From unknown Tue Jun 24 13:59:08 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#70730] [PATCH] gnu: Add r-memes. Resent-From: nafkhamdc Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 May 2024 09:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 70730 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 70730@debbugs.gnu.org Cc: nafkhamdc X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.171472814016125 (code B ref -1); Fri, 03 May 2024 09:23:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 May 2024 09:22:20 +0000 Received: from localhost ([127.0.0.1]:46289 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2p7T-0004C1-Vz for submit@debbugs.gnu.org; Fri, 03 May 2024 05:22:20 -0400 Received: from lists.gnu.org ([2001:470:142::17]:54120) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2p7Q-0004Bv-NM for submit@debbugs.gnu.org; Fri, 03 May 2024 05:22:19 -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 1s2p6v-0005hH-5f for guix-patches@gnu.org; Fri, 03 May 2024 05:21:45 -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 1s2p6s-00042y-QR for guix-patches@gnu.org; Fri, 03 May 2024 05:21:44 -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=1714728084; x=1716542485; bh=Fbl1On6A3N41dar KqX3IOls24KIOBoC7FrTo2eWP/YI=; b=KiZqBrvscHVzOBVqUyTeFgYLjEmi+zR tBBICto2wBUmppwzUOs/2P9C/OwrNnTbmNsvzs0cdZ6j80UAu7VSlFjX7lJ5hwfd bj7u+01yTOXdjCpYnjALG+nwVfa2W5dIv6tmdZswOUT3nGb3T49M698nDzmvCuaX OCF/UHlxeL3Y= 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 7509530016F for ; Fri, 3 May 2024 11:21:24 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.2.1544.11; Fri, 3 May 2024 11:21:23 +0200 From: nafkhamdc Date: Fri, 3 May 2024 09:19:33 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-AS-Result: No-10--7.008900-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6UEZ1mm50iAbnOjEKYddvv63O2+pOfl+vcwLJ9PZUBQhdvd jZ1tR/4hz0ptPRZypjnk9EII6md85IdGq5XlvEmXUrLQDoO1CVc4bHpbh2+3eH3eGsncjJZ7we4 VjBiLYh0+iqzT7heZRSrO7EhDfsNia+tg/CRYQwrk+QJ4zu017TJ6n7CimhQ1QxtMHgTkdcRcuK 3do5hdrQObIzLs3GAWEgg3cwDHl/2jYFSFiWs3onGDuy8y1qkusB15x1ZALMUfik2cUsCLrnHpf bTiOtIGV6eGIFynDoSnxyAHkRR34HeHWMfhzfSDftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.008900-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-SNTS-SMTP: A6AFBF28FE165CF08621BB920947CFB90050ECE134E504D5FA38876B8FA3B1D12000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-memes): New variable. Change-Id: Ibdf5173d35ef81d27da6831148e66be83f856deb --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fca094977..5029afbefa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2092,6 +2092,53 @@ (define-public r-macrophage in Nature Genetics, January 2018.") (license license:gpl2+))) +(define-public r-memes + (let ((commit "55f0df1fe65c8ead5252542fdc0da0ff2339049e") + (revision "1")) + (package + (name "r-memes") + (version (git-version "1.11.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snystrom/memes") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mp3a610v293prmyid3w1w8fkjkppjnim60h7p9vz2884d0wdvk4")))) + (properties `((upstream-name . "memes"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-cmdfun + r-dplyr + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-magrittr + r-matrixstats + r-patchwork + r-processx + r-purrr + r-readr + r-rlang + r-tibble + r-tidyr + r-universalmotif + r-usethis + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/snystrom/memes") + (synopsis + "Motif matching, comparison, and de novo discovery using the MEME Suite") + (description + "This package facilitates motif analysis using MEME Suite tools. +Memes provides data aware utilities for using GRanges objects as +entrypoints to motifanalysis, data structures for examining & editing +motif lists, and novel data visualizations. Memes functions and data +structures are amenable to both base R and tidyverse workflows.") + (license license:expat)))) + (define-public r-methylclockdata (package (name "r-methylclockdata") base-commit: aa9ac252206615713ab988d7068da9e14a9bccc0 -- 2.34.1 From unknown Tue Jun 24 13:59:08 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: nafkhamdc Subject: bug#70730: closed (gnu: Add r-memes.) Message-ID: References: <87msp3lxqe.fsf@elephly.net> X-Gnu-PR-Message: they-closed 70730 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 70730@debbugs.gnu.org Date: Sun, 05 May 2024 22:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1714946882-30961-1" This is a multi-part message in MIME format... ------------=_1714946882-30961-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #70730: [PATCH] gnu: Add r-memes. 