From patchwork Mon Nov 13 12:34:43 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 56407 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6784F27BBE9; Mon, 13 Nov 2023 12:36:58 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3E2AE27BBE2 for ; Mon, 13 Nov 2023 12:36:53 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1r2WB7-0003lr-Qi; Mon, 13 Nov 2023 07:36:33 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1r2WAw-0003ii-9o for guix-patches@gnu.org; Mon, 13 Nov 2023 07:36:24 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1r2WAv-0002cm-KD for guix-patches@gnu.org; Mon, 13 Nov 2023 07:36:21 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1r2WBa-0003Cz-QR for guix-patches@gnu.org; Mon, 13 Nov 2023 07:37:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#67147] [PATCH 1/2] gnu: Add r-illuminahumanmethylationepicmanifest. Resent-From: nafkhamdc Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 13 Nov 2023 12:37:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 67147 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 67147@debbugs.gnu.org Cc: nafkhamdc X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169987896312243 (code B ref -1); Mon, 13 Nov 2023 12:37:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Nov 2023 12:36:03 +0000 Received: from localhost ([127.0.0.1]:57625 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r2WAd-0003BP-7Y for submit@debbugs.gnu.org; Mon, 13 Nov 2023 07:36:03 -0500 Received: from lists.gnu.org ([2001:470:142::17]:50414) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r2WAa-0003At-1y for submit@debbugs.gnu.org; Mon, 13 Nov 2023 07:36:01 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1r2W9o-0003OZ-Ob for guix-patches@gnu.org; Mon, 13 Nov 2023 07:35:13 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1r2W9m-00024X-Aw for guix-patches@gnu.org; Mon, 13 Nov 2023 07:35:12 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1699878891; x=1701693292; bh=0wRq6x5x78whZEK oTYnpbjp3ha/JNUGnDaU08SY8SJ4=; b=dLMPHgD4rUT9bZUM+dkSJJbpa6rjcGM 67P1dZB93wUyzYsgB8EqA5pqlBopJh1AW8PodvXHu0WT80Cjg5S9Stsbjza4zwyA YAKOqgb5ISQh/bEqFrriV/pvN4FFgP419MBH2sq1iMG9TZyDHDLiBPxjVJatJzP4 fqRbAxVTJKG8= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4AC1116011B for ; Mon, 13 Nov 2023 13:34:51 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Mon, 13 Nov 2023 13:34:50 +0100 From: nafkhamdc Date: Mon, 13 Nov 2023 12:34:43 +0000 Message-ID: <2242fe308a88534c92a63bfc7b193ecdaa20983b.1699878884.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX6.mdc-berlin.net (141.80.113.56) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27994.007 X-TM-AS-Result: No-10--6.689700-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2t6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/o5C9bTTxaUYue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedJEb gebEoSmWnce8Faqbp2S+qB4NDWY7MgNVHXM3C8e7jpxdo/JwVm27/cF+aeNZMD2veI3/hwm9KfR F/WYdhbn0tCKdnhB589yM15V5aWpj6C0ePs7A07YFInLyeDAoZFpqkt0WBwsYaugN2C+pKCP9j4 nnU0KXNAak+2SD9lzKqt9XhIBwD/g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.689700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27994.007 X-TM-SNTS-SMTP: 23DB2EE8F8DB9D4E3E0D8BCAEACBD834ED4E0DC9A9055A27019382323BBA1FC92000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable. Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686 --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) base-commit: 77386bdbfe6b0c649c05ab37f08051d1ab3e5074 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7feea35d74..b99a343dbc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15657,6 +15657,38 @@ (define-public r-giotto spatial single-cell expression data.") (license license:expat)))) +(define-public r-illuminahumanmethylationepicmanifest + (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3") + (revision "1")) + (package + (name "r-illuminahumanmethylationepicmanifest") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) + (build-system r-build-system) + (home-page + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest") + (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi") + (description + "It's a drop-in replacement for the @code{IlluminaHumanMethylationEPIC} package. +It utilizes a Manifest based on 1.0B5 annotation. As of version 0.3.0, +the @code{IlluminaHumanMethylationEPIC} package by Author: Kasper Daniel +Hansen [cre, aut] still employs the 1.0B2 annotation manifest. A corresponding +annotation package, @code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, +is available to ensure proper annotation. The decision to maintain the same +name is due to complications in downstream processing caused by array name +lookup in certain preprocessing options.") + (license license:artistic2.0)))) + (define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38 (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a") (revision "1")) From patchwork Mon Nov 13 12:34:44 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 56406 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id AB3D027BBE9; Mon, 13 Nov 2023 12:36:45 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,TVD_SPACE_RATIO, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 79BA627BBE2 for ; Mon, 13 Nov 2023 12:36:41 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1r2WB5-0003jS-Ob; Mon, 13 Nov 2023 07:36:31 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1r2WAx-0003ij-Dk for guix-patches@gnu.org; Mon, 13 Nov 2023 07:36:24 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1r2WAw-0002cq-7D for guix-patches@gnu.org; Mon, 13 Nov 2023 07:36:23 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1r2WBb-0003DE-MV for guix-patches@gnu.org; Mon, 13 Nov 2023 07:37:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#67148] [PATCH 2/2] gnu: Remove r-illuminahumanmethylationepicmanifest. 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Change-Id: I59962a34eaecd53125ccf0cfd65286b7d52c6cce --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 754ba98afc..08b84c644e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1317,9 +1317,9 @@ (define-public r-fdb-infiniummethylation-hg19 annotations.") (license license:artistic2.0))) -(define-public r-illuminahumanmethylationepicmanifest +(define-public r-illuminahumanmethylationepicmanifest-old (package - (name "r-illuminahumanmethylationepicmanifest") + (name "r-illuminahumanmethylationepicmanifest-old") (version "0.3.0") (source (origin (method url-fetch)