From unknown Mon Aug 18 04:43:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#36797] [PATCH 08/11] gnu: Add r-flowpeaks. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36797 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36797@debbugs.gnu.org Cc: zimoun X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255420632 (code B ref -1); Wed, 24 Jul 2019 18:23:08 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:34 +0000 Received: from localhost ([127.0.0.1]:37995 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuL-0005Mc-PM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:46513) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuG-0005LT-OL for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41121) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuF-0003J5-Hb for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -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 1hqLuE-0007IU-Gy for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:44509) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuE-0007HO-B6 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: by mail-wr1-x436.google.com with SMTP id p17so47980433wrf.11 for ; Wed, 24 Jul 2019 11:22:26 -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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=iDV2GYp7W51EI4bxEMsoW6UwQkUSpzQUAQVK/aRGqgsvSwg2wpmZthZAX7oR8KsmGl z4AT0inmfNoky032YuXIdWTPtN1+pPWFmYQ45t2wwgLNM1zRvgHyxpZDPS2e9ZZXcI6g 3c/U6t+ibWfcElrnLIWjbi4Nbdv8bMtJQDQTO4L+qanSMRYw3Ws6Kj3AepdrqJPk9gSG cy8TR2wFcsWUBNHwNzFd1/Ahy4sKdrVM2s3gMONKaGhDAeAbQfUZXE1xI6nb8wyI/dQb PPshM1//9hH0wuHCz+GaTgqcHRNOJuAipKg651xOmpZQ50EPCX4n8D64VhB3uoZmqbZD 0y9A== 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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=HfJ+GGSef49HFIs51BbECV6+Uj4DJDpA7rpYIMLv71+bqY8n/ZCHLsVpOwn6pjOano 0SSpDb85/hDHxV1AuV+WvmwNsJz8gHMLFjzveXT81tky2/yOp9R54YAQFPC7C7GfiBvl +4GLfB/JGBnCXRDfZHAp/M9foXccaV/038BTNwSUj8nP7lOk0mZmEliNgNbaHV3jJZJT 3A0FMrDl23l+8iWNali6+mqeuCZuGKVhT8l2u8QJckSEh5+9g6DJPGP035OYFWZcKno8 BnmYnnZz3Tu0Jo98pa97H9gAvqWbJSNtsMdcgy0Wu60Crk3hTMWmu8Q0KKGE5nPfSlEP bOEw== X-Gm-Message-State: APjAAAV6hjK2MtKmMx2YHzDN3N5qJtEj4ffR9+M/Fz5BsJw/cJ27Y8r6 0i0GeT9TSniUxM/uIpLGqj7rtFgy X-Google-Smtp-Source: APXvYqwd+3sdFWK0fNREs4/OvU/T3Ar2hlq3Wx+JFBQIIu/56Bg8qBuTO2LAKV9l8PNSMiKx20e6Zw== X-Received: by 2002:adf:ea88:: with SMTP id s8mr82370761wrm.68.1563992545301; Wed, 24 Jul 2019 11:22:25 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.24 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:24 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:01 +0200 Message-Id: <20190724182204.6818-9-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::436 X-Spam-Score: -1.3 (-) 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-flowpeaks): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f023665c2..ab4d9f4075 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4907,3 +4907,26 @@ and to both short and long sequence reads.") (description "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.") (license license:artistic2.0))) + +(define-public r-flowpeaks + (package + (name "r-flowpeaks") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowPeaks" version)) + (sha256 + (base32 + "1ncz7n6n39svi444yy29ip53398392s3m6z0h2a77rhcnzg456wy")))) + (properties `((upstream-name . "flowPeaks"))) + (build-system r-build-system) + (inputs `(("gsl" ,gsl))) + (home-page + "https://bioconductor.org/packages/flowPeaks") + (synopsis + "An R package for flow data clustering") + (description + "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.") + (license license:artistic2.0))) ;TODO: artistic1.0 does not exist + -- 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 ; 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Wed, 24 Jul 2019 12:17:37 -0700 (PDT) MIME-Version: 1.0 From: zimoun Date: Wed, 24 Jul 2019 21:17:26 +0200 Message-ID: Subject: Merge 36789 36790 To: control@debbugs.gnu.org, 36789@debbugs.gnu.org, 36790@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: control 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 (-) merge 36789 36790 thanks From unknown Mon Aug 18 04:43:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#36797] [PATCH 08/11] gnu: Add r-flowpeaks. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 20:52:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 36797 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimon.toutoune@gmail.com Cc: 36797@debbugs.gnu.org Received: via spool by 36797-submit@debbugs.gnu.org id=B36797.156400147322884 (code B ref 36797); Wed, 24 Jul 2019 20:52:01 +0000 Received: (at 36797) by debbugs.gnu.org; 24 Jul 2019 20:51:13 +0000 Received: from localhost ([127.0.0.1]:38119 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqOED-0005x2-Aa for submit@debbugs.gnu.org; Wed, 24 Jul 2019 16:51:13 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21289) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqOEC-0005wt-9z for 36797@debbugs.gnu.org; Wed, 24 Jul 2019 16:51:12 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1564001469; cv=none; d=zoho.com; s=zohoarc; b=iff3ubJZUjy52cNc4Ik6jEJ80mlj87xKqc1k2HKwHdWl2RVm55UcKVPTDj4j9apqzGFHjbLg4GOqDRKGYdJwc9AkiYA+7pgBtLC7WLgM2pgrEKePc7UmmNJKPmW8mJV6a2j6dP3Hk3hPYrKNRiE8IxS+mRFNcX5UPfzaZniZPYQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1564001469; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=BbtTGoDWNvc/O9SZxj8c7Mo7/0cKw3v+E8Uw5jNkjUY=; b=UBSs30w6VtxeNFlzHi0Nf15WAYkkV1fSmUdCH2TSznt7s2Hnon2Go9oUuv9uYE00Po8tW0g/D++fFAr80Vgm+72+hMQV8XuOrc21oyNrLGFd/2DTvyPB5SzLdNLTZJq7OItRvq+aPTRp8zD5wT5RbIZmsgi9hlITCFv9IzC+HPA= ARC-Authentication-Results: i=1; mx.zoho.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=1564001469; 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; l=416; bh=BbtTGoDWNvc/O9SZxj8c7Mo7/0cKw3v+E8Uw5jNkjUY=; b=BhgEtpQCZTWxQv8uQzbSaz0VkRYFeVGONelAj4GVCGOlpURqHs/0YRX+ixyZ795/ 7ofGKJnqgKHidWvMF0SE2GaIYYhtu+94CICHfagqY6lS1YvDNAnQyt3SMbXmyKk+woQ Pp1/3RZYL+O8nQCtltcTVXMm4rLK8kVC95NbB7K4= Received: from localhost (p54AD48C4.dip0.t-ipconnect.de [84.173.72.196]) by mx.zohomail.com with SMTPS id 1564001467619383.5697228292387; Wed, 24 Jul 2019 13:51:07 -0700 (PDT) References: <20190724182204.6818-1-zimon.toutoune@gmail.com> <20190724182204.6818-9-zimon.toutoune@gmail.com> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus In-reply-to: <20190724182204.6818-9-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: Wed, 24 Jul 2019 22:51:04 +0200 Message-ID: <87tvbb9mx3.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-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: > * gnu/packages/bioconductor.scm (r-flowpeaks): New variable. [=E2=80=A6] > + (license license:artistic2.0))) ;TODO: artistic1.0 does not exist Unfortunately, version 1.0 of the Artistic License is too unclear to be considered a free license. I have excluded this package from the set of patches that I=E2=80=99ll apply to the master branch. --=20 Ricardo From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36797: closed (patches merged) Message-ID: References: <20190724182204.6818-9-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36797 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36797@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304882-6704-1" This is a multi-part message in MIME format... ------------=_1582304882-6704-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 08/11] gnu: Add r-flowpeaks. