From unknown Fri Jun 20 07:12:16 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#63803 <63803@debbugs.gnu.org> To: bug#63803 <63803@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-mbecs. Reply-To: bug#63803 <63803@debbugs.gnu.org> Date: Fri, 20 Jun 2025 14:12:16 +0000 retitle 63803 [PATCH] gnu: Add r-mbecs. reassign 63803 guix-patches submitter 63803 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 63803 normal tag 63803 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue May 30 09:38:41 2023 Received: (at submit) by debbugs.gnu.org; 30 May 2023 13:38:41 +0000 Received: from localhost ([127.0.0.1]:60501 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q3zYe-0007AS-N8 for submit@debbugs.gnu.org; Tue, 30 May 2023 09:38:41 -0400 Received: from lists.gnu.org ([209.51.188.17]:42530) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q3zYc-0007AC-6c for submit@debbugs.gnu.org; Tue, 30 May 2023 09:38:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q3zYO-0003eF-Mv for guix-patches@gnu.org; Tue, 30 May 2023 09:38:26 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q3zYL-0005Zi-TQ for guix-patches@gnu.org; Tue, 30 May 2023 09:38:24 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1685453882; x=1687268283; bh=GASCs8m39SnN1/H C3+qgZZ8yYW+xriJx/bLoUdKY7TY=; b=lX3nxrcPbIyVgnl1egtq9SZ7uHzLuF+ 1kWkKQv+Obx7kNB0n+dCsivi9OW1oE3nyHBhOW6Lcnv2m+rTTJlCdB9HbZQuGc2n QGO/hR8fC0ztuO0V5wBxNUX3JV/xaaFN6gFekzkB6Jr6PoqDKomHW1NOwO44wOch wYTR5zpB3Cac= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 817E230018D for ; Tue, 30 May 2023 15:38:02 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Tue, 30 May 2023 15:38:01 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-mbecs. Date: Tue, 30 May 2023 15:37:50 +0200 Message-ID: X-Mailer: git-send-email 2.40.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27660.007 X-TM-AS-Result: No-10--8.544700-5.000000 X-TMASE-MatchedRID: LWf8uVYp427/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEN+a z/Eyz14URRa406V/YwyBUGewL2YXt0fr6WG4Th9aDDzmS9l9fYoXivwflisSrMIubEPSkNnJwtU WziB5M+5BqOVCqBA4MbNcoBDf0EjVRnwNpu3iDO4IEFbf6bO4WheN9Hd3TB5GbX86JY8z1zvzwI gLJMuJGOOiItOm8H/EdkF/vvQ1KEkLDDuhlfYt1OOnF2j8nBWbv5r6/gUXfW5TvZg4AwMmOJ4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyBU9TwbPjFWN8lP6F/raTZjDXppATdWjcs5LQz9vqPhQadbH V44otFHdI4YcM75JnXT6MtOX0lpXvuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.544700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27660.007 X-TM-SNTS-SMTP: DC60DEA9FF9B6D2D983982729AFB3796B53B53090C1EF2D49FAFD261387DACC32002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-mbecs): New variable. --- gnu/packages/bioconductor.scm | 51 +++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 265a70cdd4..b75b9f1886 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10118,6 +10118,57 @@ (define-public r-ripseeker processing to visualization and annotation.") (license license:gpl2))) +(define-public r-mbecs + (package + (name "r-mbecs") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MBECS" version)) + (sha256 + (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz")))) + (properties `((upstream-name . "MBECS"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + ;; Fontconfig needs an writable cache + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-cluster + r-dplyr + r-ggplot2 + r-gridextra + r-limma + r-lme4 + r-lmertest + r-magrittr + r-markdown + r-matrix + r-pheatmap + r-phyloseq + r-rmarkdown + r-ruv + r-sva + r-tibble + r-tidyr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/rmolbrich/MBECS") + (synopsis + "Evaluation and correction of batch effects in microbiome data-sets") + (description + "The @acronym{MBECS, Microbiome Batch Effect Correction Suite} provides a +set of functions to evaluate and mitigate unwated noise due to processing in +batches. To that end it incorporates a host of batch correcting algorithms +(BECA) from various packages. In addition it offers a correction and reporting +pipeline that provides a preliminary look at the characteristics of a data-set +before and after correcting for batch effects.") + (license license:artistic2.0))) + (define-public r-mbkmeans (package (name "r-mbkmeans") base-commit: 3807876af4b53babdbc2f1d730e4763ff651f316 -- 2.40.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 01 03:21:58 2023 Received: (at 63803-done) by debbugs.gnu.org; 1 Jun 2023 07:21:58 +0000 Received: from localhost ([127.0.0.1]:36777 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q4cdC-0006Nt-BA for submit@debbugs.gnu.org; Thu, 01 Jun 2023 03:21:58 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21066) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q4cd6-0006Nf-71 for 63803-done@debbugs.gnu.org; Thu, 01 Jun 2023 03:21:56 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1685604108; cv=none; d=zohomail.com; s=zohoarc; b=kKk5eFaV0/FdqJVl/Ppfbuli6/Psq/e40qrv0EkjAjLYo0g5pc0w8O4YSaFyF8elxQKsHJ1nV073oat4/InbZ8GUpkTl1K12JsR4wa43E97Jy6fPEVjAvKrtkWbwY4XP4huyyix6vjlqK6fArMSne8lHf0oa6ItZRYyBkrOUwsI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1685604108; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=RA2Yxo4nd6uXY9Mm1pES+sTL+0GkQcfLyUU4M1hnMb0=; b=UGjlGMc06EWGbKs1Zyf2aovvrM8p/c633DZ94+vexQ3F5tKTcRT/KPcJBD473y0eB0u15Hb73s+iA6S8GE8dBiusHqtgeqZMyZ0Hg7ahdSyqaOjqVTKZ+2r0hcHMzFiFzgBUV0vnzlP6SbPGiXSZu3iCEDT/D5gdXXZa8WPsblg= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1685604108; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=RA2Yxo4nd6uXY9Mm1pES+sTL+0GkQcfLyUU4M1hnMb0=; b=ipQVgshxR0T4YEQeKjMsVL/4+mq9UbfoMbi05rNB6NSp10n/5jQLuNXfbGoNPmpL ySmSNGsjVJW+yKFrIX2/voOBo+O77oxuglEJiBzWTQSPD9MniBy5MP1LtWNySYn55Bs R/7qSiQFT1gmI4/BivPQpre0ECh0zBW67enQAiLg= Received: from localhost (78-108-142-46.pool.kielnet.net [46.142.108.78]) by mx.zohomail.com with SMTPS id 1685604107668286.2972624880282; Thu, 1 Jun 2023 00:21:47 -0700 (PDT) References: User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#63803] [PATCH] gnu: Add r-mbecs. Date: Thu, 01 Jun 2023 09:18:22 +0200 In-reply-to: Message-ID: <87a5xjtzp3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 63803-done Cc: 63803-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioconductor.scm (r-mbecs): New variable. Applied, thanks! --=20 Ricardo From unknown Fri Jun 20 07:12:16 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 29 Jun 2023 11:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator