From unknown Wed Jun 18 23:07:19 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#46524 <46524@debbugs.gnu.org> To: bug#46524 <46524@debbugs.gnu.org> Subject: Status: [PATCH 0/2] Add r-samr and r-gsa. Reply-To: bug#46524 <46524@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:07:19 +0000 retitle 46524 [PATCH 0/2] Add r-samr and r-gsa. reassign 46524 guix-patches submitter 46524 Tim Howes severity 46524 normal tag 46524 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 15 00:40:42 2021 Received: (at submit) by debbugs.gnu.org; 15 Feb 2021 05:40:42 +0000 Received: from localhost ([127.0.0.1]:37147 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWck-0000cL-DN for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:40:42 -0500 Received: from lists.gnu.org ([209.51.188.17]:40168) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWcj-0000cE-2L for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:40:41 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56302) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lBWci-0000AS-RE for guix-patches@gnu.org; Mon, 15 Feb 2021 00:40:40 -0500 Received: from lavabit.com ([38.147.122.66]:55007) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lBWcg-0006KP-Vw for guix-patches@gnu.org; Mon, 15 Feb 2021 00:40:40 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id GRTA05R8T7GF for ; Sun, 14 Feb 2021 23:40:37 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1613367637; bh=Nlm2LtQYkW/gzM+UVWn/5mgudE/SnsbSjjHxO+kmha8=; h=From:To:Subject:Date:Message-Id:X-Mailer:MIME-Version: Content-Transfer-Encoding; b=hZK5dfHjs5ZJ+CBsRt6Ejn/r7gf0kQjFvsxCk6Kv49OBHIhrTyQFzC79hm2ybLS9M X7tEcxvdgmwgqp2paoouDTzoaI3KnounC2GJYZZsq4TMhdBkqiUosVQoogFSW8bITN /6SrifuyhqWnSNF1oRuQOy2RiqtNp2lzuWEIHLNLZztroUJa0Qxb5n8oDb/BffbX7E MKDPI5FRmXjvjnkefbQ1Ly8QAwEFQkYpQ3HuKIkouQqgaisrlSoo6kmJUx8UeUUlHI Bq9XV9YGtl/LMLc2RRyEkIhDV6i52VtIP67bU0XLVqbbcb008dXEYjjW7h2W+q4wLk xdSSiJWQkyUEw== From: Tim Howes To: guix-patches@gnu.org Subject: [PATCH 0/2] Add r-samr and r-gsa. Date: Sun, 14 Feb 2021 21:40:29 -0800 Message-Id: <20210215054029.47677-1-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=38.147.122.66; envelope-from=timhowes@lavabit.com; helo=lavabit.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) Hello, This adds the packages samr and GSA for gene expression analysis in R. Tim Howes (2): gnu: Add r-gsa. gnu: Add r-samr. gnu/packages/cran.scm | 52 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 15 00:44:50 2021 Received: (at 46524) by debbugs.gnu.org; 15 Feb 2021 05:44:50 +0000 Received: from localhost ([127.0.0.1]:37162 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgk-0000jV-CW for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:50 -0500 Received: from lavabit.com ([38.147.122.66]:25308) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgj-0000jD-7Y for 46524@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:49 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id HIZPDQXN6WYY for <46524@debbugs.gnu.org>; Sun, 14 Feb 2021 23:44:43 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1613367883; bh=bgQ6LLKNBmxwA3n/uDLR348l0LueRjrte/FqngTlvTM=; h=From:To:Subject:Date:Message-Id:X-Mailer:MIME-Version: Content-Type:Content-Transfer-Encoding; b=NDSL58S1ixlA/dMUI5CS7w4FMsrJl85gZuzTmPwOwZRL/7BSsBpzrbAWs+ci/OKYd Bf3CMrUorMvz26TaLHW+n1cHuFWjYnFv1/7zekLmndLJ8Y84KGGbNp5D3+nDrFKtS7 l+bLj1qyVCigTW2Pb2hbMMZdsvVZArKCTUrByets95VSNN2IsgLggttZ2gzB4OojT0 KtXhH3YRD1vMf0X6WucHClYvsxOar4n1KnBi2GzHAC3bClN/TlsmpkLTuMpJ/7qPNh Epb7e9FRKoZDIXu5hquanItq2RY3IxCuUdWRcq8r0bUD5wYiYF4A2z1gCdZnm+/Kwf KDjOEFkqJyLrQ== From: Tim Howes To: 46524@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add r-gsa. Date: Sun, 14 Feb 2021 21:44:36 -0800 Message-Id: <20210215054437.47745-1-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 46524 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 (-) * gnu/packages/cran.scm (r-gsa): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1fe90619cd..86b2df0a9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,6 +33,7 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -26851,3 +26852,23 @@ from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) + +(define-public r-gsa + (package + (name "r-gsa") + (version "1.03.