From unknown Sat Aug 16 10:47:15 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#43400 <43400@debbugs.gnu.org> To: bug#43400 <43400@debbugs.gnu.org> Subject: Status: [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) Reply-To: bug#43400 <43400@debbugs.gnu.org> Date: Sat, 16 Aug 2025 17:47:15 +0000 retitle 43400 [PATCH 00/12] Move some BioConductor to (gnu packages biocond= uctor) reassign 43400 guix-patches submitter 43400 zimoun severity 43400 normal tag 43400 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:04:39 2020 Received: (at submit) by debbugs.gnu.org; 14 Sep 2020 16:04:39 +0000 Received: from localhost ([127.0.0.1]:55956 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHqy7-0008JN-Cw for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:04:39 -0400 Received: from lists.gnu.org ([209.51.188.17]:57842) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHqy3-0008JC-25 for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:04:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53858) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kHqy0-0007mY-QE for guix-patches@gnu.org; Mon, 14 Sep 2020 12:04:32 -0400 Received: from mail-wr1-x42b.google.com ([2a00:1450:4864:20::42b]:44701) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kHqxv-0001s7-Tb for guix-patches@gnu.org; Mon, 14 Sep 2020 12:04:31 -0400 Received: by mail-wr1-x42b.google.com with SMTP id s12so197263wrw.11 for ; Mon, 14 Sep 2020 09:04:27 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Hop5ueb8mZcSp2uO8dLBEAwYJWqK64vugx+2SojS2WI=; b=lgR7C8W7vNiU1u1tq5Ra3U7+PBV+GKAYQ4mlqRSnukSdASFc2N2e5dvUPvGgAQSQRG I8EZ3lFhvUf2FJFscLM580g/oxqIF89aJbEmkOjWJDDRG2husz2EWAGop15tvxi7dviF OCfjTeAnzVuJDgRabkOVcZGw8XT2IumJAJ2c07rFuxabrEoA3JQxYF4FAbQmzPlgnnBd g9phtdW5NXKEnG+fnjH+WOGcyw4EqjRPij+o7D6zYaQjALyj3YmNp0Ldh+HEoTHV8TNL 84mcx01PWUXKFczQNi2UuOcbF75kRTmQomnGdFc4w/u0x9lVmnLb0Oiqlqo8AcetfcFU DtyQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Hop5ueb8mZcSp2uO8dLBEAwYJWqK64vugx+2SojS2WI=; b=riQvTIBxrtxQqqyhisRs4MVxVEACJbHeDfvbKmD70nqLmJxKSpJzf9k0QInIawWm/W Gn/+1mbt2tsI6oFRdEAauT+i8z5iXpmxeGkhIz+dpJZb1xLdbewJZKRFlb64n+qMw51q sg/bEkVmISFdgdwF/UgV6FZ5gPlwYv6cq4efuIPPGTLCH+XqCBIzl9dPeib3wH1OWyf3 nfLxDdr8euqTBbeTFbsEhhuV7ujz3COZF5HHrE69J6cWYLKYGZ/Yh2X40PlHaUGeBvsh V5Xw3auTWz0yiAK87xrsgKAz8r8jqntG8GH5MOkoLMLSwWj6KchC91Q0jsDN/Qw4ndvb UFbw== X-Gm-Message-State: AOAM530s8c1vIGlaMKPQlLqyApAIMZJlrtiFEVzuHBt3p/RzDhk4lZCo VudOiEFai6t1mGFKyZmi8E2VE+mx61I= X-Google-Smtp-Source: ABdhPJwZ+NWdevGu0ONd2wWvIgEe/NlFqs5+5QWKpRy9y2oqcEB6+QGx2XouZ2YgUZnetlG4pTbcdw== X-Received: by 2002:a05:6000:1c4:: with SMTP id t4mr17344456wrx.350.1600099466335; Mon, 14 Sep 2020 09:04:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id v4sm19017444wml.46.2020.09.14.09.04.25 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:04:25 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) Date: Mon, 14 Sep 2020 18:04:14 +0200 Message-Id: <20200914160414.7572-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::42b; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x42b.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.6 (/) X-Debbugs-Envelope-To: submit Cc: zimoun 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: -2.3 (--) Dear, More janitoral stuff. The process is the same as described in the cover letter of #43345 . All the best, simon zimoun (12): gnu: r-fourcseq: Move to (gnu packages bioconductor). gnu: r-preprocesscore: Move to (gnu packages bioconductor). gnu: r-rgraphviz: Move to (gnu packages bioconductor). gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). gnu: r-scran: Move to (gnu packages bioconductor). gnu: r-scater: Move to (gnu packages bioconductor). gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). gnu: r-beachmat: Move to (gnu packages bioconductor). gnu: r-rhdf5lib: Move to (gnu packages bioconductor). gnu: r-hdf5array: Move to (gnu packages bioconductor). gnu: r-hitc: Move to (gnu packages bioconductor). gnu: r-fithic: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 432 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 337 ------------------------- gnu/packages/cran.scm | 44 ---- gnu/packages/graph.scm | 28 --- gnu/packages/statistics.scm | 21 -- 5 files changed, 432 insertions(+), 430 deletions(-) base-commit: c22c6de453a4685bc65bf38f92f823c733d62290 -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:02 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:02 +0000 Received: from localhost ([127.0.0.1]:55963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1N-0008QH-TT for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:02 -0400 Received: from mail-wm1-f43.google.com ([209.85.128.43]:39235) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1M-0008Pk-I6 for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:00 -0400 Received: by mail-wm1-f43.google.com with SMTP id b79so606464wmb.4 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=GkEdJ9O/6Iw5vepk2vkugGFivnPxN1wyv4xLhvAKu9k=; b=Vr+3GCRT+C5yLGIbKr+WD+gHUjZDGcpogWKTyuhJvSZey+XJDajZOol5lTq7MwDWDj lmnwc1IrSKsrTelQdosq2u5s3sXgMkdVwRl/1LVIppFLkPzxTvWKz0vXeb5aUHaqbuVq BcijZGUh1kW83eGC5aiLyUDf7L5f8OFcIlcSWLWZjFP//QoRbb3k0x166OcWJfmn0b2X XLXhg6xiuA0njSKeUYtutFDnSjQkmT+Z62BtJ62KVuA8glyCjFSPlakLgG+OYRHTeomW oBQ1LD81Ypfp6neo74Vszt4+a2mT6yReIujjRxqXgHfAUzr7ddXxFpAHvW0SsaSS6wA8 dpag== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=GkEdJ9O/6Iw5vepk2vkugGFivnPxN1wyv4xLhvAKu9k=; b=jp2Kt2IUYV9G4yJNMvusn0hvznibELufRAcGs0XU8+pW53Amfgidzc8ffpY+fSXwaS SiFPryTjwFmXfI8h/qVFIN6KoNp28/67NuWht0plgqcM/rXklpUaID7d4I9FIYn1FgJO yien6SN6efboiW1ZUiU1PKN4dci881cofs6lM8UPSZWUzNSNOUvbFXqc4GTaQ9pkuQ2E cznuEiCqf/lezAKloGuu7L12hJTxfh2io0Lx5vq6RenbVR+rCMKS5Xql6Nvh+d8aFKnT CdltM9GRGl23E4IykFnHrBx3tFSOy/d4Sfx1iljThz0g8yLqyOwmYjN8NkdCFqYJ1Oe2 7gqA== X-Gm-Message-State: AOAM530A9VjXOXPbOVYlocpwfkg1ghvtsdWYebcjZ+8S2cPDUEKEppDK X5TZJOeUSu1VIFzdwBJ7k4nBn8P7pNg= X-Google-Smtp-Source: ABdhPJwzqOLGc7VAcvBeoEnz0p3iY6slE70cm8Y5rfqBp6Bfk3dywoMWhOdTjmGoRjF1CW2gfafCKQ== X-Received: by 2002:a7b:c847:: with SMTP id c7mr81483wml.149.1600099674556; Mon, 14 Sep 2020 09:07:54 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:54 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 02/12] gnu: r-preprocesscore: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:37 +0200 Message-Id: <20200914160747.8983-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/statistics.scm (r-preprocesscore): Move from here... * gnu/packages/bioconductor.scm (r-preprocesscore): ...to here. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ gnu/packages/statistics.scm | 21 --------------------- 2 files changed, 21 insertions(+), 21 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 01c4748500..57755e1116 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8286,3 +8286,24 @@ a Python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.") (license license:gpl3+))) + +(define-public r-preprocesscore + (package + (name "r-preprocesscore") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "preprocessCore" version)) + (sha256 + (base32 + "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) + (properties + `((upstream-name . "preprocessCore"))) + (build-system r-build-system) + (home-page "https://github.com/bmbolstad/preprocessCore") + (synopsis "Collection of pre-processing functions") + (description + "This package provides a library of core pre-processing and normalization +routines.") + (license license:lgpl2.0+))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 70a85e8b60..f6de1a329c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4079,27 +4079,6 @@ framework, with additional code inspection and report generation tools.") hierarchical clustering dendrograms.") (license license:gpl2+))) -(define-public r-preprocesscore - (package - (name "r-preprocesscore") - (version "1.50.