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36797@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304882-6704-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304882-6704-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:34 +0000 Received: from localhost ([127.0.0.1]:37995 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuL-0005Mc-PM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:46513) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuG-0005LT-OL for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41121) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuF-0003J5-Hb for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -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 1hqLuE-0007IU-Gy for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:44509) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuE-0007HO-B6 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: by mail-wr1-x436.google.com with SMTP id p17so47980433wrf.11 for ; Wed, 24 Jul 2019 11:22:26 -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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=iDV2GYp7W51EI4bxEMsoW6UwQkUSpzQUAQVK/aRGqgsvSwg2wpmZthZAX7oR8KsmGl z4AT0inmfNoky032YuXIdWTPtN1+pPWFmYQ45t2wwgLNM1zRvgHyxpZDPS2e9ZZXcI6g 3c/U6t+ibWfcElrnLIWjbi4Nbdv8bMtJQDQTO4L+qanSMRYw3Ws6Kj3AepdrqJPk9gSG cy8TR2wFcsWUBNHwNzFd1/Ahy4sKdrVM2s3gMONKaGhDAeAbQfUZXE1xI6nb8wyI/dQb PPshM1//9hH0wuHCz+GaTgqcHRNOJuAipKg651xOmpZQ50EPCX4n8D64VhB3uoZmqbZD 0y9A== 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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=HfJ+GGSef49HFIs51BbECV6+Uj4DJDpA7rpYIMLv71+bqY8n/ZCHLsVpOwn6pjOano 0SSpDb85/hDHxV1AuV+WvmwNsJz8gHMLFjzveXT81tky2/yOp9R54YAQFPC7C7GfiBvl +4GLfB/JGBnCXRDfZHAp/M9foXccaV/038BTNwSUj8nP7lOk0mZmEliNgNbaHV3jJZJT 3A0FMrDl23l+8iWNali6+mqeuCZuGKVhT8l2u8QJckSEh5+9g6DJPGP035OYFWZcKno8 BnmYnnZz3Tu0Jo98pa97H9gAvqWbJSNtsMdcgy0Wu60Crk3hTMWmu8Q0KKGE5nPfSlEP bOEw== X-Gm-Message-State: APjAAAV6hjK2MtKmMx2YHzDN3N5qJtEj4ffR9+M/Fz5BsJw/cJ27Y8r6 0i0GeT9TSniUxM/uIpLGqj7rtFgy X-Google-Smtp-Source: APXvYqwd+3sdFWK0fNREs4/OvU/T3Ar2hlq3Wx+JFBQIIu/56Bg8qBuTO2LAKV9l8PNSMiKx20e6Zw== X-Received: by 2002:adf:ea88:: with SMTP id s8mr82370761wrm.68.1563992545301; Wed, 24 Jul 2019 11:22:25 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.24 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:24 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 08/11] gnu: Add r-flowpeaks. Date: Wed, 24 Jul 2019 20:22:01 +0200 Message-Id: <20190724182204.6818-9-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::436 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-flowpeaks): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f023665c2..ab4d9f4075 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4907,3 +4907,26 @@ and to both short and long sequence reads.") (description "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.") (license license:artistic2.0))) + +(define-public r-flowpeaks + (package + (name "r-flowpeaks") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowPeaks" version)) + (sha256 + (base32 + "1ncz7n6n39svi444yy29ip53398392s3m6z0h2a77rhcnzg456wy")))) + (properties `((upstream-name . "flowPeaks"))) + (build-system r-build-system) + (inputs `(("gsl" ,gsl))) + (home-page + "https://bioconductor.org/packages/flowPeaks") + (synopsis + "An R package for flow data clustering") + (description + "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.") + (license license:artistic2.0))) ;TODO: artistic1.0 does not exist + -- 2.21.0 ------------=_1582304882-6704-1-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36789: closed (patches merged) Message-ID: References: <20190724182204.6818-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36789 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36789@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304882-6704-3" This is a multi-part message in MIME format... ------------=_1582304882-6704-3 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 00/11] Add r packages to process flow cytometry data which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36789@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304882-6704-3 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304882-6704-3 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:24 +0000 Received: from localhost ([127.0.0.1]:37969 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Ka-1H for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:38900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuA-0005KK-KU for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41017) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLu9-0003G5-Ns for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -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 autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLu8-00079s-T9 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:21 -0400 Received: from mail-wr1-x430.google.com ([2a00:1450:4864:20::430]:38495) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLu8-00078j-N2 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:20 -0400 Received: by mail-wr1-x430.google.com with SMTP id g17so48018211wrr.5 for ; Wed, 24 Jul 2019 11:22:20 -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=a3fgK7jCKnhsRv15kj7FAOAT+XOMfQSDra35HkCurBk=; b=El7qtTq/GZlHi+fnyJDNUI8ZOEvBSn7gUPtsQkVYft35zuP6quAbCFLnJakZ7afw6+ TdnKHqMLW/eSoI0jYpx2F+dfTc9OEgRiYaUwrcKUyPB26x2o8CtFwla95U+fW0Gij1Pw HlEFIamcmo35X/rThBTNYVjLE25fQeaqVM8JNXbzfDZ/0tM5LIInIanvw2yM2sFflZTF xLCfk22EEEZMU3uEMn2ze4arTLKspS9oKFklcESRqaMMcnLRPjRPgKaaZNyJBzmHeBu9 I7cHe0gkjqMvD3yAC2+5kY2ByFRrFIfLZxXLOZSzHi9it6O1KR73JFRjf5sT4dSxWGe8 5QEg== 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=a3fgK7jCKnhsRv15kj7FAOAT+XOMfQSDra35HkCurBk=; b=NoAHigdzbGrdVk+mJZocpfGVN7qpov+STUUP5HUGs/ebElBgtglfju9Gp4wsPlSMVk 9fhxDDR6sddJ+JbRGZvC2mXQXYu05N5Dt/CFkeGRS1UvYHjE+BczKEmZhwOS5QIcUBRt YLm2Vt93hmMcv4e9JWSre/8n7wb3IWSeGYzOJrdcUOsr/ovIE3uqpU7Fb+NzchoXS+vc /HofU4nSCnmg4OcM0giSNKYjWVcYevZzWAmhZwl4i0L9G6orUgTwL8mPjv7R8h8yaPkD LMuLHmSjuRSCGz7jGUyMtxh1XkY7TQiJAcb3NZtt6mqyrhvUWAbyzN2foqTXzXU2Zt/b in7w== X-Gm-Message-State: APjAAAUhQh4ZrFniuY7FAmbmwpWhVjZ8wUynwnV0XsJ8KQT0i7N85XqN HACGgPgLaKFLdvNqW3jDWTVm2ozX X-Google-Smtp-Source: APXvYqxPjMzmNwH6CLvBCYPZpXtkX36ReSwUkIWeHSJ9walVY8hcyvxYf4WBw0U4DJG5a0Lh3iIeCw== X-Received: by 2002:adf:de90:: with SMTP id w16mr52913552wrl.217.1563992539269; Wed, 24 Jul 2019 11:22:19 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.18 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:18 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/11] Add r packages to process flow cytometry data Date: Wed, 24 Jul 2019 20:21:53 +0200 Message-Id: <20190724182204.6818-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 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::430 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 (--) Dear, This serie adds packages used in flow cytometry data analysis; and their dependencies. They are the result of the command `guix import cran --archive=bioconductor --recursive`. Please let me know if it is correct. All the best, simon zimoun (11): gnu: Add r-umap. gnu: Add r-kableextra. gnu: Add r-all. gnu: Add r-flowcore. gnu: Add r-flowutils. gnu: Add r-consensusclusterplus. gnu: Add r-flowmeans. gnu: Add r-flowpeaks. gnu: Add r-flowsom. gnu: Add r-mixomics. gnu: Add r-depecher. gnu/packages/bioconductor.scm | 288 ++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 67 ++++++++ 2 files changed, 355 insertions(+) -- 2.21.0 ------------=_1582304882-6704-3-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36790: closed (patches merged) Message-ID: References: <20190724182204.6818-2-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36790 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36790@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304882-6704-5" This is a multi-part message in MIME format... ------------=_1582304882-6704-5 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 01/11] gnu: Add r-umap. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36790@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304882-6704-5 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304882-6704-5 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:24 +0000 Received: from localhost ([127.0.0.1]:37971 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Kd-9C for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:35128) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuB-0005KS-CP for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41025) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuA-0003G6-Cy for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -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 autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLu9-0007AV-AO for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:39719) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLu9-00079M-4g for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:21 -0400 Received: by mail-wr1-x436.google.com with SMTP id x4so47968393wrt.6 for ; Wed, 24 Jul 2019 11:22:21 -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=wljyQX5T4Om4XmkiAWJsFHRSb3sTgG1+ANXwr1zpL+c=; b=NBFlpPpdptTzZRANsARv64zUWUJQvkHDh5R7eMVGR0W+0CabPRCcsiijdwPzh/xSPL CfZVUAsgbpVYHoC3iTC4IJplyE9te4fCjBBNDi7i5+eAMIccSVCk3gCxfwZIaUSCnj9R HG7qKXzJqz6V6p/lR236TxlRVaqkhKuRjQeNISR+ciZvz0JY17rn2pbw8pkkTCS0jfg5 FpD1MS1urPuo1iMFg63btjJwcEX5R5K/fWpElm2U/in/Nb7FFL/SX+vrpPOl7aYEdJDE 1uliZRz/jmUOCbBF3eIvHH2SOXnpzLJ1NXJGTUC6D+SDFJFVo/ZHdk4gT2e/EdgGh6Dc O8Qg== 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=wljyQX5T4Om4XmkiAWJsFHRSb3sTgG1+ANXwr1zpL+c=; b=coOPOw/ysEU+NRSaK/IsS8ILMkwxDXHvo/0sfWimNoU/Z41EymDJr/5s6dN2SpTmc+ 2WscNOaP0sY6nbSA+PB6/ntzTSV5pgFf7Gfg0q5BuE48uRb/UrNrFTUgozbx2rnUZ0kD 4zmMDNJS+SLTd7MGnPBReFXk+cYAy5DkH3M+25/VHb8Rb0GFWx1CAX8Y0sLagjmny2uL oHoikU0QXa+EquU7GUu0O1ac7p2pYv7pDBOnJlwVi6wJv+nmNXI+jW75Y7IpVN84Jd1s L13suhZQsYk0b3gkx6IQLHBDS56ObvUpvv8VTEt6rfGNkJFqFpWO4Tx6JGlBIjf3ZwsQ xMAA== X-Gm-Message-State: APjAAAVxP+VVshVunQ1PtQdh1FOS9/nNQx49TNH12DW4U+usUdiogJI5 E/z+O8f+UTvUVF1AdlP2KIqSo0qr X-Google-Smtp-Source: APXvYqx5+SQgoc0ZEl+FaovThgL7Cx0g06EtlJckwNwlmk3d+NE4bAtrL7H5H88BbSI4XZ/4k3OQrw== X-Received: by 2002:a5d:51c1:: with SMTP id n1mr84349538wrv.254.1563992539918; Wed, 24 Jul 2019 11:22:19 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.19 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:19 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 01/11] gnu: Add r-umap. Date: Wed, 24 Jul 2019 20:21:54 +0200 Message-Id: <20190724182204.6818-2-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::436 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/cran.scm (r-umap): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f0d819df7..768a7d09c5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14530,3 +14530,30 @@ including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) + +(define-public r-umap + (package + (name "r-umap") + (version "0.2.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "umap" version)) + (sha256 + (base32 + "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-reticulate" ,r-reticulate) + ("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/tkonopka/umap") + (synopsis + "Uniform Manifold Approximation and Projection") + (description + "Uniform manifold approximation and projection is a technique for +dimension reduction. The algorithm was described by McInnes and Healy (2018) +in . This package provides an interface to the UMAP +algorithm in R, including a translation of the original algorithm into R with +minimal dependencies.") + (license license:expat))) -- 2.21.0 ------------=_1582304882-6704-5-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36791: closed (patches merged) Message-ID: References: <20190724182204.6818-3-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36791 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36791@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304882-6704-7" This is a multi-part message in MIME format... ------------=_1582304882-6704-7 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 02/11] gnu: Add r-kableextra. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36791@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304882-6704-7 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304882-6704-7 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:31 +0000 Received: from localhost ([127.0.0.1]:37981 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuI-0005Lh-OM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from lists.gnu.org ([209.51.188.17]:56560) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Ke-AP for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41043) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuB-0003Hc-6q 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-0007BV-28 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from mail-wr1-x42f.google.com ([2a00:1450:4864:20::42f]:43436) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLu9-0007AL-Sg for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: by mail-wr1-x42f.google.com with SMTP id p13so47974634wru.10 for ; Wed, 24 Jul 2019 11:22:21 -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=7sQ4hMMewGNK1ZUfxvELsM3vEj41+txaX373UyUZUqs=; b=XYdgAYJY5iu+br3qnF+QyDWO/FlQiEh6fNqIPwb2Cq4F4krqYaX3vF7cu4GznNMpFP L7178xI+hX1ci6g5aZEOLEzXhUUR3OsoToxHQ81KHerR6C5FT+Y1xeJEyxAeqFA3pbRy pKEtFuAOesifjCKzvv0rz+AoDLJyttPv92D6mAPD/nNhL5CbdPiy9qV626os3hgQBm3o 1RyZUiOD1+OLyXwvNXGzUT8WKvUQDVlEPoiiC1XUfXSq6/oq9aTabOBQWJM5fEfluGhG Z9oDMBaJjtGr9tF4sdXtHGEqsxj2phjzt/AZXbnhseUZDMQ04Ng36m6rPuxvvcr62exd sfsw== 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=7sQ4hMMewGNK1ZUfxvELsM3vEj41+txaX373UyUZUqs=; b=jSwS85TtTE5295PVRRmcrwQqhkD66CcGz897WoYndMVi6+HKlo7EcwdvvruMaoqACp SHRhc9GHOErr5bvshZtd/0yIONEZ06NAm7zhwMHZUn08k5mmkJ5sJOeJDTwbp22n1Pf/ zcrh2Wc7vMxtZfloP9dViI1a/mDm0dokcYAffyeKnU6xpXX+EMhhx2S2w1E6jsafr5Ms LhyI54hNb9c54Ttb/ti1k+NZAs+LJlfM1MKJhX47p6DFpB4ka5hAEmxq6wIH0JXINIUV +H2a9h4Cef5bb9iRonpqJj4T0kqSmlrICxT8heh91zF31AFaYj48QJXJ2cNop4w6gz5F InNw== X-Gm-Message-State: APjAAAUwaHfnAbDiqRJtRw7eg4YeJJb+Fw0Ly1GJb0SISqnSH6fxhyoe Bex4DBKRS14Nu80jmy/o23/wRpjn X-Google-Smtp-Source: APXvYqy9rS2iAxcsrW9VrdpwvwnYN3avi70ONFvF5PWzl8rkTGt7W0ZLCglayQdJH6KUBExaGmQAag== X-Received: by 2002:a5d:6408:: with SMTP id z8mr73352019wru.246.1563992540767; Wed, 24 Jul 2019 11:22:20 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.19 (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 02/11] gnu: Add r-kableextra. Date: Wed, 24 Jul 2019 20:21:55 +0200 Message-Id: <20190724182204.6818-3-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::42f 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/cran.scm (r-kableextra): New variable. --- gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 768a7d09c5..7349a9513e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14557,3 +14557,43 @@ in . This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R with minimal dependencies.") (license license:expat))) + +(define-public r-kableextra + (package + (name "r-kableextra") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kableExtra" version)) + (sha256 + (base32 + "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) + (properties `((upstream-name . "kableExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-readr" ,r-readr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-rvest" ,r-rvest) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-viridislite" ,r-viridislite) + ("r-webshot" ,r-webshot) + ("r-xml2" ,r-xml2))) + (home-page + "http://haozhu233.github.io/kableExtra/") + (synopsis + "Construct Complex Table with 'kable' and Pipe Syntax") + (description + "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and +the piping syntax from 'magrittr'. Function 'kable()' is a light weight table +generator coming from 'knitr'. This package simplifies the way to manipulate +the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct +complex tables and customize styles using a readable syntax.") + (license license:expat))) -- 2.21.0 ------------=_1582304882-6704-7-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36792: closed (patches merged) Message-ID: References: <20190724182204.6818-4-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36792 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36792@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304883-6704-9" This is a multi-part message in MIME format... ------------=_1582304883-6704-9 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 03/11] gnu: Add r-all. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36792@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304883-6704-9 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304883-6704-9 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 ------------=_1582304883-6704-9-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36793: closed (patches merged) Message-ID: References: <20190724182204.6818-5-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36793 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36793@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304883-6704-11" This is a multi-part message in MIME format... ------------=_1582304883-6704-11 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 04/11] gnu: Add r-flowcore. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36793@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304883-6704-11 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304883-6704-11 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:32 +0000 Received: from localhost ([127.0.0.1]:37987 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Ly-Ky for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:46301) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuD-0005L2-LJ for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41070) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuC-0003Ho-Kr for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -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 1hqLuB-0007Dt-JB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from mail-wr1-x431.google.com ([2a00:1450:4864:20::431]:43438) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuB-0007Cf-DF for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: by mail-wr1-x431.google.com with SMTP id p13so47974699wru.10 for ; Wed, 24 Jul 2019 11:22:23 -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=rx7LUQvIHcLh54Mlx4vy8OaM3guvdfNahu+L7Qf6kUw=; b=A5n8zr5XDapjfpVzDCP8mYd8loT2PvPW6fbEIeXtGPhXeFfLZ1SiVMXzx83h9VIkO1 qfX0dWpJLS1w3pjqLaevfq6OWGNR6aOlgwaYokYijvC13oWJj9BcTua+DErbsVl1jZT7 iq3M6h2wAjvFReeuAHDb+BBkPS/9zzXodELyiMy+053IUgiccKEQstAcj6W9FKU/X52T SPoCfLG0aTxO34zsRbVP2r2ZcUjbPUFuZgCN/3D5ndOafPM052UDlYA+u1phIoWN/cMQ AMS1gQUxFWX8OKcMityO/yZYS497/YDKgR1zfkTdJDQXVkp7iJoDdf56Yto+nfgcJ4XA qGDg== 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=rx7LUQvIHcLh54Mlx4vy8OaM3guvdfNahu+L7Qf6kUw=; b=qpjlcH7FpSzrwji2etpz/4/cTVzFI4mFR2hPlSQXLEP37rCbqD+pkI3YHaV4jO9mjS cWk5rCSQJT3eWTQGU8ve2ZpYogYqhBHbVwLTW8dGCyB8dB3BVrZkD7HLTnMDbPlrL29D 5RgYAQKoiA/7OE4gcoHyOU8MlFFAXu7kqoKpwS7zv9MD2ZVFtyPmdHFDtdIFeuMvOCtS 9nxHuLyRacbthrKxXQBGpxZBFAw802Z682P/eqBBQXX0fILHOmz/jXRBdoI7514WAyZb QnuNneTP59+i5F4/+fyqVcrB3IwLxu18x7rhJiIuELSmiDouQQSx6KzDgU2zPSCWkbpp Z86w== X-Gm-Message-State: APjAAAW73DPJ79W2j+zs80qecTckXwblFfYboMgiER+4LB1Jnp6aoMAd pSAs26jZhustj1n0FCpm68kFgapO X-Google-Smtp-Source: APXvYqzFM1KPSMixiABfbX8e2HxGBDpvz061d663XnYDMnnTvhFY9LggOG04MgcQ92N7Odfpm+KNYQ== X-Received: by 2002:a5d:6a84:: with SMTP id s4mr12580003wru.125.1563992542287; Wed, 24 Jul 2019 11:22:22 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.21 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:21 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 04/11] gnu: Add r-flowcore. Date: Wed, 24 Jul 2019 20:21:57 +0200 Message-Id: <20190724182204.6818-5-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::431 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-flowcore): 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 18b5711496..3a38042537 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4799,3 +4799,33 @@ read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) + +(define-public r-flowcore + (package + (name "r-flowcore") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowCore" version)) + (sha256 + (base32 + "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + (properties `((upstream-name . "flowCore"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-corpcor" ,r-corpcor) + ("r-graph" ,r-graph) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page + "https://bioconductor.org/packages/flowCore") + (synopsis "Basic structures for flow cytometry data") + (description + "Provides S4 data structures and basic functions to deal with flow cytometry data.") + (license license:artistic2.0))) -- 2.21.0 ------------=_1582304883-6704-11-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36794: closed (patches merged) Message-ID: References: <20190724182204.6818-6-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36794 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36794@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304883-6704-13" This is a multi-part message in MIME format... ------------=_1582304883-6704-13 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 05/11] gnu: Add r-flowutils. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36794@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304883-6704-13 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304883-6704-13 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:32 +0000 Received: from localhost ([127.0.0.1]:37989 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuK-0005MC-Fa for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:54749) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuE-0005L9-C3 for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41084) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuD-0003I5-8B for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -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 autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuC-0007Ex-AZ for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from mail-wr1-x42d.google.com ([2a00:1450:4864:20::42d]:33639) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuC-0007Do-3W for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: by mail-wr1-x42d.google.com with SMTP id n9so48094453wru.0 for ; Wed, 24 Jul 2019 11:22:24 -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=OSpLDtjNGjfHmKRoGp1RTvE1NGPzUJ5XElI50Q6CEgw=; b=iegAibzrIREiO2fEUC8nsqr/ZpvTb4LNilB7sQXLjOV7c3LtbKvApSV20IiU0xQRk8 6Rltj5m7r1iwW2nLAO5227OcYLiOJtZ7kDY3to/1tQKMRJz9Grgo0gKz4mwRpG+jiJ2m tIokIp4HTZ+yZ1FJBzPe/hv9cywbLj0qoMSfecGfvxeJe4FWnYJMC/Rv6bj+1+JsMh0c exB64vzd7SbYzpEmx5NLgUHQO/qjCh0EpEFER9nNdNQNLtwwiNa0Pj5fJ52Ib3u+WbRz 4X2cYHvpD1qXQ2BMONNs1UOlcwEbaoIB6vLGJctLuflZ/DAnnCbAuodp6dkrONzqCGac rG5w== 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=OSpLDtjNGjfHmKRoGp1RTvE1NGPzUJ5XElI50Q6CEgw=; b=GgzU5p31ukxyJ40bTvhG7s4H5YDWTgOIDhoPTAlp6K2MMoxTrrmK2bD17Ru+D/yuTU MhpfVDjppGpNiztwKKHRgtbLDMi/PqI8hw5MgRPwhebLXC/Yg3LtK2lY1DNr90aBQeCv dbZpKuZYNMBTHZFEWhKyOanNBjuEyG9Aqj1zmUyaaS8Iea0k8nb4whSgcYuD7b69yZCj j2HObMAZ5PM9fbB4Fkgn6ZIpT2qhA8U6v9i7Kam60CzU189Pq7zSmUH97Tqp9xemujkb OLwX5NzO0/XT9CAUiYEGCbkwCrG4i0sIgznTOfhfOz0DPgQNFP7de/eWtZaVKbFMuxmq U0Tg== X-Gm-Message-State: APjAAAWiwiHI4fCHNVMeuXV3FUO8PeYZnYp0GJL2aCTwAQcggqrCha0h vMNYFunmlg4w5nQkdqo/nNXnq8+M X-Google-Smtp-Source: APXvYqzDEnKHSSGDJ2R+27497B6eZ63kVT1UTmRh53JrwGtXP6YT1Y0UQw6blGZ/M63N0NOOA7KPpg== X-Received: by 2002:adf:de10:: with SMTP id b16mr55952468wrm.296.1563992542948; Wed, 24 Jul 2019 11:22:22 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.22 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:22 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 05/11] gnu: Add r-flowutils. Date: Wed, 24 Jul 2019 20:21:58 +0200 Message-Id: <20190724182204.6818-6-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-flowutils): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a38042537..d79ff729fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4800,6 +4800,33 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flowutils + (package + (name "r-flowutils") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowUtils" version)) + (sha256 + (base32 + "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + (properties `((upstream-name . "flowUtils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-flowcore" ,r-flowcore) + ("r-graph" ,r-graph) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml))) + (home-page + "https://github.com/jspidlen/flowUtils") + (synopsis "Utilities for flow cytometry") + (description + "Provides utilities for flow cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") -- 2.21.0 ------------=_1582304883-6704-13-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36795: closed (patches merged) Message-ID: References: <20190724182204.6818-7-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36795 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36795@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304883-6704-15" This is a multi-part message in MIME format... ------------=_1582304883-6704-15 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 06/11] gnu: Add r-consensusclusterplus. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36795@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304883-6704-15 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304883-6704-15 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:33 +0000 Received: from localhost ([127.0.0.1]:37991 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuK-0005ML-QO for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:33 -0400 Received: from lists.gnu.org ([209.51.188.17]:42064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuF-0005LG-7A for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41096) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuE-0003Ix-6a for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -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 1hqLuD-0007GU-4l for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:39999) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuC-0007Eu-Ut for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: by mail-wr1-x42e.google.com with SMTP id r1so47997542wrl.7 for ; Wed, 24 Jul 2019 11:22:24 -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=24W40LvZghPcbKV/H18xen7gsRhPS5H4z1oHo7bo37o=; b=rnqbXAjUbGifnfSO2GeQGZh0dc4in9l2FFDzbMa2r4+No3iWfFlW5kDSK6zMOmgtW3 2SMnZYV32ponjO/9S3WMrTgZZW3TKj4vKT4TA+OGqPVCsQ1Kg/CCrAgV51LJK+EL2pVb cl24I9l58S9hW8+IEZdFFQpSsJBtn4bLc2hnYKPB7QwnLTbuHGXvcXIRuSnwsn6wg0xw CKaCaxReizbyFrqw+dZBWZlq7BHHAEUibamWkZ+gsjagf9A9YRWbwwaoKCFu2Mz/vNMO 2ILflRcwss1a3vBgqXZOJRwqeeQP6EK/MvHX/VMjFqxFDsTVNvuDJG3/uJOprycZTT9w vTbQ== 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=24W40LvZghPcbKV/H18xen7gsRhPS5H4z1oHo7bo37o=; b=SIN8y4AD5vmwGOSqg6BYKYwOO3Bat+E6o7eBKJ0ikn4zdU3Jmj11ZqlmS/vkLTXlc7 CZFhqzi/V+vj0RzPAAzwf4mSFwLj2AlCumAIucL/vzR+yQF+oIk3+/1xk9A/Wcd4qjUm 0PMwv9ppAz1eIl4igDEPm9dRvEi0571rA/08p13G89s3ERE8fYbAn0qas1lSkc1ZJzXb gfcq4YDbwbB/xUYaUq14h96eG+L9qxdwp1Y9Zu23Jf1lY9wxAm6MM10NgumSP9llRH+w F86v+QC/uJJpCLUuyk2ICKqeSMgzax+I44cgwh/1mz681GFFHcgnMftPc/Msoi7SYwvi KdcA== X-Gm-Message-State: APjAAAXTDYOX7U62k1YMrKv+k/n+FLIJscrU9reWMjLutN92HPDg3f0Q aDAKjFMkKQFHSwy2hCdzY/qtD6mh X-Google-Smtp-Source: APXvYqwCXWThIC3B+SGJ91uJCfiUoKLOXuqkMDur6pAOubKmN3dlEbtcvfcg0Cj8OD6alf5bvtf3oQ== X-Received: by 2002:a5d:618d:: with SMTP id j13mr88213012wru.195.1563992543841; Wed, 24 Jul 2019 11:22:23 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.22 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:23 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 06/11] gnu: Add r-consensusclusterplus. Date: Wed, 24 Jul 2019 20:21:59 +0200 Message-Id: <20190724182204.6818-7-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::42e 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-consensusclusterplus): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79ff729fc..d5bd512972 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4827,6 +4827,31 @@ and to both short and long sequence reads.") "Provides utilities for flow cytometry data.") (license license:artistic2.0))) +(define-public r-consensusclusterplus + (package + (name "r-consensusclusterplus") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ConsensusClusterPlus" version)) + (sha256 + (base32 + "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + (properties + `((upstream-name . "ConsensusClusterPlus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-all" ,r-all) + ("r-biobase" ,r-biobase) + ("r-cluster" ,r-cluster))) + (home-page + "https://bioconductor.org/packages/ConsensusClusterPlus") + (synopsis "Clustering algorithm") + (description + "Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") + (license license:gpl2))) + (define-public r-flowcore (package (name "r-flowcore") -- 2.21.0 ------------=_1582304883-6704-15-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36796: closed (patches merged) Message-ID: References: <20190724182204.6818-8-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36796 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36796@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:04 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304884-6704-17" This is a multi-part message in MIME format... ------------=_1582304884-6704-17 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 07/11] gnu: Add r-flowmeans. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36796@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304884-6704-17 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304884-6704-17 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:33 +0000 Received: from localhost ([127.0.0.1]:37993 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuL-0005MU-Cc for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:33 -0400 Received: from lists.gnu.org ([209.51.188.17]:48146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuG-0005LM-1R for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41112) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuF-0003J1-0q for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -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 1hqLuD-0007Hc-Ui for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from mail-wr1-x433.google.com ([2a00:1450:4864:20::433]:33645) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuD-0007GY-Oh for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: by mail-wr1-x433.google.com with SMTP id n9so48094525wru.0 for ; Wed, 24 Jul 2019 11:22:25 -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=0foQD19vAMQrvcRH4ETjIMv5JzK13UlFkevMaKX88ck=; b=Yt14iPtbAHIlIr2twiukipiepKskFRoRYJ/6HzWUFW5fvCsTXeBOpSZz7CZUsYrrlm ZFD7kF9lgOsUKspSIF1OI1oAgZhZgv75HxtW7EbEWGN8iKVMDv3qV90DaOUEH+wzqd9D kx38SdkCvN/OKI7ysV186CWXTl7GDm0EeTLtVx5l7d2rQm/1MUh57dIXHXPI9yy38328 ko5VqPXzudjbBlwQz4DcvBywjknBddDDHpqvGxAFQz5Kl6f83HqEWCGFuJbkei9AK3/a iMBFvlj9CRerYSWVFyvHnAQDdycwiAYLoEODX8amswODkWOC99CmLHTvjJFjSkT4p0MX GTBA== 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=0foQD19vAMQrvcRH4ETjIMv5JzK13UlFkevMaKX88ck=; b=iR9UAloC+ZMj/NVRecf34BLin0gQsUX2qzezTmF6aQ/Lc5jmRZu+haAyzJ4iE2vQmZ fqZ/EHwUsPs1rPasgalXPgHESRtl5tNLNM6QNFFbglih09gDMFxREMoIpJIFXJk+CJFC /aPKi0jzefN4M1EbawsrKqUH+iqVY6qrQ23Tq8EKLr6gWHSCWNdT1JNJwSJTP9urhe59 sXendYIJiHK5aMW5eZiMHOozx61D+h6qnVcBDL1mJ8lOKeFUT462eKGjEwfYM7YZxwgK EPzNXBVUDIVrb3+7MfcURv2CgmJgx8uTd2y9dZTTd2APWnF/1YuTW1D6q8T7JQO4X1// fWww== X-Gm-Message-State: APjAAAXDFAs784XTgUyXz5UZGIUgjF5Cm2h2f+uxcl/jVtFFy7rdCLiN rcYAzQnxtDPHhd4GRnpIebc++rNO X-Google-Smtp-Source: APXvYqwYq0dfkdXt1gxoLntVS7kilXWftZ8hRBQZHMCpQ13GcBfbe/RIAbN0UZldoS/eSElsqWN9Aw== X-Received: by 2002:a5d:51c8:: with SMTP id n8mr78520379wrv.46.1563992544648; Wed, 24 Jul 2019 11:22:24 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.23 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:24 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 07/11] gnu: Add r-flowmeans. Date: Wed, 24 Jul 2019 20:22:00 +0200 Message-Id: <20190724182204.6818-8-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::433 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-flowmeans): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5bd512972..0f023665c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4881,3 +4881,29 @@ and to both short and long sequence reads.") (description "Provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowmeans + (package + (name "r-flowmeans") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowMeans" version)) + (sha256 + (base32 + "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + (properties `((upstream-name . "flowMeans"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-feature" ,r-feature) + ("r-flowcore" ,r-flowcore) + ("r-rrcov" ,r-rrcov))) + (home-page + "https://bioconductor.org/packages/flowMeans") + (synopsis + "Non-parametric Flow Cytometry Data Gating") + (description + "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.") + (license license:artistic2.0))) -- 2.21.0 ------------=_1582304884-6704-17-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36798: closed (patches merged) Message-ID: References: <20190724182204.6818-10-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36798 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36798@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:04 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304884-6704-19" This is a multi-part message in MIME format... ------------=_1582304884-6704-19 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 09/11] gnu: Add r-flowsom. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36798@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304884-6704-19 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304884-6704-19 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:34 +0000 Received: from localhost ([127.0.0.1]:37997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuM-0005Mk-8b for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:46489) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuH-0005La-TM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41139) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuG-0003JC-Sm for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -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 1hqLuF-0007Jz-H0 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from mail-wm1-x336.google.com ([2a00:1450:4864:20::336]:37215) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuF-0007If-Af for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: by mail-wm1-x336.google.com with SMTP id f17so42458535wme.2 for ; Wed, 24 Jul 2019 11:22:27 -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:in-reply-to:references :mime-version:content-transfer-encoding; bh=Jy5PfItzZJVOlLqCCQqbG/YxP5343aRlpYkP9syQYug=; b=m9lGmm/xWzn683krnhDieT9FvrdJYmEBju8anez8FZ/2JOpnPj4p42R6iImYPFgd7v 6l/rf2nl61VccRcdlztzzLoF7BU/geVAjnb64ORTQrEeIOyvpCY7Kr2R7LKeG9+jMHIe j1XrDb1kM2wYAixlWDYnoZfWTglxcj7tcpXuSyosToNHaT2lo7NjBdUjVRHiXeLYIk3o lSg9i5ujx4qqZkW15G7dArVS5hoj8Ont/Pm73ow7MQP9kJ5Bjr4rVIsc0UXY72ROhXCl /rffSQ7x0UTrZzrwvqfXuT5wIetHrsNFnmM2jy+tPZCLyiHeO3tiZfWTU8oZclJLYrkJ alew== 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=Jy5PfItzZJVOlLqCCQqbG/YxP5343aRlpYkP9syQYug=; b=tT1vLR4rrw9bLRvAvj2chFkxVUR9j78fV+9lnphSOD84vnZEQbwgUgc2uxnSvZ6LHC t3iQRwaEnvlI+zk5J+UKDfzV3RHEMnLwIcczkhgmPFR8pFbgH+g3zFiDtST/H8xL4jrG rIcjbfSYF6+0xq2ayoyDWXjlsBjI/di2nOGWHn7yl2fBOo/5b8LK7IbEBMW6q+wf9Oen LNkBd6tc7i4GMkzMJWACfhQdGi7vWQ50tm/FWGuAfDXvo0XbtQ2jQXwh8cIPq2nYfeYf GFJDWywDKZQ8mjsOiN3+sHxTUDhdbsPCEL59bNayxxwNOLsEmDxfZu/nuRz4wfHg3p5W NiuA== X-Gm-Message-State: APjAAAWMIBKvy4oBfdymMeYkLFpuDz54PP3ksO3mv8lywqBDHiXGbTUR FM1oDAI05vgeptIn8GK80QvTn+pG X-Google-Smtp-Source: APXvYqwQ48qRtiK2RON5XQId43FA96hyYW6rs0IfMgkQVI5V0LkDH3RyjFCcTNu8yUaNx7w3GtjLWQ== X-Received: by 2002:a05:600c:2199:: with SMTP id e25mr72471457wme.72.1563992546181; Wed, 24 Jul 2019 11:22:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.25 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:25 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 09/11] gnu: Add r-flowsom. Date: Wed, 24 Jul 2019 20:22:02 +0200 Message-Id: <20190724182204.6818-10-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::336 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-flowsom): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab4d9f4075..dd6570ed17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4930,3 +4930,32 @@ and to both short and long sequence reads.") "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.") (license license:artistic2.0))) ;TODO: artistic1.0 does not exist +(define-public r-flowsom + (package + (name "r-flowsom") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FlowSOM" version)) + (sha256 + (base32 + "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + (properties `((upstream-name . "FlowSOM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-consensusclusterplus" + ,r-consensusclusterplus) + ("r-flowcore" ,r-flowcore) + ("r-flowutils" ,r-flowutils) + ("r-igraph" ,r-igraph) + ("r-tsne" ,r-tsne) + ("r-xml" ,r-xml))) + (home-page "http://www.r-project.org") + (synopsis + "Using self-organizing maps for visualization and interpretation of cytometry data") + (description + "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") + (license license:gpl2+))) + -- 2.21.0 ------------=_1582304884-6704-19-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36799: closed (patches merged) Message-ID: References: <20190724182204.6818-11-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36799 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36799@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:04 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304884-6704-21" This is a multi-part message in MIME format... ------------=_1582304884-6704-21 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 10/11] gnu: Add r-mixomics. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36799@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304884-6704-21 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304884-6704-21 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:50 +0000 Received: from localhost ([127.0.0.1]:37999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLub-0005NC-Os for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:53309) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuI-0005Li-U9 for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41156) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JD-NB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:30 -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 1hqLuG-0007LN-E5 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x444.google.com ([2a00:1450:4864:20::444]:37543) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007KG-7w for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x444.google.com with SMTP id n9so22935346wrr.4 for ; Wed, 24 Jul 2019 11:22:28 -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=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=sha95n4lGaGvY2bGThdgOf385qekX03bv61eBfpv2LEvAVZRVjU63K52ANguH9HtTz 04XNqFy8KXEQX+hDGGtS8ua4fn6ISFhGcSag6a0gUB1k2Lb3BM7oIFshmokDRh7cjiIO 6MVRaWwz/kNYDrDhuABoFnTHbei4fzV8ZRGfEXCsy+QHfmj9xzRfoJ5VzzRn3KZD9BHW Qbci9qgUSjY72Gqp2GxX73Rn+oqAS4bRrwNdUf1jxORL4nqh+2gW8JKKeIvr1JrCjkQX 2yaxMYuWcMc0uTHWVAw97UEKDg5ZxaPGwdIORcK3eU9jrW8UVjh4A3//Vu+i0ywKufQ1 lKpQ== 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=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=NYjBxCF1GICvMFMKa1ZbaSVZqFtFj9hfBXAX5CfTPUYf7cAFMmLkVfwxkYXnM7Xwxq XW7bwhuxaaN7IRgMlutbKFRRLlLhIc9kL0GN2r60hz+SlmbIkzyu705NRl56TCb7Pyct xHzi3MvRoG8j/yQXxM5zUCIqq0hs8SPVh6RkdEPbySU8f75OCh8pa9u99Q/2s50Rc3p3 J3pJhPpoIELMqb0fIHontAAjwMnPzc9horqZeHZrWAI4MtK9Vi16jeo/qAo9Q077B29j QessCVsxH8KbsCUmTjUuzVmrsSzYLbZtFk+vARDF0er86HhogxVgLHz5tI31VYufYvpM U/Fg== X-Gm-Message-State: APjAAAWSKC6b8Y5X4Sv3PJV8B8coepefU4Jc9S0QOePuT8oK244TXUSO hle41XYFNndUCmqG9ZUnDCVfa641 X-Google-Smtp-Source: APXvYqzyl11IBqOyaqgmhhrD+fF562RdIWpPtMnE28DsPNfTMy9rUwVULK1zqzOsXyGJRCib3fIPHg== X-Received: by 2002:adf:ec0f:: with SMTP id x15mr54221988wrn.165.1563992546975; Wed, 24 Jul 2019 11:22:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:26 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 10/11] gnu: Add r-mixomics. Date: Wed, 24 Jul 2019 20:22:03 +0200 Message-Id: <20190724182204.6818-11-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::444 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-mixomics): New variable. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd6570ed17..64625aedd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4959,3 +4959,57 @@ and to both short and long sequence reads.") "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") (license license:gpl2+))) +(define-public r-mixomics + (package + (name "r-mixomics") + (version "6.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mixOmics" version)) + (sha256 + (base32 + "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + (properties `((upstream-name . "mixOmics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-dplyr" ,r-dplyr) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.mixOmics.org") + (synopsis "Omics Data Integration Project") + (description + "Multivariate methods are well suited to large omics data sets where the +number of variables (e.g. genes, proteins, metabolites) is much larger than +the number of samples (patients, cells, mice). They have the appealing +properties of reducing the dimension of the data by using instrumental +variables (components), which are defined as combinations of all variables. +Those components are then used to produce useful graphical outputs that enable +better understanding of the relationships and correlation structures between +the different data sets that are integrated. mixOmics offers a wide range of +multivariate methods for the exploration and integration of biological +datasets with a particular focus on variable selection. The package proposes +several sparse multivariate models we have developed to identify the key +variables that are highly correlated, and/or explain the biological outcome of +interest. The data that can be analysed with mixOmics may come from high +throughput sequencing technologies, such as omics data (transcriptomics, +metabolomics, proteomics, metagenomics etc) but also beyond the realm of +omics (e.g. spectral imaging). The methods implemented in mixOmics can also +handle missing values without having to delete entire rows with missing data. +A non exhaustive list of methods include variants of generalised Canonical +Correlation Analysis, sparse Partial Least Squares and sparse Discriminant +Analysis. Recently we implemented integrative methods to combine multiple +data sets: N-integration with variants of Generalised Canonical Correlation +Analysis and P-integration with variants of multi-group Partial Least +Squares.") + (license license:gpl2+))) -- 2.21.0 ------------=_1582304884-6704-21-- From unknown Mon Aug 18 04:43:12 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#36800: closed (patches merged) Message-ID: References: <20190724182204.6818-12-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 36800 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 36800@debbugs.gnu.org Date: Fri, 21 Feb 2020 17:08:04 +0000 Content-Type: multipart/mixed; boundary="----------=_1582304884-6704-23" This is a multi-part message in MIME format... ------------=_1582304884-6704-23 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #36797: [PATCH 11/11] gnu: Add r-depecher. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 36800@debbugs.gnu.org. --=20 36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D36797 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1582304884-6704-23 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 36797-done) by debbugs.gnu.org; 21 Feb 2020 17:07:52 +0000 Received: from localhost ([127.0.0.1]:47963 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmK-0001jl-0U for submit@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:52 -0500 Received: from mail-qv1-f47.google.com ([209.85.219.47]:32976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BmI-0001jT-Ax for 36797-done@debbugs.gnu.org; Fri, 21 Feb 2020 12:07:50 -0500 Received: by mail-qv1-f47.google.com with SMTP id ek2so1307297qvb.0 for <36797-done@debbugs.gnu.org>; Fri, 21 Feb 2020 09:07:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=Z01QM3huQL9maU2X2ZyEekh9Spe6h2m0PxZhm5NjuB8wMIb4Yi2gbzMHFMwthKoXF4 /1HWoDul5PcvCwKKIdGsLI3YJtJaTB9Pr9ngBQJhEyJruhfE/042gjRVqFeuw4Pghng/ 47CPvu4/jJ3MdBoRE9F5IM9U+hzit22LSONTunmMdsGzqI9zc61qRGKIBVXcDYF7F2qt DAabKhog6GFz/I50mHwRh4WDq/LEH7jDYNuvlEvtt5vp4B9+lJkc27Dtfbaz/44W6hHs VRCV5eQ/z4xPFYrA3qP8863JcNduWzRTHy0EKcaoao8/fO+tOnqtThyaPKqhC8++kiGN 5AUA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=89FU/LZLfY9nYtoc9Xp5IIFzSE8fp03TqDVIpr+1YkE=; b=SepEQHm5QaG2Ym2y6vKSZZliu6ghSR+KFD9aB7jBduDwwndxmCAM3IJ6h/G4WnLBxd r+msMiEXUV+iQNNehTKqkZ3WYc+wt/E8iFHmmeH7MC8VRhhZlmAwsY4DfRO4Iogklw5P DXS6LbuCMAo14pNDBS3i+C7/7y3ZAxnUPRNr1IoLyLGECzXdjH0GixopcZKeS1f93G4n 10e8ItBRcbar4LubWF86ovfLZ1VRQi46bLAL6+DChK6YTDz3a9sIRoEvMhE0Kvyz7plT 1zenVSn2iH1+au6Y9nI3Y0P+bsJInxdySkxItBvVgL6iXYISV3VCtXr02pGf+pxQCDQs IpmQ== X-Gm-Message-State: APjAAAX37rTuJiQ3nxUTmi64jayWynzOed6ye/ZiAgk679Lt8LT6A4Ct 06kVm0XJdtvJm6+ONW2Rjhln2iZFuLB0c3qVJL1xZ/11 X-Google-Smtp-Source: APXvYqzVjAfvguWHSmIcZihj89aJNHlmJ2CHns1pYWbiVmnbLtc50tH9CRCYbwoBvbsODKnoh5LzQJ7sawXm59fonmk= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr31769085qvw.67.1582304864628; Fri, 21 Feb 2020 09:07:44 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 18:07:33 +0100 Message-ID: Subject: patches merged To: 36797-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36797-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Dear, All the patches are merged now; except r-flowpeaks. Because this package use Artistic1.0 which is not enough clear to be considered "free" [1,2] (GNU's point of view [3]) and upstream are not responsive, let clean the bug tracker. :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16 [2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html [3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense All the best, simon ------------=_1582304884-6704-23 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:51 +0000 Received: from localhost ([127.0.0.1]:38001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuc-0005NE-Ch for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:57385) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Lp-5J for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41160) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JI-VI for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:31 -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 1hqLuG-0007Ls-QE for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:46471) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007Kn-JF for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x42e.google.com with SMTP id z1so47975368wru.13 for ; Wed, 24 Jul 2019 11:22:28 -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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=arjY1DZIzQFyagrcaZBJyzZ2T2ROcRfcO6JCf37Y0fghwUjtnc7OdUi8mBBGcf8vOi ZGDuTAgOX2CvpF9UcTW284RetJLpHQ1zXiompK5fWQuW7PmuCatMG1lo9WpjywY/YV5Q EfPTDnZoyzcZkUluAxxn0SKMvzl0Aa5J0sGlMYz8KMKR83H+9HU8DFBRye5YybG6UW2G nzEUl5tfma6hqjPXAz3S6Ekb2A0nBwfOAI9ttyYtxkwh6y68FV7uB8tLmoVRNBI2Q8yb jHlocUl0Mz9XvnrHuFI6ra+sYTU9TbpNMl9LLLiq3DPfu4+f9SzX/cnACGdRTpKjZ2RE hcgw== 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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=Pwlk9A9Gu+hpb4t3Mn4826eHGjShPwrSED0X/aZVCIqSMY5jUHl3atnReblnYK+WKr VTaMic5wdkQ3Xtnxxiv4tXT2c/gSNH3+jV9i8MSeSYWwW3AGP85B965X26ZYkeTJT46t xdrgimk56G7blGSlXXhH937fT/Ciav+QtnONZcQvRM9CcJdbuuq18MZZcLiaWSHrOqT6 7WNM4PREytEV3rGT1gTXZZX2VNDmMahYtpEPWSINa9mXaDUfFC5KFzBLaB/stVo/bVZ/ R7EtXXZ91z8G3+t0poFeOG/Yd0XU6moO54uQ7/hGZc9HWtMZlx8Zudx08tV99tu2e2r2 HCjA== X-Gm-Message-State: APjAAAU1uMGMqkFXk0hGZEcKfoT41oRw8NYO9mICyBdhO1MifSsCqsQ6 WPfY5minMAVBRLzYS4LV8g/qgyvD X-Google-Smtp-Source: APXvYqzOY7O3H+91cgitdfrLSWMNn7eNp4gW4U+Wte0ELZHg89wmje+qFFkYGN0VOfFAZrqCrP8PQQ== X-Received: by 2002:adf:e444:: with SMTP id t4mr84470240wrm.262.1563992547529; Wed, 24 Jul 2019 11:22:27 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:27 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 11/11] gnu: Add r-depecher. Date: Wed, 24 Jul 2019 20:22:04 +0200 Message-Id: <20190724182204.6818-12-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::42e 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-depecher): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64625aedd4..7c9a3b7417 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5013,3 +5013,47 @@ data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.") (license license:gpl2+))) + +(define-public r-depecher + (package + (name "r-depecher") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DepecheR" version)) + (sha256 + (base32 + "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + (properties `((upstream-name . "DepecheR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beanplot" ,r-beanplot) + ("r-biocparallel" ,r-biocparallel) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-mixomics" ,r-mixomics) + ("r-moments" ,r-moments) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2) + ("r-viridis" ,r-viridis))) + (home-page + "https://bioconductor.org/packages/DepecheR") + (synopsis + "Determination of essential phenotypic elements of clusters in high-dimensional entities") + (description + "The purpose of this package is to identify traits in a dataset that can +separate groups. This is done on two levels. First, clustering is performed, +using an implementation of sparse K-means. Secondly, the generated clusters +are used to predict outcomes of groups of individuals based on their +distribution of observations in the different clusters. As certain clusters +with separating information will be identified, and these clusters are defined +by a sparse number of variables, this method can reduce the complexity of +data, to only emphasize the data that actually matters.") + (license license:expat))) -- 2.21.0 ------------=_1582304884-6704-23--