From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 27 04:58:48 2023 Received: (at submit) by debbugs.gnu.org; 27 Dec 2023 09:58:48 +0000 Received: from localhost ([127.0.0.1]:35358 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQga-0005Fq-4w for submit@debbugs.gnu.org; Wed, 27 Dec 2023 04:58:48 -0500 Received: from lists.gnu.org ([2001:470:142::17]:46108) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQgY-0005Fb-Bx for submit@debbugs.gnu.org; Wed, 27 Dec 2023 04:58:46 -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 1rIQgR-0000VM-Mm for guix-patches@gnu.org; Wed, 27 Dec 2023 04:58:40 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rIQgP-0001Hu-De for guix-patches@gnu.org; Wed, 27 Dec 2023 04:58:39 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:subject :subject:from:from:content-language:user-agent:mime-version:date :date:message-id:received; s=mdc; t=1703671098; x=1705485499; bh=amq0/pkUXgi7ts78qMwZVW6D1A0DrTzxT6H0limEWc4=; b=mLzRy+D7spnR Gd1aSY/3WsbloeUBs7WAV43wT/N/7JKrgkbGrhSQbyvY9Qxwl4b7B2qZpekmtV2b 6zlHo8EzUFkrBgMj3P5vjLWglcYXTPgS+ZFF882fs0bsoQLt8NHC5WtgaddBOF6h IEf8NvdfeuMp3rwRxk4nEUzkaikMzBU= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id CFA97A02C7 for ; Wed, 27 Dec 2023 10:58:18 +0100 (CET) Received: from [192.168.1.248] (95.89.229.232) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Wed, 27 Dec 2023 10:58:18 +0100 Message-ID: Date: Wed, 27 Dec 2023 10:58:17 +0100 MIME-Version: 1.0 User-Agent: Mozilla Thunderbird Content-Language: en-US To: From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Subject: [PATCH] gnu: Add r-scgate, r-stacas and r-projectils. 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From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 27 05:03:39 2023 Received: (at 68056) by debbugs.gnu.org; 27 Dec 2023 10:03:40 +0000 Received: from localhost ([127.0.0.1]:35371 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlH-00080h-Fz for submit@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:39 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:41971) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlE-000804-Tj for 68056@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:37 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1703671412; x=1705485813; bh=lXSNUZYgGRzIVEc qMWVDkgrXUYvXMzsberqtthaP2DI=; b=NagOfSVH+d6AR+U45dRVEoi4EWMOflu 7CpurOsyYyFEvi/4vfrX5LhM9Wrh2NvhXzcdJs3SNob9l6K26cDYfF7xGRacjhW8 6aLi4Pb30Gsh+OoJo/BWrp2y0f1H+Gec3i+k/EXfUPyZPYQO+N/sIPMAPo/qQqQo TTr1e0V4xncQ= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 61D74A02C7 for <68056@debbugs.gnu.org>; Wed, 27 Dec 2023 11:03:32 +0100 (CET) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Wed, 27 Dec 2023 11:03:31 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <68056@debbugs.gnu.org> Subject: [PATCH 1/3] gnu: Add r-scgate. Date: Wed, 27 Dec 2023 11:02:34 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.219.20] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-AS-Result: No-10--10.389500-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb16fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHJEg +DBUO6yjIOF3/3JJdN8gfrq5NRrgE5ZDQBqP32VoqIkSpQVZGCBB0ENZnw1vtzcKpAqTAv4qMnZ m8tXkF+043xuKaGMWOGr4YPOFlg2WtYv/FAmebjqubsOtSWY2QX7bicKxRIU2No+PRbWqfRMprJ P8FBOIaA/zV34DQstXRrdMKeCSIxihLR3ZeUpCGvv5Dmx/qaui73QOMlQZBQQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--10.389500-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-SNTS-SMTP: F14F28D62E13A72982A27B0126426E34DB368A64CFE71D09BDB16295D9C257C92000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 68056 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: -3.3 (---) * gnu/packages/bioinformatics.scm (r-scgate): New variable. Change-Id: Ibcf9eaef67398aa00473d29d651c6d32e425d989 --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e7b99ee61..d572980965 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10301,6 +10301,47 @@ (define-public r-sccustomize visualization and analysis of single-cell data using R.") (license license:gpl3+)))) +(define-public r-scgate + (package + (name "r-scgate") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scGate" version)) + (sha256 + (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (properties `((upstream-name . "scGate"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-patchwork + r-reshape2 + r-seurat + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/scGate") + (synopsis + "Marker-based cell type purification for single-cell sequencing data") + (description + "This package provides a method to purify a cell type or cell population of +interest from heterogeneous datasets. scGate package automatizes marker-based +purification of specific cell populations, without requiring training data or +reference gene expression profiles. scGate takes as input a gene expression +matrix stored in a Seurat object and a @acronym{GM, gating model}, consisting of +a set of marker genes that define the cell population of interest. It evaluates +the strength of signature marker expression in each cell using the rank-based +method UCell, and then performs @acronym{kNN, k-nearest neighbor} smoothing by +calculating the mean UCell score across neighboring cells. kNN-smoothing aims +at compensating for the large degree of sparsity in scRNAseq data. Finally, a +universal threshold over kNN-smoothed signature scores is applied in binary +decision trees generated from the user-provided gating model, to annotate cells +as either “pure” or “impure”, with respect to the cell population of interest.") + (license license:gpl3))) + (define-public r-markdownhelpers (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe") (revision "1")) base-commit: 0d13d095420861022e68e87ceebd5e037e12a8b3 -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 27 05:03:40 2023 Received: (at 68056) by debbugs.gnu.org; 27 Dec 2023 10:03:40 +0000 Received: from localhost ([127.0.0.1]:35374 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlH-00080m-RH for submit@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:40 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:53171) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlF-000806-CT for 68056@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:37 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1703671413; x=1705485814; bh=80H//L2PYqVnrQA6JQZQWWY0HiqxDGkI0Mmtt/EI8hw=; b=Y1MZ4hgKX0rR EPs5L02D6WXu61/JaxztqjSQf+2GyNWPF0GYpouTwnaSnnG9CTfmIX9MubyJWgOx fDH8lY5het+zOgu26WBrteK7gPAwkJ0ZhLNvGPHqx6CGOwDMbtvCgNKlalSxczyr ZAL+r3Ldkc0ObwgpV9aLmI8UvAtF0w4= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id E6BABA02D0 for <68056@debbugs.gnu.org>; Wed, 27 Dec 2023 11:03:32 +0100 (CET) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Wed, 27 Dec 2023 11:03:32 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <68056@debbugs.gnu.org> Subject: [PATCH 2/3] gnu: Add r-stacas. Date: Wed, 27 Dec 2023 11:02:35 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.219.20] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-AS-Result: No-10--1.596400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/KIqAq0jIHikJ1hMCC63pY2Lg EVfggSljfZBOSPspI/lLcDE3RV/2HDhvVpbWTycPdCok3ibXlQeuLFZZYlisfHxPMjOKY7A9qHX ONfTwSQsRB0bsfrpPI34T9cYMsdwwk4rhfSn26VG9iu7SFrKikUV+uSwZOK+JArjStyojHmARx8 +SZIxLzFYtcHAkkwTOaj9uCj2ndII+Hyv9lU5NhVr+RpvthbbDcUke23u350xU7OJY7bdPeD9iv /sJMsVc7Oyi/ulxQeKUgZdIaXg4f X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.596400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-SNTS-SMTP: B55830E302E0383607CFFA4467CDEDC21434072206E9DC91CF4DB7479FA917932000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 68056 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: -3.3 (---) * gnu/packages/bioinformatics.scm (r-stacas): New variable. Change-Id: I258a315465ed88b8013d26a36718250c950aa107 --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d572980965..d736abe07e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1069,6 +1069,42 @@ (define-public r-singlet similar.") (license license:gpl2+)))) +(define-public r-stacas + (package + (name "r-stacas") + (version "2.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/carmonalab/STACAS") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm")))) + (properties `((upstream-name . "STACAS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocneighbors + r-biocparallel + r-ggplot2 + r-ggridges + r-pbapply + r-r-utils + r-seurat)) + (home-page "https://github.com/carmonalab/STACAS") + (synopsis "Sub-type anchoring correction for alignment in Seurat") + (description + "This package implements methods for batch correction and integration of +scRNA-seq datasets, based on the Seurat anchor-based integration framework. In +particular, STACAS is optimized for the integration of heterogenous