From unknown Thu Jun 19 14:00:17 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#36792 <36792@debbugs.gnu.org> To: bug#36792 <36792@debbugs.gnu.org> Subject: Status: [PATCH 03/11] gnu: Add r-all. Reply-To: bug#36792 <36792@debbugs.gnu.org> Date: Thu, 19 Jun 2025 21:00:17 +0000 retitle 36792 [PATCH 03/11] gnu: Add r-all. reassign 36792 guix-patches submitter 36792 zimoun severity 36792 normal tag 36792 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Jul 24 14:22:31 2019 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:31 +0000 Received: from localhost ([127.0.0.1]:37984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Lk-2V for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:36130) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Kw-Un for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41054) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuB-0003Hg-Pm for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuA-0007CQ-ML for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from mail-wr1-x42d.google.com ([2a00:1450:4864:20::42d]:46470) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuA-0007BH-GA for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: by mail-wr1-x42d.google.com with SMTP id z1so47975081wru.13 for ; Wed, 24 Jul 2019 11:22:22 -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=EBGiqIJ6MqoHCF1xFEtWHJ1TQ7cJOOpwKR35oebI/2o=; b=DPDpblrdhpnvpvcjT+K7QEilzzelwPmzzIBsCzwrYw1bGYRCNRU9JPE3U+zDb3pFX7 MenSkp6C/5IJ+L/6azdKGT4Se++aiFOzef5+daafcPaGs0uJDSqKP8egdvMouhQKu/G9 lJj+/OXKE3zK2SoLTGqCiZxPOVrTf0hKLuDipq2paItNDWij43PC2X2gSUHts+wswkBD cxT5mO0yGZEzltWP+3E/pRKoF8sJ/APm8NpYDmTNCNlO82XJ9jNiCcCEXAVLLnCV3qQ/ uEoQf0ShTSKv0TsMY5s5fnYBWdC7cocQ7qQZMeFGTXZ+5AgnxPhtqJN76FqyT/VG/b2e 36xQ== 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=EBGiqIJ6MqoHCF1xFEtWHJ1TQ7cJOOpwKR35oebI/2o=; b=EXKKhcsxH8tC7jWwSIJD4BIgTevyoQB8h2vwaRgm5bt4ZPEFcdfYGu1rKauykeGEDj eZ3RWhn7C6bS3NZlO3QdpOzrAN+ob9kI/Bz+LwXquKRWfdzFrKw2MRHsqXIb8sJDs8tq OFoS4gMEakFgyRbmfxHS2IbEzmbGX8cAvJMAasaqM3BVFDi6fEf8fmoqxF38dKRDJAnw dx418MD+CoqEjm8lHYxVZ8+ju4RciigcT8US7ajK/578/vU5Bbl7AajjtRKaMM5diX4Y XZqK9o09msEMyLESymQ5x0dm0v6joO1eJrbKlCabfGeDVfZm8IiO0gm3ohi4ioHXLmB8 Zg1w== X-Gm-Message-State: APjAAAVwKefCmBI+4EqBMvsMG4rO1AuCysny0zYee7WdPyBKVJowxKFV UabghP0REqJWsSwHGIsIrNJGNA+a X-Google-Smtp-Source: APXvYqx30FcyPS2v/zaUpi8X7US4YuGoKBjpwGy+V25kGjDlzOHRaZ7e4KntlCNReAbTHjMxRkH5Ow== X-Received: by 2002:adf:e444:: with SMTP id t4mr84469995wrm.262.1563992541413; Wed, 24 Jul 2019 11:22:21 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.20 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:20 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 03/11] gnu: Add r-all. Date: Wed, 24 Jul 2019 20:21:56 +0200 Message-Id: <20190724182204.6818-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4864:20::42d X-Spam-Score: -1.3 (-) 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 (--) * gnu/packages/bioconductor.scm (r-all): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5a2d66b2d..18b5711496 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -865,6 +865,36 @@ which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) +(define-public r-all + (package + (name "r-all") + (version "1.26.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ALL_" version ".tar.gz")) + (sha256 + (base32 + "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) + (properties + `((upstream-name . "ConsensusClusterPlus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase))) + (home-page + "https://bioconductor.org/packages/ALL") + (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") + (description + "The data consist of microarrays from 128 different individuals with +acute lymphoblastic leukemia (ALL). A number of additional covariates are +available. The data have been normalized (using rma) and it is the jointly +normalized data that are available here. The data are presented in the form of +an exprSet object.") + (license license:artistic2.0))) + ;;; Packages -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Jul 24 14:36:31 2019 Received: (at control) by debbugs.gnu.org; 24 Jul 2019 18:36:31 +0000 Received: from localhost ([127.0.0.1]:38044 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqM7q-0005tE-Mh for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:36:31 -0400 Received: from tobias.gr ([80.241.217.52]:34870) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqM7o-0005t1-Oj for control@debbugs.gnu.org; Wed, 24 Jul 2019 14:36:29 -0400 Received: by tobias.gr (OpenSMTPD) with ESMTP id 65ffc8bb for ; Wed, 24 Jul 2019 18:36:28 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=tobias.gr; h=from:to :date:message-id:mime-version:content-type; s=2018; i= me@tobias.gr; bh=snX8gkIGwvvMEOtUu1R0ewv6IhNBYe75nf1jTlPDTEg=; b= SKr2Nv4IaVdOgC7U4A5T1waVQ3bmHeD75MNbHb6ontzKUAnC6AyGAK69j7/mLSyq n5TkkJZbjt4m+cMYNmomsc7Jb8jfsrESeUhfOx6FFLs2CiDgGn3nppkYdKFCyieN 6Dx1nzpofFJCIu8XT/N6hGOtrt0H2heZAaRoK+X/o/u9/rFUrUC3cGKJMvs5wicm +hXhxFncsAid/LS+/6qt464n6YFucXB15p9Y4vpfsrh39E2tXATEVI3jXVhsl0I3 AZoN5GIDMLw1lsqgIrZBUJcC8EjaNpNamWID3v7BJWjq/sfaCz+n/b1H1MdkLo0X 9z3P1vmgpYkapiHIfOxzSQ== Received: by submission.tobias.gr (OpenSMTPD) with ESMTPSA id aaceb1cb (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256:NO) for ; 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