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "GSA" version)) + (sha256 + (base32 + "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1")))) + (properties `((upstream-name . "GSA"))) + (build-system r-build-system) + (home-page + "https://statweb.stanford.edu/~tibs/GSA/") + (synopsis "Gene Set Analysis") + (description "Inference on gene sets in microarray studies.") + ;; Any version of the LGPL + (license license:lgpl3+))) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 15 00:44:52 2021 Received: (at 46524) by debbugs.gnu.org; 15 Feb 2021 05:44:52 +0000 Received: from localhost ([127.0.0.1]:37164 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgm-0000jf-Kw for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:52 -0500 Received: from lavabit.com ([38.147.122.66]:6440) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgj-0000jE-M4 for 46524@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:50 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id CQON08BU2Y86 for <46524@debbugs.gnu.org>; Sun, 14 Feb 2021 23:44:44 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1613367884; bh=tRtrFYvr3xZTAiItyf41/hMgBaJKE52eBaXg3a4+xII=; h=From:To:Subject:Date:Message-Id:X-Mailer:In-Reply-To:References: MIME-Version:Content-Transfer-Encoding; b=a3ZYYEcfMsZ7maYGvTmaPVvcKMzTU1PluB3Ba4W+v2BGf4rjWL0um0l3Sx2+TWKtx rF1YmXwIe5XPYMihGiN9Sa13LU7tHcpt972/e+a+Mwj3kTwysHCi5gLzxVFstwNO/V OQ4mt5ErH7ZHKSVyIyBzA5UxstQgqt1gNxSaoOjwJBM8B6z1NXAp2VXnb6/HqsOiXg N1x5e2O/ogYouKUFfK/D8WdR1gJ5mPUR3BqqcpL9TYBDpZyOT4sh36g6h4yY948wJK UmZn5XUygrCoQu1WLPZFM8j8WXg8KDBA/gg+IWsfM8D4nD47795eknHIzU6PENjBni ngKTVQWBBu0oQ== From: Tim Howes To: 46524@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add r-samr. Date: Sun, 14 Feb 2021 21:44:37 -0800 Message-Id: <20210215054437.47745-2-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210215054437.47745-1-timhowes@lavabit.com> References: <20210215054437.47745-1-timhowes@lavabit.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 46524 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 (-) * gnu/packages/cran.scm (r-samr): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 86b2df0a9f..d151f1cb50 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26872,3 +26872,34 @@ package online.") (description "Inference on gene sets in microarray studies.") ;; Any version of the LGPL (license license:lgpl3+))) + +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page + "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis + "Significance Analysis of Microarrays") + (description + "Significance Analysis of Microarrays for differential expression +analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 26 05:14:58 2021 Received: (at 46524-done) by debbugs.gnu.org; 26 Mar 2021 09:14:58 +0000 Received: from localhost ([127.0.0.1]:40406 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lPiYU-0007zq-5M for submit@debbugs.gnu.org; Fri, 26 Mar 2021 05:14:58 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lPiYS-0007zi-54 for 46524-done@debbugs.gnu.org; Fri, 26 Mar 2021 05:14:56 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1616750091; cv=none; d=zohomail.com; s=zohoarc; b=Pp+10Qd/gvmEGo74JqpMKKKoHz9Bu4L5/fQvNb63Q1YRf7n2/nAAxk1cawb7eLotmjYFgVkySoDhoCgUjn6QzeaBeLiArBQbKROGGohGQJTU5jbnU5SEuGS3pEBVBOqi+t/eI4GhOMLejJRn+Zfq9ABK+A3uV7EPdNwz3NIyVJk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1616750091; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=yBtzgB64Wj6oOE/wrmSCn7zJQT2GuYhgHVHGTVY2bzo=; b=PSpo+cDHoMKKNUqgK7F1JSl7K2iOA4IPC/zUROmKzap7Kc82upae8KRwG5qwlocbhyvXWs2ngN2eFqJ/HkpdUV2O2QaE4v9PJa9sFXeCJawb/qMxLAk0YzJa/7XB+k/iB4HjdHeTuW57mjaunBqeYt8s5S0uSZyh/ff0zmAfFqU= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1616750091; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=yBtzgB64Wj6oOE/wrmSCn7zJQT2GuYhgHVHGTVY2bzo=; b=Orm73gtydUyB4wBSBZgQuROubW4W21TnutN3vgPWz6VMT0k7EHtTZ3qh3s3soisc VKZVFufMJDEmFJoK5Uh7GjMwNwAmUxEKCwwBmao7dtxF/L2jp8rrnW3yCf/7JzfquD7 QpDmYh+sKBuANWPC3Z68/jIKRCa/0XQjZqhnctBs= Received: from localhost (p54ad4990.dip0.t-ipconnect.de [84.173.73.144]) by mx.zohomail.com with SMTPS id 1616750089871496.2045127836982; Fri, 26 Mar 2021 02:14:49 -0700 (PDT) References: <20210215054029.47677-1-timhowes@lavabit.com> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus To: Tim Howes Subject: Re: [bug#46524] [PATCH 0/2] Add r-samr and r-gsa. In-reply-to: <20210215054029.47677-1-timhowes@lavabit.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 26 Mar 2021 10:14:47 +0100 Message-ID: <87lfaatgxk.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 46524-done Cc: 46524-done@debbugs.gnu.org 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 (-) Hi Tim, I=E2=80=99m sorry for the delay! > This adds the packages samr and GSA for gene expression analysis in R. > > Tim Howes (2): > gnu: Add r-gsa. > gnu: Add r-samr. > > gnu/packages/cran.scm | 52 +++++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 52 insertions(+) I applied these with minor changes with commit e9741ad623. Thank you! --=20 Ricardo From unknown Wed Jun 18 23:07:19 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 23 Apr 2021 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator