23 06:01:21 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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