datasets with +only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with +CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods +would tend to over-correct biological differences. The 2.0 version of the package +allows the users to incorporate explicit information about cell-types in order +to assist the integration process.") + (license license:gpl3))) + (define-public r-stringendo (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a") (revision "1")) -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 27 05:03:40 2023 Received: (at 68056) by debbugs.gnu.org; 27 Dec 2023 10:03:40 +0000 Received: from localhost ([127.0.0.1]:35376 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlI-00080t-8n for submit@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:40 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:41633) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rIQlF-000807-P0 for 68056@debbugs.gnu.org; Wed, 27 Dec 2023 05:03:38 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1703671413; x=1705485814; bh=JxtKpCu2+l9SrIo24Yu+UZjFQxahjGxUQxa8nOozEm4=; b=TlEWrx+Ac5/F St74j+uX1ygIvpppqIU0hcnZuVfKud4ecwtKWepQcRtGHBVbZaQCpxk5K52mN07+ auJeHOKsqiZ6tqct7SMFWJdKspxxJVGYkahWhwNxGw7PK6OtdfTh+JxUgv/CDJkW s3oAwMPt4ieq/u0aYzmTQaIK0xhRp2Y= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 5EFF3A02D5 for <68056@debbugs.gnu.org>; Wed, 27 Dec 2023 11:03:33 +0100 (CET) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1258.28; Wed, 27 Dec 2023 11:03:32 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <68056@debbugs.gnu.org> Subject: [PATCH 3/3] gnu: Add r-projectils. Date: Wed, 27 Dec 2023 11:02:36 +0100 Message-ID: <94e8ffe4bb3d6ae0530bc6da99989f39a79f5f5c.1703671356.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.219.20] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-AS-Result: No-10--3.002400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/o5C9bTTxaUYue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedJEb gebEoSmXklvPIaBvBZarP+04pA0BmVvHb3MCevvjdCok3ibXlQT5//buCv56OlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYW8oa2fBdTmalZux3iEjPMv/1S5fBgdwijIlxAacSgZ4GE0x 4luZfsWtbvdVeQlG+Kt+EwDd82WzOS4kHCcW+i//cc73CVikmjHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.002400-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28082.006 X-TM-SNTS-SMTP: 99F95DC0D40C9031FA4452645E265676F76DA54C3741D73ECFC32D501819E8B32000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 68056 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: -3.3 (---) * gnu/packages/bioinformatics.scm (r-projectils): New variable. Change-Id: Ia975cfcb9c79e59b029c6839dc87b5dcb89bf72a --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d736abe07e..f959de7cd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10247,6 +10247,51 @@ (define-public r-premessa bead-based normalization and debarcoding.") (license license:gpl3)))) +(define-public r-projectils + (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709") + (revision "1")) + (package + (name "r-projectils") + (version (git-version "3.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/carmonalab/ProjecTILs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw")))) + (properties `((upstream-name . "ProjecTILs"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocneighbors + r-biocparallel + r-dplyr + r-ggplot2 + r-matrix + r-patchwork + r-pheatmap + r-pracma + r-purrr + r-rcolorbrewer + r-reshape2 + r-scales + r-scgate + r-seurat + r-seuratobject + r-stacas + r-ucell + r-umap + r-uwot)) + (home-page "https://github.com/carmonalab/ProjecTILs") + (synopsis "Reference-based analysis of scRNA-seq data") + (description + "This package implements methods to project single-cell RNA-seq data onto +a reference atlas, enabling interpretation of unknown cell transcriptomic states +in the the context of known, reference states.") + (license license:gpl3)))) + (define-public r-presto (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") (revision "0")) -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 30 11:29:23 2024 Received: (at 68056-done) by debbugs.gnu.org; 30 Jan 2024 16:29:23 +0000 Received: from localhost ([127.0.0.1]:36571 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUqzC-0001Bc-Vd for submit@debbugs.gnu.org; Tue, 30 Jan 2024 11:29:23 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21779) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUqzB-0001BU-4h