From unknown Wed Aug 20 03:37:18 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#56024 <56024@debbugs.gnu.org> To: bug#56024 <56024@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-alpine. Reply-To: bug#56024 <56024@debbugs.gnu.org> Date: Wed, 20 Aug 2025 10:37:18 +0000 retitle 56024 [PATCH] gnu: Add r-alpine. reassign 56024 guix-patches submitter 56024 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 56024 normal tag 56024 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 16 13:01:29 2022 Received: (at submit) by debbugs.gnu.org; 16 Jun 2022 17:01:29 +0000 Received: from localhost ([127.0.0.1]:43015 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1ss5-0006rc-ID for submit@debbugs.gnu.org; Thu, 16 Jun 2022 13:01:29 -0400 Received: from lists.gnu.org ([209.51.188.17]:57986) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1ss0-0006rR-M4 for submit@debbugs.gnu.org; Thu, 16 Jun 2022 13:01:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48080) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1srv-0001Ma-VQ for guix-patches@gnu.org; Thu, 16 Jun 2022 13:01:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:50983) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1srh-0002Rn-GI for guix-patches@gnu.org; Thu, 16 Jun 2022 13:01:08 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9F4FB300346 for ; Thu, 16 Jun 2022 19:01:00 +0200 (CEST) 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:received:received; s=mdc; t=1655398859; x=1657213260; bh=o7f12Vb3/3LbDf8MYfS7SF7ffzvHbzad9RV32yStVZI=; b=lqVkSEJrgJGQ Yyy1/GgX7Rvt19cyQ+/c7S0RuPAZFG4CcZt63FjPBXXverFKsus8E+NjjqtrE4+g 0ObQMs9MSR/Ei0mmshdxrbYSBF3MAymtl+yPPgGJ5yatzaKddIXlbjrlLf+sg1QD MvOdSoszZ/nR77VVs4ymOEXpFfNWcWs= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 702sQbfkOxEv for ; Thu, 16 Jun 2022 19:00:59 +0200 (CEST) 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 for ; Thu, 16 Jun 2022 19:00:59 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.9; Thu, 16 Jun 2022 19:00:59 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-alpine. Date: Thu, 16 Jun 2022 19:00:48 +0200 Message-ID: <20220616170048.28808-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26960.000 X-TM-AS-Result: No-10--2.517600-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCwHDvci4zWajQ6QlBHhBZuwT1z kvtd51LjyC7TvwUXkXHFRlzRkyh3++ineqRpWTZwOy1AV8tUD8IZS+fz1TDIS64sf0Egj7iqsqx rFSI3/KcX4oKkYTfsImyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5e1THoW6brZyWN4v Os3xfy8+U0z3bnUgq1TKs/xOx2aSjtt8QypjkQTif74aHo1A17BCqvbEhNPJV4sx2yOw0Ze6c+n Av+kfGYNQSQFNny84vGXJMJdBHjGKgDk8Dh1C7G5iklHaSF5d37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.517600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.000 X-TM-SNTS-SMTP: 66DABE68EB6D0A56FD883483027AE4ABF146D1569F207EF314460201F7B842AF2002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@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: -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 (--) * gnu/packages/bioconductor.scm (r-alpine): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..e0797206f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,46 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript abundance +in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million mapped reads). It +is currently designed for un-stranded paired-end RNA-seq data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 24 08:44:47 2022 Received: (at 56024-done) by debbugs.gnu.org; 24 Nov 2022 13:44:47 +0000 Received: from localhost ([127.0.0.1]:57740 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyCX1-0005E7-2x for submit@debbugs.gnu.org; Thu, 24 Nov 2022 08:44:47 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyCWz-0005Dz-Sx for 56024-done@debbugs.gnu.org; Thu, 24 Nov 2022 08:44:46 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1669297484; cv=none; d=zohomail.com; s=zohoarc; b=NPmlfSF5Rd7tkbmTJgfISJVpx+6f9w2bWjeDHnfQQ7QupRIJxx66imizxLDJ1RFZS1EIrBIhO7YEaq7L7zQSCHj6XK/4uVVjoAnDG5Ak3PrQcau/IAh8TuDgj1TxPVl4lzNt3GtFNIh30LXtrmlC4i7zISmJu1/yU2VGJtKb1Qc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1669297484; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=fMyH3B6Q+E/tB10+UBQrtvdrSkMyLmU6WEPCTq2Ho54qHpRjtdo4vbvngAxODueErxwAuVqgF2dKhhXVO9ppjI7V/Nh4iKqjhLm848E/TpJKppsFnIVBFraKrMS329rAQdBEk1IP4HkfPWBvATxXg5etPrJIIv5TWjbZ2qzTDnM= 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=1669297484; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=QvR38ubw0NPKdB3l96HMkcvx4VRthZuCnlmYY+NksWoiAdRoqsqxHdBpg555IpDI pUJ64iOUlrkvrqU5PAsjWoP8pmDK3suW7wMEmxCCkhiW2L7e61t5hJOmes2QB7LSLVC DG9/t2YOcSgTsjUrVBD4OX4ZXkmGDSbTUQxisJHM= Received: from localhost (145-109-142-46.pool.kielnet.net [46.142.109.145]) by mx.zohomail.com with SMTPS id 1669297481795655.5545839063388; Thu, 24 Nov 2022 05:44:41 -0800 (PST) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56024-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-alpine. 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