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "preprocessCore" version)) - (sha256 - (base32 - "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) - (properties - `((upstream-name . "preprocessCore"))) - (build-system r-build-system) - (home-page "https://github.com/bmbolstad/preprocessCore") - (synopsis "Collection of pre-processing functions") - (description - "This package provides a library of core pre-processing and normalization -routines.") - (license license:lgpl2.0+))) - (define-public r-fastcluster (package (name "r-fastcluster") -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:03 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:03 +0000 Received: from localhost ([127.0.0.1]:55966 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1O-0008QR-8q for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:03 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:38544) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1M-0008Pj-8I for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:00 -0400 Received: by mail-wr1-f51.google.com with SMTP id g4so260476wrs.5 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Si/ab2uYi+yX7lgCqvxxVrMZR9akjslFB91Jum1G8K0=; b=lUrfLzKT8WBvBomdNY3RPWTYHCIPXgd16JL6KFQgyXzhiG3tn0eOaL9rCxhhLQ7vAI omkodIpFPq+rsOr9rl9XvDvR0m0SO7iNJ/05zW4mDRxDktPDLh5dZbijW8w/H+mh+I4G O8fR6hOuyt2dTBs6PYGW+UxRMoC7lZG3IBMn0iaLgWvtcCldJXyf+yHLUPpcfithK6dJ t+b/xqZkQEkvJ0EToAfPlJpR2TCTVpah9FhgU7tCGhTMh8pM94Pk/ZVzhqBysVjNYr4T WqUWyltm423oc0VkapTWUCRFI4eGBKnX/+geU7fXQ8BIyQq6zRrZjyl6P5uOWSuDR1k9 MMxQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Si/ab2uYi+yX7lgCqvxxVrMZR9akjslFB91Jum1G8K0=; b=LpwMwZxbVqenihVlwBdZp0ovyS9PH3vTp1PUt9KvFoslV83Ri+Wq4IxX57eR+/USKf 7dEMcLC9U5XR3/u8t25qH9yRyweNNlWjunMi09e5n50KZFRowzD4rDSJ5ZPbMVlgKlvN usNMEfnWegog5S8wfrrSvaWHlP18d7vrRKWuKPK/+hgOicJ/PL9FfAG/sxUHNFeO1X54 OIfUO2uGN+pe7UZsY/ck+JqHPvSsuwGHtOHsnT6mZQeucqj4H7dqzsrFWSX7QXXM+SDF bpbapMlI3d0OWVmMOy8fWeVsVrq8k61702faFE9D5G5mZ2yjIKmgYZGhqeuCDDDRdsYV EL5w== X-Gm-Message-State: AOAM531jSx+bX4uf4UsvyZMBBcymrzNLozEY/i9EmDddDLc7OLx45an6 5exNCl8uEv4iRlVVDDHKNWlWT72Ild0= X-Google-Smtp-Source: ABdhPJxrUsv0dNOkmyUDj7vRcqaelPywADa7sFwnpMQZK5oD3EvmaogFeGhiIsum4Pmb2csljyqleg== X-Received: by 2002:a05:6000:1083:: with SMTP id y3mr16503811wrw.405.1600099674004; Mon, 14 Sep 2020 09:07:54 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:53 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 01/12] gnu: r-fourcseq: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:36 +0200 Message-Id: <20200914160747.8983-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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-fourcseq): Move from here... * gnu/packages/bioconductor.scm (r-fourcseq): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 44 ---------------------------------- 2 files changed, 45 insertions(+), 44 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db1fdcad17..01c4748500 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo +;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; ;;; This file is part of GNU Guix. ;;; @@ -8241,3 +8242,47 @@ with: @end itemize ") (license license:gpl2+))) + +(define-public r-fourcseq + (package + (name "r-fourcseq") + (version "1.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FourCSeq" version)) + (sha256 + (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) + (properties `((upstream-name . "FourCSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-fda" ,r-fda) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gtools" ,r-gtools) + ("r-lsd" ,r-lsd) + ("r-matrix" ,r-matrix) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") + (synopsis "Analysis of multiplexed 4C sequencing data") + (description + "This package is an R package dedicated to the analysis of (multiplexed) +4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific +interactions between DNA elements and identify differential interactions +between conditions. The statistical analysis in R starts with individual bam +files for each sample as inputs. To obtain these files, the package contains +a Python script to demultiplex libraries and trim off primer sequences. With +a standard alignment software the required bam files can be then be +generated.") + (license license:gpl3+))) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be66533b0b..1ba763ff66 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22572,50 +22572,6 @@ Try a demo of the LSD by running @code{demotour()}.") ;; Either version (license (list license:gpl2 license:gpl3)))) -(define-public r-fourcseq - (package - (name "r-fourcseq") - (version "1.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "FourCSeq" version)) - (sha256 - (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) - (properties `((upstream-name . "FourCSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") - (synopsis "Analysis of multiplexed 4C sequencing data") - (description - "This package is an R package dedicated to the analysis of (multiplexed) -4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific -interactions between DNA elements and identify differential interactions -between conditions. The statistical analysis in R starts with individual bam -files for each sample as inputs. To obtain these files, the package contains -a Python script to demultiplex libraries and trim off primer sequences. With -a standard alignment software the required bam files can be then be -generated.") - (license license:gpl3+))) - (define-public r-phylogram (package (name "r-phylogram") -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:04 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:04 +0000 Received: from localhost ([127.0.0.1]:55969 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1P-0008Qr-Ai for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:03 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:55449) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1N-0008Pm-6I for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:01 -0400 Received: by mail-wm1-f51.google.com with SMTP id d4so557184wmd.5 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=C8fm1RxcCX3R/MoquebhsUmZaVj8+soVwUL3uUmbwOg=; b=cOrTFWfgbr+viQu/r6gJ8T5ALngYGM6cpzOjTepldaxOvLna5x3wydrJw4i6/QbJk9 e+9fjaKZBapOUjY15ILxzf8THBC0u1HInHk25AG1NXJARLAPh6ZMHOWtcX2P5anL7nTG 0VY7zofkQDGxkN/O1VQpBI/J/RVbRh/9Zgq/pPhyqjW02BKQVj0mANqNME0TA/vJHZlI NzpBftCjIocRvCgCkNbcthTkzGHmibg3EWc5TAkb8yWb5WMGYHIymXoIsGdWS2LHlTMs QfmVC6Zyd39s2oI66AKdGb2HyXucVT4dsSYWt8junEdhixl84jxeEosMQBRW5CfWob4o GIUg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=C8fm1RxcCX3R/MoquebhsUmZaVj8+soVwUL3uUmbwOg=; b=A87Gvdtj3QnarBcvzhrF5RtCB+H2/OmBrG3yGenBykScBBIpnPxbCMFdE4NbpBX+aX NWV/2SgpryadA2rhmSnEpzjraK7NcQWEwyDAiyXdmkJvf1zkadNFCyK2ASheuVgQRobh RRDuNnAFWQSkZBLxg5d3wnJEXwxWMzsvbOu35PUqtiY/BDyWi+Zs7ibZl0xSy2Rfqnii AoxuU76PjldBrqHxKNZb6xRoR9A5yyN8dxXbFU8T6FiJsqK9ky9wAl4wcplEgRRjCuqW xLy4GsUy4Z1hL3aFWz4mRHHpHmG+tj7XCLpOyidiOkjxbn4D5QNXsWJSjUx1jUtiKNa+ zgeQ== X-Gm-Message-State: AOAM532RfuPfdntxeTx0PkGf46VM+Cht8RlYAapq7xl46CZSyrb5UjVR +Cq3sL2k2LxAuLrcna3AFHzEfQYYGlU= X-Google-Smtp-Source: ABdhPJypPV/O+QkzWTZ7RioGRoWt1k4r1k8lpcjcf/Ib4aBf4UE/SU+UmcKqhf53h23x/gB0Vkc8ZA== X-Received: by 2002:a1c:31c6:: with SMTP id x189mr97539wmx.83.1600099675416; Mon, 14 Sep 2020 09:07:55 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:54 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 03/12] gnu: r-rgraphviz: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:38 +0200 Message-Id: <20200914160747.8983-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/graph.scm (r-rgraphviz): Move from here... * gnu/packages/bioconductor.scm (r-rgraphviz): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/graph.