for 68056-done@debbugs.gnu.org; Tue, 30 Jan 2024 11:29:22 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1706632150; cv=none; d=zohomail.com; s=zohoarc; b=azWGRfJEMDhWMcZDpJHNheMrrJefrQGEh1rHILhpa3j8NU0dftGqsmZgMzWKtZFRahNwhknrsFiiEyONPoCCgNiL3/U+8N9s5Lbn/G1HpfKzO+KlaJY5PrvCMdu4pUM02D+4h9zh5t60aiQGBlHw6kflJn7qs6h0zKxzp6EeKVI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1706632150; h=Content-Type:Content-Transfer-Encoding:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=U9fiyA8pcycMawqe+rMFcK1llpAemXkoPq7aFM8z4cE=; b=CjkP0ixWjXBmhxifva85y1dpWE6ensNL4wd/DSZbElBv2LKXZcpTfgP4kIAd8hK8E8J4iocqoQPoY7NgMVsDDQ+s7mhyIN9R+pfW2JajEF6BXS+yYUMFoSrM/VuQdCYgsFZWJYVGAJUHCu3lWadwg0Fs5fxRCkv0p5unZadsQRs= 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=1706632150; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=U9fiyA8pcycMawqe+rMFcK1llpAemXkoPq7aFM8z4cE=; b=I2/rTysN0gwpo1sa9HLHinP5AHVrvRMC2eFAZXWntqmD8ojIwKL3WJ6R4/JohHJY C7xjjsrDJ87e16tE1z5LWgFe+EInhAXUZqg6XiTPjgjNUha8pc39FirGjy5sylBhtEy aDlq/CVHVAkVI1W+S2UQVbeYYGy0BUGfnAK8bZxM= Received: from localhost (102-111-142-46.pool.kielnet.net [46.142.111.102]) by mx.zohomail.com with SMTPS id 1706632147019470.27797539129006; Tue, 30 Jan 2024 08:29:07 -0800 (PST) User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 68056-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-scgate, r-stacas and r-projectils. Date: Tue, 30 Jan 2024 17:27:51 +0100 Message-ID: <874jeuhjjj.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: 68056-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 patches. For r-stacas and r-scgate we already have Bioconductor packages. Since we also have a package for r-projectils I=E2=80=99m closing this issue. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 30 12:07:07 2024 Received: (at 68056-done) by debbugs.gnu.org; 30 Jan 2024 17:07:07 +0000 Received: from localhost ([127.0.0.1]:36602 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUrZi-0004wC-9z for submit@debbugs.gnu.org; Tue, 30 Jan 2024 12:07:07 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21048) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUrZW-0004vc-5o for 68056-done@debbugs.gnu.org; Tue, 30 Jan 2024 12:07:05 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1706634402; cv=none; d=zohomail.com; s=zohoarc; b=XgzaXo3JgUADzKkPcIhLJgrdMLG8/ITSkeAhd9NW8ravRtQ5asBl0S2vuzhXcXtfrrvR1HtrzTz36shwd4hjL7judxoN56J6QqE1cqPTVndkY2RqrQ7xbgHaciY2UFIrEqzTsMCicESfRFy6Yj0zLn9LNUYeEZJjc1/1nhjY1Sk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1706634402; h=Content-Type:Content-Transfer-Encoding:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=vudmmyy6PjTb19BmX2J1jzsiDNXg3FnVfjfByXuvuiQ=; b=h2N5m29BKLeoYo1bFRAcIZEpY+meyYK/y5AnWzi/kRTnf834R+HleR3Pmk1ZSws7GVnTpRs+USGfXGfWXzb/KVt9R9W7aX/jIMfKBA4ApSWjGJypQ1rATi9dllYJH/UZyRpmem8hAySDKvua8lT9PxeeJsKPNhOHN9QPiafr74E= 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=1706634402; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=vudmmyy6PjTb19BmX2J1jzsiDNXg3FnVfjfByXuvuiQ=; b=H3uNDRPvs8WYAZInpLralN7C+oN0AcMJpLU0+olc1bMKwysZKf7/b6QHuiNdg6HF IBFRwt8OXjJTYtZ/5DMLOpeePPSIXrIsyPrFUdUjMkwMWk039SW8GrFkfO+31/DpY/V Ab60PFTNeuwoLLylN3UL0k1WtLbB+/k9kS6vrYUI= Received: from localhost (102-111-142-46.pool.kielnet.net [46.142.111.102]) by mx.zohomail.com with SMTPS id 1706634400837424.9891365787689; Tue, 30 Jan 2024 09:06:40 -0800 (PST) References: <874jeuhjjj.fsf@elephly.net> User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 68056-done@debbugs.gnu.org Subject: Re: [PATCH] gnu: Add r-scgate, r-stacas and r-projectils. Date: Tue, 30 Jan 2024 18:05:57 +0100 In-reply-to: <874jeuhjjj.fsf@elephly.net> Message-ID: <87zfwmg38h.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: 68056-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 (-) Ricardo Wurmus writes: > Thanks for the patches. > > For r-stacas and r-scgate we already have Bioconductor packages. Since > we also have a package for r-projectils I=E2=80=99m closing this issue. Turns out that *I* actually applied them about a month ago, but I had edited the package definitions to use bioconductor-uri instead of an arbitrary git checkout. Sorry for the confusion! --=20 Ricardo From unknown Sat Jun 14 14:29:32 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 28 Feb 2024 12:24:08 +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