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 70730@debbugs.gnu.org. --=20 70730: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D70730 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1714946882-30961-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 70730-done) by debbugs.gnu.org; 5 May 2024 22:07:28 +0000 Received: from localhost ([127.0.0.1]:33797 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3k12-00082z-Cc for submit@debbugs.gnu.org; Sun, 05 May 2024 18:07:28 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21130) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3k0w-00082s-Pi for 70730-done@debbugs.gnu.org; Sun, 05 May 2024 18:07:26 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1714946815; cv=none; d=zohomail.com; s=zohoarc; b=fdl4UBn0JRfbwgUhakA1blszAjX+xqj7mdk2tBONUto1JIzcHBhLHNXRhEe+5kCtyls2gx2ZZBTKt3physZsRTyc5LRu/Xh+bSrVqsIiliGO3jVsMAWQpua8asEHILdN9bTnpC2qpyaW1MKiCTS4xigxS8pNvIDiEOiFsfqE19E= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1714946815; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=WDqeFZSMU0+bJvMjlESenZtp/wulLHHndTEUwb1B1f8e+mXnBRvvCOd0ONDiyOEQ00ZE5xR0aywRMKhqNXjWayi3lJdpaBEYtaCYRD9CcM0Puv+NU9/DLm9CvNV6vktMBzzZe7aRCVfCjGcptlfDrlYtvkWvvpmcKTfGZGsOUb4= 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=1714946815; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=LEvMzDUlqUaLsNbzNKb7pbf6Cx4FbEOB57U+sdM13yLNSfoJA50sXeVKbV3urNjZ YpgBsZ5zMPU/R3Gpls7l5yN3Gcq54Eluo1921DvHpG1xsbJVV+6THjE6jET9wL8Y8tm KYLuBwNVzNcS2zlqh2xlS0lzkcyFpqTlj2hL/HbA= Received: by mx.zohomail.com with SMTPS id 1714946813414464.0606355481624; Sun, 5 May 2024 15:06:53 -0700 (PDT) From: Ricardo Wurmus To: 70730-done@debbugs.gnu.org Subject: gnu: Add r-memes. User-Agent: mu4e 1.12.4; emacs 29.3 Date: Mon, 06 May 2024 00:06:49 +0200 Message-ID: <87msp3lxqe.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 70730-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 (-) Applied, thank you! -- Ricardo ------------=_1714946882-30961-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 May 2024 09:22:20 +0000 Received: from localhost ([127.0.0.1]:46289 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2p7T-0004C1-Vz for submit@debbugs.gnu.org; Fri, 03 May 2024 05:22:20 -0400 Received: from lists.gnu.org ([2001:470:142::17]:54120) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2p7Q-0004Bv-NM for submit@debbugs.gnu.org; Fri, 03 May 2024 05:22:19 -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 1s2p6v-0005hH-5f for guix-patches@gnu.org; Fri, 03 May 2024 05:21:45 -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 1s2p6s-00042y-QR for guix-patches@gnu.org; Fri, 03 May 2024 05:21:44 -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=1714728084; x=1716542485; bh=Fbl1On6A3N41dar KqX3IOls24KIOBoC7FrTo2eWP/YI=; b=KiZqBrvscHVzOBVqUyTeFgYLjEmi+zR tBBICto2wBUmppwzUOs/2P9C/OwrNnTbmNsvzs0cdZ6j80UAu7VSlFjX7lJ5hwfd bj7u+01yTOXdjCpYnjALG+nwVfa2W5dIv6tmdZswOUT3nGb3T49M698nDzmvCuaX OCF/UHlxeL3Y= 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 7509530016F for ; Fri, 3 May 2024 11:21:24 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.2.1544.11; Fri, 3 May 2024 11:21:23 +0200 From: nafkhamdc To: Subject: [PATCH] gnu: Add r-memes. Date: Fri, 3 May 2024 09:19:33 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-AS-Result: No-10--7.008900-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6UEZ1mm50iAbnOjEKYddvv63O2+pOfl+vcwLJ9PZUBQhdvd jZ1tR/4hz0ptPRZypjnk9EII6md85IdGq5XlvEmXUrLQDoO1CVc4bHpbh2+3eH3eGsncjJZ7we4 VjBiLYh0+iqzT7heZRSrO7EhDfsNia+tg/CRYQwrk+QJ4zu017TJ6n7CimhQ1QxtMHgTkdcRcuK 3do5hdrQObIzLs3GAWEgg3cwDHl/2jYFSFiWs3onGDuy8y1qkusB15x1ZALMUfik2cUsCLrnHpf bTiOtIGV6eGIFynDoSnxyAHkRR34HeHWMfhzfSDftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.008900-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-SNTS-SMTP: A6AFBF28FE165CF08621BB920947CFB90050ECE134E504D5FA38876B8FA3B1D12000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: nafkhamdc 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-memes): New variable. Change-Id: Ibdf5173d35ef81d27da6831148e66be83f856deb --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fca094977..5029afbefa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2092,6 +2092,53 @@ (define-public r-macrophage in Nature Genetics, January 2018.") (license license:gpl2+))) +(define-public r-memes + (let ((commit "55f0df1fe65c8ead5252542fdc0da0ff2339049e") + (revision "1")) + (package + (name "r-memes") + (version (git-version "1.11.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snystrom/memes") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mp3a610v293prmyid3w1w8fkjkppjnim60h7p9vz2884d0wdvk4")))) + (properties `((upstream-name . "memes"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-cmdfun + r-dplyr + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-magrittr + r-matrixstats + r-patchwork + r-processx + r-purrr + r-readr + r-rlang + r-tibble + r-tidyr + r-universalmotif + r-usethis + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/snystrom/memes") + (synopsis + "Motif matching, comparison, and de novo discovery using the MEME Suite") + (description + "This package facilitates motif analysis using MEME Suite tools. +Memes provides data aware utilities for using GRanges objects as +entrypoints to motifanalysis, data structures for examining & editing +motif lists, and novel data visualizations. Memes functions and data +structures are amenable to both base R and tidyverse workflows.") + (license license:expat)))) + (define-public r-methylclockdata (package (name "r-methylclockdata") base-commit: aa9ac252206615713ab988d7068da9e14a9bccc0 -- 2.34.1 ------------=_1714946882-30961-1--