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 57755e1116..dea0862b64 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8307,3 +8307,31 @@ generated.") "This package provides a library of core pre-processing and normalization routines.") (license license:lgpl2.0+))) + +(define-public r-rgraphviz + (package + (name "r-rgraphviz") + (version "2.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rgraphviz" version)) + (sha256 + (base32 + "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) + (properties `((upstream-name . "Rgraphviz"))) + (build-system r-build-system) + ;; FIXME: Rgraphviz bundles the sources of an older variant of + ;; graphviz. It does not build with the latest version of graphviz, so + ;; we do not add graphviz to the inputs. + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-graph" ,r-graph))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://bioconductor.org/packages/Rgraphviz") + (synopsis "Plotting capabilities for R graph objects") + (description + "This package interfaces R with the graphviz library for plotting R graph +objects from the @code{graph} package.") + (license license:epl1.0))) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index a307fee808..db390fed5e 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -121,34 +121,6 @@ more.") (home-page "https://pypi.org/project/python-igraph/") (synopsis "Python bindings for the igraph network analysis library"))) -(define-public r-rgraphviz - (package - (name "r-rgraphviz") - (version "2.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rgraphviz" version)) - (sha256 - (base32 - "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) - (properties `((upstream-name . "Rgraphviz"))) - (build-system r-build-system) - ;; FIXME: Rgraphviz bundles the sources of an older variant of - ;; graphviz. It does not build with the latest version of graphviz, so - ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-graph" ,r-graph))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (home-page "https://bioconductor.org/packages/Rgraphviz") - (synopsis "Plotting capabilities for R graph objects") - (description - "This package interfaces R with the graphviz library for plotting R graph -objects from the @code{graph} package.") - (license license:epl1.0))) - (define-public r-rbiofabric (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") (revision "1")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:10 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:10 +0000 Received: from localhost ([127.0.0.1]:55978 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1W-0008Rj-0K for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:10 -0400 Received: from mail-wr1-f52.google.com ([209.85.221.52]:45158) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1O-0008Po-21 for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:02 -0400 Received: by mail-wr1-f52.google.com with SMTP id x14so201288wrl.12 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=NNeDv+bV3g6qLALFROO8O5RDlHRQWuGTwUQ9lkdK1YU=; b=N891d2iM2LgqQ2xppjdadBFGvJOGTc7IbTU8Kg3vF9YZVg03ERy3WNcrtz8BxliKeU xPV/sFjNWHdukBlEQDYCS+5IpmPZb/h7cKu3hFS1AZrf9xujcweau2fua7HrBr2FNBqS jDg6ZkWLIB72q8aNihAyc8E34oN3sjRd9uT9NsVgmlpQCCwNpOrtoONdDiKCDZF2EV7a W5lM+AyaEC2cESSddHd0ulQSfBTda8iCP4zAls3KqjGKoMpIyAGpdIbybUmCTkAP5BD3 3SRDo6MUArMVuIdllw3f/kDiGwp2XoH+JVlX2Fu+Swxln2+bm/MgzBe/qwuSZSuDiPZO poKg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=NNeDv+bV3g6qLALFROO8O5RDlHRQWuGTwUQ9lkdK1YU=; b=qDVdiIhkJyqC+G0HP+2YX6u8G5vpztENDHg3YDlBxl0qaFNXRzc22GLKAYIOL0DgiP fQhE1Gq6sb3dos7MYaExcHwWCeyVUwYeoUB8iXrKvmJZKRlQURzCXfIH2MFWgpwyCx+W JFTORBsOSIjcH/eMgfga2gv/XmKTm8ggsMgtCQmt0YePTYQ+VfofAkt0TMx5iXdmRs+t xbY17Yowl7vY3xxC9pnJ5KQeBe3Z1T+anqmQU5BEjgCIvXATsEPSxvCdA7jEN7pnfoRp 1GzrK3BluQso3ogEomp1R69M9YOBIFiNkdVnZwO93MtXOso+b4FrrrxrHp2lGpEkAE6w SQ9A== X-Gm-Message-State: AOAM531Pd+IS7vz/he5jwSnKLy/erex3yXWS9OnBxhA3nvMEIGaSZHTC qmRXiXCguhy0x/+5vckflaI0bhZNNbA= X-Google-Smtp-Source: ABdhPJzN9FTpffl3/jdQfWjpCkt9b5gXqXGyKwwtXj2yb1uxrcq87gHyQbkhYYJashxb23tLQ8NBGQ== X-Received: by 2002:a5d:4e0b:: with SMTP id p11mr16181657wrt.32.1600099676232; Mon, 14 Sep 2020 09:07:56 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.55 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:55 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 04/12] gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:39 +0200 Message-Id: <20200914160747.8983-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-delayedmatrixstats): Move from here... * gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 --------------------------------- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dea0862b64..e81e9cd726 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8335,3 +8335,39 @@ routines.") "This package interfaces R with the graphviz library for plotting R graph objects from the @code{graph} package.") (license license:epl1.0))) + +(define-public r-delayedmatrixstats + (package + (name "r-delayedmatrixstats") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedMatrixStats" version)) + (sha256 + (base32 + "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) + (properties + `((upstream-name . "DelayedMatrixStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-hdf5array" ,r-hdf5array) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") + (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") + (description + "This package provides a port of the @code{matrixStats} API for use with +@code{DelayedMatrix} objects from the @code{DelayedArray} package. It +contains high-performing functions operating on rows and columns of +@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, +@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions +are optimized per data type and for subsetted calculations such that both +memory usage and processing time is minimized.") + (license license:expat))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ffa2618458..ccdc693e08 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10900,42 +10900,6 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) -(define-public r-delayedmatrixstats - (package - (name "r-delayedmatrixstats") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedMatrixStats" version)) - (sha256 - (base32 - "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) - (properties - `((upstream-name . "DelayedMatrixStats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") - (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") - (description - "This package provides a port of the @code{matrixStats} API for use with -@code{DelayedMatrix} objects from the @code{DelayedArray} package. It -contains high-performing functions operating on rows and columns of -@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, -@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions -are optimized per data type and for subsetted calculations such that both -memory usage and processing time is minimized.") - (license license:expat))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:10 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:10 +0000 Received: from localhost ([127.0.0.1]:55980 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1W-0008Rq-Cm for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:10 -0400 Received: from mail-wm1-f41.google.com ([209.85.128.41]:32811) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1O-0008Pq-Pj for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:03 -0400 Received: by mail-wm1-f41.google.com with SMTP id e11so9189390wme.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=3AE8XJVj92n6rfCjbWovIOQdzoIyucUx0ssj7sr2pRU=; b=dwNJkg8zQeyqX92Pvure4XP8rAZApneaC7jUR5T5Z6BGVXhSClV9hPWDujoOiicQyc FJ8n7MUmxxh9eTjEMjz5o2qQfd+NlL8II23BL+3Ioc7fGnyw8/xar6h6UCPKz+iqb6DO sRYX02q5Ui3qZt4N4M6U35jrTYqa18F9upKO/5hxVMKNxNnLXVbW0MapRv9QAvKbns3I /4yQVDp3f6j2RVkQHjJ81hDOPf5ROkSP+hxHe+yFyf4i4wuTvOY7oB+h6ryBh0beYpxe DgQOCb9ZGOR0/pyRMThhIC4Jd3lwG9lLI9RFo94fA2/wPBrGNP8z1AfWu7Gy3pka4BxS 9gZQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=3AE8XJVj92n6rfCjbWovIOQdzoIyucUx0ssj7sr2pRU=; b=gndkK6Fd02Mt06dNmZa2N+GOqHwE1/DZAKX+Fd8eWWh8OloBVrrwHhtUnytdIp8ig+ KkkKPRHpJiIws4xzxClPiLwmecuS8SlCyl5x6UC67IqPDCDlLV/zckAQyrnFfNq/mMkT 97pPKo9/4QFBD4AdEuyeKG/5vpMy+72n+4buUbJitYarmAm8czerfB7W1g8SATcobhs3 1p5givOhVCjbJDpRbu2ZsOrL67LS8PgDeDYXCTKWkXU8HY85N0hroiHOsypyaoQI1Tqr cYuG00ISlAt7cZ5K/t86xI8wJitDOBxQAc5jQDuUosFYtgy2oE6BN85vxtEHQzA3EzSo ol/Q== X-Gm-Message-State: AOAM533GfirQB+iCoKYAG44Uk81GjVcS0+UY+Kxsma2hRGRvGiEAuzVj eK1Vk7Va81arJNDjIJsTwUIuGeZxjF4= X-Google-Smtp-Source: ABdhPJw+IJNgHuFHWJPjYYp5WPZgF5FUuexmjHeCtHLytwHlrKvOmGZGYmGYreCl1HTqOq18r7i7jQ== X-Received: by 2002:a1c:c2c6:: with SMTP id s189mr122234wmf.146.1600099676952; Mon, 14 Sep 2020 09:07:56 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:56 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 05/12] gnu: r-scran: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:40 +0200 Message-Id: <20200914160747.8983-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e81e9cd726..77de0e2275 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8336,6 +8336,49 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-scran + (package + (name "r-scran") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scran" version)) + (sha256 + (base32 + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-bh" ,r-bh) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dqrng" ,r-dqrng) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-statmod" ,r-statmod) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/scran") + (synopsis "Methods for single-cell RNA-Seq data analysis") + (description "This package implements a variety of low-level analyses of +single-cell RNA-seq data. Methods are provided for normalization of +cell-specific biases, assignment of cell cycle phase, and detection of highly +variable and significantly correlated genes.") + (license license:gpl3))) + (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccdc693e08..dcafbb2d21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10857,49 +10857,6 @@ various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.") (license license:gpl2+))) -(define-public r-scran - (package - (name "r-scran") - (version "1.16.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "scran" version)) - (sha256 - (base32 - "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/scran") - (synopsis "Methods for single-cell RNA-Seq data analysis") - (description "This package implements a variety of low-level analyses of -single-cell RNA-seq data. Methods are provided for normalization of -cell-specific biases, assignment of cell cycle phase, and detection of highly -variable and significantly correlated genes.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:11 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:11 +0000 Received: from localhost ([127.0.0.1]:55982 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1W-0008Rx-PJ for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:11 -0400 Received: from mail-wm1-f49.google.com ([209.85.128.49]:50486) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1Q-0008Ps-2O for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:04 -0400 Received: by mail-wm1-f49.google.com with SMTP id e17so590922wme.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=vw0BxB24GTNnXlmSVSp1zzGQZ2VIFQPPulQb+0BwQpI=; b=cdDRhjFUL6FX5UoiPMCOCX6S9ObMv5pw++fIe63KmW4toRM9wB2XgsSe1wrxKvamwz pPLplPCVVFgUgitp6lNT3vCVGY12Tj56zqpfJSg7gsv809V2jTWzlROLdTJQlXeBLUdx d44ZNIM5AhUT4y9iVSWFojq3c/e67/ZfcfyDPcqdvyjcohvnFaRPuVSPCYyEQNNS0Vjx yLK+m6iFdrrGZkDcgNZwYbQKQ5viAN7PWW6+2+jJJBiF8+yvqN92heh1C40RNQfM6NNf QQBo9pmBdNnoGSQ4sEizeMLeo+Z5xqdpY4ca5FWZb04KxGkSV2WDJaQfef9jZS+aKeOC rT2Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=vw0BxB24GTNnXlmSVSp1zzGQZ2VIFQPPulQb+0BwQpI=; b=V+wFL5F3VbfeqKcOFSZjSLNaVJuAjrLrb1HbISGXk9D4PjBMA4W5zzKHq9gtOVegC3 NtHVVOzCINinOGdsR51ePY1SkQ14kTSMA8URVDgQOkB+r8MXkq2KTG14dsWJlK6HJbVJ BTc7p4Bf06SpeNmUsY8+XXrwgNw+vYpefYf6pUmEhcAkgDcj1xVwp/uxNH51x+oRfQ6T +DxGqJu7VN3EuEU3ck1NsxpziFPXc1DGOszQf5hTCljb6VasDrR9f19sK4Ht0kEbOmSy nDQTWJ7297o6iH20+M1YyK+a4TYrNriscnWsAKxirxEGfha7dplJP6OCh5/slSvY9BSK 6IKQ== X-Gm-Message-State: AOAM530qk9g0rB0vv+mQkHBC9/ucG0numOxI4+AY24IF2SDvUj4lWiPE tPjLyXlN+KA7gl8jYbod3bmg2I8usX0= X-Google-Smtp-Source: ABdhPJxitjYaBifEXekpJlDEYer8LIrNxTXk1zC1qp4xL/B/n2sr8mQnxfT0cdPPs8O8a86WVT3nyA== X-Received: by 2002:a1c:39c4:: with SMTP id g187mr121291wma.126.1600099678214; Mon, 14 Sep 2020 09:07:58 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:57 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 06/12] gnu: r-scater: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:41 +0200 Message-Id: <20200914160747.8983-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-scater): Move from here... * gnu/packages/bioconductor.scm (r-scater): ...to here. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 37 --------------------------------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77de0e2275..52685a4df1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8336,6 +8336,43 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-scater + (package + (name "r-scater") + (version "1.16.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scater" version)) + (sha256 + (base32 + "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/davismcc/scater") + (synopsis "Single-cell analysis toolkit for gene expression data in R") + (description "This package provides a collection of tools for doing +various analyses of single-cell RNA-seq gene expression data, with a focus on +quality control.") + (license license:gpl2+))) + (define-public r-scran (package (name "r-scran") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dcafbb2d21..8dea6df8a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10820,43 +10820,6 @@ factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) -(define-public r-scater - (package - (name "r-scater") - (version "1.16.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "scater" version)) - (sha256 - (base32 - "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/davismcc/scater") - (synopsis "Single-cell analysis toolkit for gene expression data in R") - (description "This package provides a collection of tools for doing -various analyses of single-cell RNA-seq gene expression data, with a focus on -quality control.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:11 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:11 +0000 Received: from localhost ([127.0.0.1]:55984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1X-0008S5-5t for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:11 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:50482) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1Q-0008Pu-R1 for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:05 -0400 Received: by mail-wm1-f42.google.com with SMTP id e17so590971wme.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=uvM4H5/W/ophYQMaL/xksv8cYQyQ8aJM7OhpC/nOOtc=; b=qK3PpXCTqVnGk77lryoJ22M4j2CsxIdTer+gs1k2fyHXTcd77Z0vFi1ENK5byih+Mj YhaFeqlWWyeGB4YEihk+hCN31bBWKYbkVVrvtST8wsDpke2lqdHT4gB955DwAzDbBhuq oqBjNE9MVYI25raN6rU8QkVH8SDJvvGq/ZKYqa6dMvBVs2GvpcpUJwRQjFjlPdA6r1vd NSzaypY39+Sr/Smv4+v2oR0Y0hRDskkB7Z0EIeHkLFmbXp48FkrzUwVZZ6YPOFvdc1cF gbquuZw4i77LITrmo62CF7Km0a6oVnbF1BuyuJyRbyZca0myjIDa7YlzuxvbJLgZP7Iw NB+w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=uvM4H5/W/ophYQMaL/xksv8cYQyQ8aJM7OhpC/nOOtc=; b=Iuqu5PeiPCTD9r9NqNrJrgIwGeGkKwLWgK1gzfcEAI8OzsERpgZPtN0zeYQlISH/cJ zCKKwhtOki30Wm2BEsavjZkLyhoA16QsfS8JWDZGjMLoPu6OXNInrWXBBn/IVJhKYV7E 01+1gP9N7dFjuAxdDefeP1eBM4JSFjKqpcQRFjyc/pSJEoT0Kyoxeo7ErztpvlGlzrd9 lLY6xyL9CLula5T6y358NmCD4wKWn8ZHnGUgcQkNHsOzbottMSdcBvInGWnJiefmRSUE 2ueatfqBFXjxKCL9bXd4cIRzPnFZiB7ECyDYiwBkbXpG0MDNbNjxmgKRTX4W9Ze6Ssrs jIEQ== X-Gm-Message-State: AOAM533r8pG0ELMEPwvSGVDsakzpjjhyfHewbTXlGjZyRJBqKsuyFnkW 7zO4j7ZvuhQOosnwU/6Eo8y2KCBGaK8= X-Google-Smtp-Source: ABdhPJxrAPaAf4FqXitwSiW5b3Gz9odzckgbkwq7h/0BUeQ/GRKqIDvrx3TWmy9Hsw+rMzSPP50SVw== X-Received: by 2002:a1c:62d4:: with SMTP id w203mr114048wmb.146.1600099679015; Mon, 14 Sep 2020 09:07:59 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.58 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:58 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 07/12] gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:42 +0200 Message-Id: <20200914160747.8983-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-singlecellexperiment): Move from here... * gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52685a4df1..d9f7a9fb67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8336,6 +8336,35 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-singlecellexperiment + (package + (name "r-singlecellexperiment") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SingleCellExperiment" version)) + (sha256 + (base32 + "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) + (properties + `((upstream-name . "SingleCellExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/SingleCellExperiment") + (synopsis "S4 classes for single cell data") + (description "This package defines an S4 class for storing data from +single-cell experiments. This includes specialized methods to store and +retrieve spike-in information, dimensionality reduction coordinates and size +factors for each cell, along with the usual metadata for genes and +libraries.") + (license license:gpl3))) + (define-public r-scater (package (name "r-scater") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dea6df8a1..ef6d6fc2d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10791,35 +10791,6 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) -(define-public r-singlecellexperiment - (package - (name "r-singlecellexperiment") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "SingleCellExperiment" version)) - (sha256 - (base32 - "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) - (properties - `((upstream-name . "SingleCellExperiment"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/SingleCellExperiment") - (synopsis "S4 classes for single cell data") - (description "This package defines an S4 class for storing data from -single-cell experiments. This includes specialized methods to store and -retrieve spike-in information, dimensionality reduction coordinates and size -factors for each cell, along with the usual metadata for genes and -libraries.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:12 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:12 +0000 Received: from localhost ([127.0.0.1]:55986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1X-0008SC-JR for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:11 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:52675) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1R-0008Px-DB for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:05 -0400 Received: by mail-wm1-f42.google.com with SMTP id q9so577974wmj.2 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=4qwhLrE7+oySAiwAMhiEwKlRjbB6BtbNSN2GlmLDJuA=; b=QEytrCz6zXIL4bPfxiTVbnNQ8kKYUoBWf3R3byzEJ+pR56AKF/cw6AW4ToSLoZuKH+ Go1Qb8W5/zRWcr5XQQ55Fp5FbS0Pb4OFoUgRbDVz+fiVeIo1vuIUPgdd/WcqDjbTOJbt X655bBykQIYJiepqOfpo0PmfkUiINEIflbUMorDT0VZLD58BnWY+JmJz93WanWaxi4EO edecajXMriUMMWvWf5i8OhzTITKgH+RUBlALsZkSAeAPKtEEZct6GirSYfTUv59UXgR9 AoSzr9wnYXXM9ZnFZYlEINdr5h1fdcnz/m87CPPeEnqdkJNbMV6jRmQz94wuS3+zj7G4 QTHA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=4qwhLrE7+oySAiwAMhiEwKlRjbB6BtbNSN2GlmLDJuA=; b=NcwhPrkmTDDjvg2SVrK1k+/7ZW0Qt2kukOmRjvh0wWSj9v2mVHp62ZGHneN6vDeQ9l AWGVNoo4DDAxFtfmBF9KY5mer8PIsNWSiTsXFG7VFoPa+5WM/Qw6W9qN1nAK74/QLpMd Tf3QSJQa+iEihq5L/c8au5X84W7fSsM0gGjnN+/fgeEmNJzNSVGJeySBqqQYDO9oKC7v gBuCGrPSFxL3v+tALSsBlMFgzHYF0DhmXmkCwyH4jARX8LsLA7QLndDWg92/Rsm/AA1h b43RIMA0zrO2Q18cYxYramkoUENfzgpzxMKiS4ji4jYZsMxbg/zCUGasHpkP2DY3fJ3/ Tonw== X-Gm-Message-State: AOAM533uR4Fzi+gVqQEEUbMIlLj3ReK5VfnShyU7cTtbCjnoo77G9ifx N1IZCCtueYmwlzNCp1lsFvn8423Zbjs= X-Google-Smtp-Source: ABdhPJylWfc/oCJAcsj4KWXr+DkA/3R1fs2jZe+7RrbYPZhfAVCxAyy9B4b6s5pJ6ImFTWv27sKjfA== X-Received: by 2002:a1c:4b0e:: with SMTP id y14mr114603wma.156.1600099679748; Mon, 14 Sep 2020 09:07:59 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.07.59 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:07:59 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 08/12] gnu: r-beachmat: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:43 +0200 Message-Id: <20200914160747.8983-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-beachmat): Move from here... * gnu/packages/bioconductor.scm (r-beachmat): ...to here. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 25 ------------------------- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9f7a9fb67..0ecb460bc4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8336,6 +8336,31 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-beachmat + (package + (name "r-beachmat") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beachmat" version)) + (sha256 + (base32 + "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/beachmat") + (synopsis "Compiling Bioconductor to handle each matrix type") + (description "This package provides a consistent C++ class interface for a +variety of commonly used matrix types, including sparse and HDF5-backed +matrices.") + (license license:gpl3))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef6d6fc2d8..a84d19727c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10766,31 +10766,6 @@ block processing.") packages.") (license license:artistic2.0))) -(define-public r-beachmat - (package - (name "r-beachmat") - (version "2.4.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "beachmat" version)) - (sha256 - (base32 - "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/beachmat") - (synopsis "Compiling Bioconductor to handle each matrix type") - (description "This package provides a consistent C++ class interface for a -variety of commonly used matrix types, including sparse and HDF5-backed -matrices.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:12 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:13 +0000 Received: from localhost ([127.0.0.1]:55988 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1X-0008SJ-Uv for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:12 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:52687) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1T-0008QM-6P for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:07 -0400 Received: by mail-wm1-f51.google.com with SMTP id q9so578065wmj.2 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:07 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=yiBgfilDskVqsbwUlYpzifkisiJw9rRlDq9lRcXYm7k=; b=llIf/kSWPTT6XdW1SE2aMflQTSwd0b9y5dBpG1qW+h3GU4USnX8vRAx0gq6xN8zzSw rHq3fnwefxVFMdL4JoVxWuIG9yNt6FD7YiMRTRV4IUQevt8DoRsbGg6aM2Cv1yG/vbeX AIlNejputddUW+hnnHjzCuq89886StGRrkTY+c9lb3JiIBYSbYASw1b45+LKbLijSLYQ EcqBP4hkkfFrpANf54txJDcsxxT5PhmspkHaSwvkzGwi6/vB1QpPf7AEC5PlBxhls8bt iXGmkDCh/7eEINaF/x1aVCRcNfkXN/mjsc8f/t3GG9wG2Y5zyC1N5KAPVX9Z1n7JYpbm evhQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=yiBgfilDskVqsbwUlYpzifkisiJw9rRlDq9lRcXYm7k=; b=oHLIpI/CPFajJWGyBU4k0fUUs9W11vzX432PohGBfVCZI4M3aJsjHK0RLAZPmTSD8t kZJOZ18BdwG6Q+Fe7xc1faWhR4Rz5s9J04uvifu5QAQaPKqbrmhK5G+ljx97TG8xydqZ KLYmt8r84mmSQO0PrIKbTdsCjvYDd/3mum5xA1kLKX84kz/AaBgtO/zTMaD9zbZSuf8x def50Zn/FSfH4Sv6OI03U4FtT3oOpZAB+n5pyN1ah/P79PKe3v7o9BwsZ7sjEzQGdNtK liu6DTUcS9ZQBfhE2PfEYOQ1wmXUp3xH09YS/9VHg1zsJVTYkdypPu2tlNd28rQMITvZ H+Xg== X-Gm-Message-State: AOAM532TF+4Ae0A/jfza/pAxLnWDuCexGd43e8KUQXPcrfgaLknHFXsA 9Tu7b1VpC/bfL8Lf7GnvNzTlJiCPO/A= X-Google-Smtp-Source: ABdhPJwbZvc28kuwYqx9H8HZ09rRhFjaINxFh6TRueqAUZ4QjYcU/9XRoc9iRMUXgm/V8FeScm6/3g== X-Received: by 2002:a05:600c:4104:: with SMTP id j4mr147137wmi.36.1600099681229; Mon, 14 Sep 2020 09:08:01 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:00 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 11/12] gnu: r-hitc: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:45 +0200 Message-Id: <20200914160747.8983-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6a09c4ce4..5878c43a3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8337,6 +8337,35 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-hitc + (package + (name "r-hitc") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HiTC" version)) + (sha256 + (base32 + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) + (properties `((upstream-name . "HiTC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "https://bioconductor.org/packages/HiTC") + (synopsis "High throughput chromosome conformation capture analysis") + (description + "The HiTC package was developed to explore high-throughput \"C\" data +such as 5C or Hi-C. Dedicated R classes as well as standard methods for +quality controls, normalization, visualization, and further analysis are also +provided.") + (license license:artistic2.0))) + (define-public r-hdf5array (package (name "r-hdf5array") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d874fe9a13..6bbcc3fe00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10625,35 +10625,6 @@ intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.") (license license:gpl2+))) -(define-public r-hitc - (package - (name "r-hitc") - (version "1.32.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HiTC" version)) - (sha256 - (base32 - "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) - (properties `((upstream-name . "HiTC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) - (home-page "https://bioconductor.org/packages/HiTC") - (synopsis "High throughput chromosome conformation capture analysis") - (description - "The HiTC package was developed to explore high-throughput \"C\" data -such as 5C or Hi-C. Dedicated R classes as well as standard methods for -quality controls, normalization, visualization, and further analysis are also -provided.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:13 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:13 +0000 Received: from localhost ([127.0.0.1]:55990 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1Y-0008SU-Ur for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:13 -0400 Received: from mail-wm1-f66.google.com ([209.85.128.66]:53361) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1T-0008QX-Mu for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:08 -0400 Received: by mail-wm1-f66.google.com with SMTP id x23so575020wmi.3 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:07 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=b2OYHRwW703vxSoHixOMwkUvsf6nu3+9eIZ5a4JWVLQ=; b=TX2jFvH7oOwsmAstyJ7DJnI2VjhvP5Gitan4/Ak0p2fYOodgjGZu8kv4IykO7z0JIJ /i1GSCUjFu+RQfPP/TtnTRzvzsjTqYv9DbBmKxVqlAY0x/9N/ivaNLeXejwMjtIAwhtn /nASSab0YT4NNWUQLv/ucidzFUPRaQKppO7u/8sZb5GzTlcDYI6puIgXJU+2n5ChUpF+ XCgZVnt5gsQKDSxVar+7Fk4CQg/ngsuv+d9Y8ZTaZKpRbLp9uMzFuNGbFBMaohpI8F8H kIq+KHGklJwFSKKcgPApaTqhkNJvmUhb3kmwJQV2/XXUJxgc6y+XZ7/uTdlP8YvT80oE iiyw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=b2OYHRwW703vxSoHixOMwkUvsf6nu3+9eIZ5a4JWVLQ=; b=W02XhQshtbMNr1dTC4LzXGdXSBjK+lx4o83wR+UIfnkig05GFg8Z7Al3dgEPEOiaD/ yxsN81kD1OW983afyjuEmvM0AXRK/TjdrrDJHefKudIm2wSyj0FKJbemVzZrdqvb2K1y G/ncthhhC4Dmq0H9651ZG5XbrcXPpLAdiAyvinHKUPyX3HejmEY1HNVvGvScyxyZOYbd 8R8HIZQRz54Cnp/sOn9SBMhw07JkTkwyH0nxw+7ZcYkPozlB1BGgminyOYjZ2+kn1fWm 4x6Q+E3VpwryNeEbCCp/iH+3WOmRfUN5d4y5Psir4sONsZrz3qtr/CYba2VzGk96vnG7 2pHA== X-Gm-Message-State: AOAM5331xU8kVVkzkiVvVMG4xjhcyDPCuF/paB0N6OXJc4S8qnrzk+uG lVMNHeYhDS9OAjKV3zu0scLkoa2jnUo= X-Google-Smtp-Source: ABdhPJzrpwjCFlMQFen0UwEGsJMAm7jGnIZsZGffOBkKHCjXpxCQs/n2Eqg9+XpwCWi5keHguEQcng== X-Received: by 2002:a05:600c:230c:: with SMTP id 12mr103005wmo.23.1600099681860; Mon, 14 Sep 2020 09:08:01 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:01 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 12/12] gnu: r-fithic: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:46 +0200 Message-Id: <20200914160747.8983-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-fithic): Move from here... * gnu/packages/bioconductor.scm (r-fithic): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5878c43a3d..9473f3a286 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8337,6 +8337,32 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fithic + (package + (name "r-fithic") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "FitHiC" version)) + (sha256 + (base32 + "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) + (properties `((upstream-name . "FitHiC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-fdrtool" ,r-fdrtool) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/FitHiC") + (synopsis "Confidence estimation for intra-chromosomal contact maps") + (description + "Fit-Hi-C is a tool for assigning statistical confidence estimates to +intra-chromosomal contact maps produced by genome-wide genome architecture +assays such as Hi-C.") + (license license:gpl2+))) + (define-public r-hitc (package (name "r-hitc") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6bbcc3fe00..71369affaf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10599,32 +10599,6 @@ EMBL-EBI GWAS catalog.") visualizations for publication-quality multi-panel figures.") (license license:gpl2+))) -(define-public r-fithic - (package - (name "r-fithic") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "FitHiC" version)) - (sha256 - (base32 - "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) - (properties `((upstream-name . "FitHiC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/FitHiC") - (synopsis "Confidence estimation for intra-chromosomal contact maps") - (description - "Fit-Hi-C is a tool for assigning statistical confidence estimates to -intra-chromosomal contact maps produced by genome-wide genome architecture -assays such as Hi-C.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:13 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:13 +0000 Received: from localhost ([127.0.0.1]:55992 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1Z-0008Sb-BJ for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:13 -0400 Received: from mail-wm1-f65.google.com ([209.85.128.65]:50234) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1U-0008Qp-Eq for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:08 -0400 Received: by mail-wm1-f65.google.com with SMTP id e17so591169wme.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:08 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=RUmD3Qbk2Qu7nZdCvedNLapmlrQ62L+fb463AHm6F1c=; b=QYiQK7moPEoEe0dSOkGzUByeQ5mdwV7RBFXb768DWjkj6vn0jZSFLtorxpFlya6oRJ 7ZoRHL9+UjVAbhum1uVK2CIAZxcHJIdU/5GBYMnGh/a5MJGbozp9W94MYTvQsn5L8HKl zj5GtEyo+v9xOjYe18lfYT6ltz60UzQ1e1bFscA4ffcX2L/Gla6XxsYIbMUmov+clI3w flCTkrHydGuXrLBryRPOE6BMhFkhXmaO+xim0plrAZ9Z9eVDuCTYFtNp7g2u3aMb38x0 v0TnKJzfEUL9TQ4Tu317CCD92E/YzdQIBUpbV9TPTuJo+DCqiTwIta8v+ql/PKxf0Ebc YDlw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=RUmD3Qbk2Qu7nZdCvedNLapmlrQ62L+fb463AHm6F1c=; b=OTlw+a40DMjdQdYn5LZKVPgfMhfkDl30533O+DGuGpZEfamav4AvJmg68FLr0o9q6d 0i8zGvvDTfwuRJcSRxW63MRywuMj6aZDPcUGM0NS8Ta2xp4ZDQDY+o7Y9D3LUlbVs++b kxCLd859LptY6o4fGU8LXaRtk+rd53ODScOIIYCdHXoJaxI3dMJnlGo5wtwojGO9MqhH t5IWL72id3CyAagd2GLK/6D0T1sn8HO207dp0FFYyHB17QFI9MoZwU6Lj7pwpWaLlXg9 zRPM0ChEfRL+9Pdl/ihSEj9qATZQ6mPXbLwg/pkfo+C8QQ+ryR8w9ae/xjgwuJz+cVfb P1wg== X-Gm-Message-State: AOAM533x5OZIxfRYEKu9su1f2PdB3IZ3uCHZa8xqsvV6ySDynsmOtvt2 XKTrqjAUkyn/cykKCfGGV673n4As8fU= X-Google-Smtp-Source: ABdhPJwKh1krrrGDSE3xR3WL+MFsZ28dpzQ4JJ1zmK8aL6O41fPTkeOvUIydCE8H0VSXZCjKImkzCg== X-Received: by 2002:a7b:cd89:: with SMTP id y9mr134390wmj.72.1600099682653; Mon, 14 Sep 2020 09:08:02 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:02 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 10/12] gnu: r-hdf5array: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:47 +0200 Message-Id: <20200914160747.8983-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-hdf5array): Move from here... * gnu/packages/bioconductor.scm (r-hdf5array): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e63c486ee..b6a09c4ce4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8337,6 +8337,36 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-hdf5array + (package + (name "r-hdf5array") + (version "1.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HDF5Array" version)) + (sha256 + (base32 + "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) + (properties `((upstream-name . "HDF5Array"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/HDF5Array") + (synopsis "HDF5 back end for DelayedArray objects") + (description "This package provides an array-like container for convenient +access and manipulation of HDF5 datasets. It supports delayed operations and +block processing.") + (license license:artistic2.0))) + (define-public r-rhdf5lib (package (name "r-rhdf5lib") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8bd42c9429..d874fe9a13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10654,36 +10654,6 @@ quality controls, normalization, visualization, and further analysis are also provided.") (license license:artistic2.0))) -(define-public r-hdf5array - (package - (name "r-hdf5array") - (version "1.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "HDF5Array" version)) - (sha256 - (base32 - "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) - (properties `((upstream-name . "HDF5Array"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/HDF5Array") - (synopsis "HDF5 back end for DelayedArray objects") - (description "This package provides an array-like container for convenient -access and manipulation of HDF5 datasets. It supports delayed operations and -block processing.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 12:08:24 2020 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:24 +0000 Received: from localhost ([127.0.0.1]:55994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1j-0008T1-Or for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:24 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:35455) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1S-0008QB-Ir for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:10 -0400 Received: by mail-wm1-f44.google.com with SMTP id y15so635862wmi.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:06 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=Yaf+qkABzTAsimJvzt6Vmu8oDVZ3zYmNV6OyFMBKM1U=; b=F5QWRcePWNMmKPk/bUNey/Ma5dnX8se7Sy2DUw9jAyJ5nSWpTJn55YcfFo2UgmKRfa 16riQfFUEiGMXzw5Jy9KsjN4noVTkGYcdBMlun4XiSun9JF9dzB9ASX5WVpbcj+3NSNM mVaHA170LH6/jQS61s0fzyuBtdjBrkbiP6b/TtW01PO26hQetnF8f3d14x7YR7xhdrL1 P96If4j8GcfhQYzP3jh49BG6Dos3xNeZx0esUB833B/NfCRwviGXI0iMWAiCl5BwWBaw zpyCkvX+dA6cVmExyRzXDNDVj8h3Uj8hxq1GaPCyGAcII2AnhKXPd8PrsnD4KY4g5jhQ 3EFQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=Yaf+qkABzTAsimJvzt6Vmu8oDVZ3zYmNV6OyFMBKM1U=; b=hqDOoZwsO5IJvUzndYbCfa/fATS8iQh+LJKvITJx4SV0g90vPoUT5ZHFoH70JI97j4 TgQjLYD9BRD8NEff85X+9nElKbenJxdgShe+tqP1ZxFr2vxJXRnbdhYDCU2KkPXJSXwn nawq81nfsC5ZeE14dmNVJhdgFZs27Zy6zczyFlDg8nlgh8KwMy+TOUsxakJDOg0vURPv RA6Y501noWKh8+QV8qEgpRPhRl5qGvmwuaI0W8kY+eXD6WIpZ4aXtv4Uih+8fe51lFn0 I0bLGR1+tOFqlryMjUToa71Xu2RatCrG9yFMR49gwmk7+O8gfU4bUwgePRp6qeYxTt9z 28Tg== X-Gm-Message-State: AOAM531N7c1+VhGJLIjiVF4MdRI2qo1+UObvP3OohzvhZmQ56+kjVh7+ htok3GR86Ga8eAcV34GEiDVg2XbBMiE= X-Google-Smtp-Source: ABdhPJzvSXuK5nUyVTz6+vlpyvfrBdnv7AmiRODMoMdtuCcbe6ORmi4v2VpEBWYptXKlsvreYbZ03A== X-Received: by 2002:a1c:b388:: with SMTP id c130mr73979wmf.175.1600099680664; Mon, 14 Sep 2020 09:08:00 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:00 -0700 (PDT) From: zimoun To: 43400@debbugs.gnu.org Subject: [PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor). Date: Mon, 14 Sep 2020 18:07:44 +0200 Message-Id: <20200914160747.8983-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43400 Cc: zimoun 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/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. --- gnu/packages/bioconductor.scm | 83 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 82 -------------------------------- 2 files changed, 83 insertions(+), 82 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ecb460bc4..0e63c486ee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -8336,6 +8337,88 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-rhdf5lib + (package + (name "r-rhdf5lib") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhdf5lib" version)) + (sha256 + (base32 + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled binaries + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") + #t)))) + (properties `((upstream-name . "Rhdf5lib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (for-each delete-file '("configure" "configure.ac")) + ;; Do not make other packages link with the proprietary libsz. + (substitute* "R/zzz.R" + ((" \"%s/libsz.a\"") "")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) + "hdf5") + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) + ;; szip is non-free software + (("cp \"\\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("hdf5" ,hdf5-1.10))) + (native-inputs + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Rhdf5lib") + (synopsis "HDF5 library as an R package") + (description "This package provides C and C++ HDF5 libraries for use in R +packages.") + (license license:artistic2.0))) + (define-public r-beachmat (package (name "r-beachmat") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a84d19727c..8bd42c9429 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10684,88 +10684,6 @@ access and manipulation of HDF5 datasets. It supports delayed operations and block processing.") (license license:artistic2.0))) -(define-public r-rhdf5lib - (package - (name "r-rhdf5lib") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhdf5lib" version)) - (sha256 - (base32 - "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete bundled binaries - (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-4.9.3/") - (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") - #t)))) - (properties `((upstream-name . "Rhdf5lib"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'do-not-use-bundled-hdf5 - (lambda* (#:key inputs #:allow-other-keys) - (for-each delete-file '("configure" "configure.ac")) - ;; Do not make other packages link with the proprietary libsz. - (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "")) - (with-directory-excursion "src" - (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) - (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) - "hdf5") - ;; Remove timestamp and host system information to make - ;; the build reproducible. - (substitute* "hdf5/src/libhdf5.settings.in" - (("Configured on: @CONFIG_DATE@") - "Configured on: Guix") - (("Uname information:.*") - "Uname information: Linux\n") - ;; Remove unnecessary store reference. - (("C Compiler:.*") - "C Compiler: GCC\n")) - (rename-file "Makevars.in" "Makevars") - (substitute* "Makevars" - (("@ZLIB_LIB@") "-lz") - (("@ZLIB_INCLUDE@") "") - (("HDF5_CXX_LIB=.*") - (string-append "HDF5_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) - (("HDF5_LIB=.*") - (string-append "HDF5_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) - (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") - (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") - (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") - (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") - (("HDF5_HL_LIB=.*") - (string-append "HDF5_HL_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) - (("HDF5_HL_CXX_LIB=.*") - (string-append "HDF5_HL_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) - ;; szip is non-free software - (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("hdf5" ,hdf5-1.10))) - (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Rhdf5lib") - (synopsis "HDF5 library as an R package") - (description "This package provides C and C++ HDF5 libraries for use in R -packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 14 15:41:08 2020 Received: (at 43400-done) by debbugs.gnu.org; 14 Sep 2020 19:41:08 +0000 Received: from localhost ([127.0.0.1]:56342 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHuLb-0005c1-Mw for submit@debbugs.gnu.org; Mon, 14 Sep 2020 15:41:07 -0400 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 1kHuLV-0005b7-DX for 43400-done@debbugs.gnu.org; Mon, 14 Sep 2020 15:41:06 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1600112459; cv=none; d=zohomail.com; s=zohoarc; b=Jsd/Wu1oMAMST9LTXlU7F4qfIXPg1LNz6AN5sdoKxMbowfPHXw8LN/vbR3F3PFxzUkDxo2bbam66xaNvhFsj79z5G+/1nmqpFQqFW0VcoVIraoT0DYR8YFdXTmHGjib+pK09kzfap2WrSN7oMvBjips1tU4XCHDJ+WcUMbsU/dU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1600112459; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=fdB34XD9pEz1m6QzoLbM7yu1km5FtAbsIkAQGFcWZGI=; b=JLFn0xaXuGUMb+w+s00y/HoiJ1IAt1mprm+N/oQJVrVMZNY0GIVFHmaA34STN0F4Bn/ocfZHKx37lWyWPbh0sqRfr8wZeimM8eiUpSGT/yv/Q8NGNhiSysb29dh61OiBSPBvnxxrILe777mTWaSiPJJg1nXxjtPlIsFP276L6O8= 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=1600112459; 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=fdB34XD9pEz1m6QzoLbM7yu1km5FtAbsIkAQGFcWZGI=; b=BreowsX7yfs/4nXMDkTtcL3aDcRHJlRwWgRiLhdsr0OFXHzTKWqyWepZeHiDtEx+ pArtEHfc1t+QiIUuJ/Uhrd5Kgao/1ILJiQzB/+6d6L9/seREVALVIyYkr3HPZlrwoU/ aWxmudLMsbqECGClhJMpykwzxY35aECXrp3X/Icw= Received: from localhost (p54ad4c23.dip0.t-ipconnect.de [84.173.76.35]) by mx.zohomail.com with SMTPS id 16001124571201015.5531451600918; Mon, 14 Sep 2020 12:40:57 -0700 (PDT) References: <20200914160414.7572-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#43400] [PATCH 00/12] Move some BioConductor to (gnu packages bioconductor) In-reply-to: <20200914160414.7572-1-zimon.toutoune@gmail.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: Mon, 14 Sep 2020 21:42:14 +0200 Message-ID: <87d02oxi09.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: 43400-done Cc: 43400-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 (-) zimoun writes: > More janitoral stuff. The process is the same as described in the cover > letter of #43345 . Thank you. I applied them all and added a commit to move a CRAN package to (gnu packages bioconductor) because r-preprocesscore had been moved. Pushed to =E2=80=9Cmaster=E2=80=9D branch with commit 3159fcf145. --=20 Ricardo From unknown Sat Aug 16 10:47:15 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 13 Oct 2020 11:24:03 +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