From unknown Sat Jun 14 18:38:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#58523] [PATCH] gnu: Add r-macrophage. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 17:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 58523 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58523@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.16657684727502 (code B ref -1); Fri, 14 Oct 2022 17:28:02 +0000 Received: (at submit) by debbugs.gnu.org; 14 Oct 2022 17:27:52 +0000 Received: from localhost ([127.0.0.1]:38512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojOTP-0001wv-NX for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:27:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:44256) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojOTO-0001wo-1J for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:27:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38150) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojOTN-0000tp-Q9 for guix-patches@gnu.org; Fri, 14 Oct 2022 13:27:49 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:48729) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojOTK-0006gi-V3 for guix-patches@gnu.org; Fri, 14 Oct 2022 13:27:48 -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=1665768459; x=1667582860; bh=ZQMO4tuUUIz3JlU KXfBPlgm/LwvY7rvDUCNF5Jrsk10=; b=KyBpOOhb7Jiic24ArZ/MxsO+LaS3857 GP9enAsl7kUxBkk1Jgntsjgsl//IgrvwNVMS2ilmvs2WfoCjq3Y55tMq8upeyuWf b0yRtt1c/JcFqBbByE+PC7hIMTIOyO62lJcmMOh5b14nKjbQ6qWxLusxfKp73pTA e/YTrd2Qd/10= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 04BDD1603E3 for ; Fri, 14 Oct 2022 19:27:38 +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 15.1.2507.12; Fri, 14 Oct 2022 19:27:38 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 14 Oct 2022 19:27:28 +0200 Message-ID: <20221014172728.3982-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-AS-Result: No-10--7.995100-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiKaVzGETDUtnArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFDnl0XDEnyb7ruNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtII8At8YCVVsfqbs +nJ/tFJER2mYLPjXkrmZw9r+P6lFy3SWdjqTh/wrGL//8mlodA27/cF+aeNZMU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8gVPU8Gz4xVjfJT+hf62k2Yw16aQE3Vo3KQDSPaIxCrZHRJq eoBGlaoLhGCx+H8KTXmgf/twp+vCOulxyHOcPoH X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.995100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-SNTS-SMTP: DA85BDBEC03E439E0385DAA56B1469839738E3205E97C5FB8BC9F5C7190C663D2002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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 (--) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioconductor.scm (r-macrophage): 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 ecb60f2e24..3692bb94af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1384,6 +1384,29 @@ (define-public r-genomationdata downloaded from Encode.") (license license:gpl3+))) +(define-public r-macrophage + (package + (name "r-macrophage") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "macrophage" version + 'experiment)) + (sha256 + (base32 + "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms")))) + (properties `((upstream-name . "macrophage"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/macrophage") + (synopsis "Human macrophage immune response data") + (description + "This package provides the output of running @code{Salmon} on a set of 24 +RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and +gene expression indicate a role for enhancer priming in immune response\", published +in Nature Genetics, January 2018.") + (license license:gpl2+))) + (define-public r-msdata (package (name "r-msdata") base-commit: 10d429f2fce321d8285684503094694ec3979865 -- 2.37.3 From unknown Sat Jun 14 18:38:28 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: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#58523: closed (Re: [bug#58523] [PATCH] gnu: Add r-macrophage.) Message-ID: References: <875ygkg4s2.fsf@elephly.net> <20221014172728.3982-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 58523 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 58523@debbugs.gnu.org Date: Sat, 15 Oct 2022 21:24:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1665869042-30240-1" This is a multi-part message in MIME format... ------------=_1665869042-30240-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #58523: [PATCH] gnu: Add r-macrophage. 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 58523@debbugs.gnu.org. --=20 58523: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D58523 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1665869042-30240-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 58523-done) by debbugs.gnu.org; 15 Oct 2022 21:23:37 +0000 Received: from localhost ([127.0.0.1]:42706 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojod6-0007r1-SB for submit@debbugs.gnu.org; Sat, 15 Oct 2022 17:23:37 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojod4-0007qm-47 for 58523-done@debbugs.gnu.org; Sat, 15 Oct 2022 17:23:34 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1665869010; cv=none; d=zohomail.com; s=zohoarc; b=AEimfh5/lRV82clKxieFxM02IDl6b//DnYy+yc6VsGiO9QJ2FR1ZN6pp5mwYP0Ze92Mzx6XFSrY7pjMnGQFPf+y9EE3JZlBVwcOXYWR0WmJ0QzOWolfWlIDTJMzq6EgSc2S5xa8c2l9sl1KbOKyWm2Crirl8WSySXLU7Zz/gw3U= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1665869010; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=6W/UtDVzY54oX65/FZNczOdbN2yO1gNeuZUXajywqH4=; b=Ju95EqBP10mh/hILXGRcHq+hfuEBFDbwDFMHNo1DeiNzj9PVsoD0b55ujWT1nwrkr8ibbfEmUCg8ARp/m1iyyGZoLYpwEjO6nszU0ssYyHeZVrxEs9W9C2mMVVPGJoQPIL4G6ZvBr/or0iLc5z+f8PIRGg9zv9PVmSchTMbDBCs= 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=1665869010; 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=6W/UtDVzY54oX65/FZNczOdbN2yO1gNeuZUXajywqH4=; b=JFkA4NLsz49LcX0cu+mz0Dgl77sW+DLTGSFProdaNa5TgM5SYJa3xYXs8C/xUkjb Pnzc5YrVYqota5/aZR8RW4X1dMoioT1f5UlHJLIA1uLacCcQle3EYnq7K5WysKtxD/8 ouUue/AcNyjYW6wFWhtVcnETvtdBXafvYmfTFzsU= Received: from localhost (73-110-142-46.pool.kielnet.net [46.142.110.73]) by mx.zohomail.com with SMTPS id 1665869008265569.232323655022; Sat, 15 Oct 2022 14:23:28 -0700 (PDT) References: <20221014172728.3982-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#58523] [PATCH] gnu: Add r-macrophage. Date: Sat, 15 Oct 2022 23:23:07 +0200 In-reply-to: <20221014172728.3982-1-madalinionel.patrascu@mdc-berlin.de> 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 Message-ID: <875ygkg4s2.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: 58523-done Cc: 58523-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: > X-Debbugs-Cc: rekado@elephly.net > > * gnu/packages/bioconductor.scm (r-macrophage): New variable. Applied, thanks! --=20 Ricardo ------------=_1665869042-30240-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 14 Oct 2022 17:27:52 +0000 Received: from localhost ([127.0.0.1]:38512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojOTP-0001wv-NX for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:27:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:44256) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojOTO-0001wo-1J for submit@debbugs.gnu.org; Fri, 14 Oct 2022 13:27:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38150) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojOTN-0000tp-Q9 for guix-patches@gnu.org; Fri, 14 Oct 2022 13:27:49 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:48729) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojOTK-0006gi-V3 for guix-patches@gnu.org; Fri, 14 Oct 2022 13:27:48 -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=1665768459; x=1667582860; bh=ZQMO4tuUUIz3JlU KXfBPlgm/LwvY7rvDUCNF5Jrsk10=; b=KyBpOOhb7Jiic24ArZ/MxsO+LaS3857 GP9enAsl7kUxBkk1Jgntsjgsl//IgrvwNVMS2ilmvs2WfoCjq3Y55tMq8upeyuWf b0yRtt1c/JcFqBbByE+PC7hIMTIOyO62lJcmMOh5b14nKjbQ6qWxLusxfKp73pTA e/YTrd2Qd/10= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 04BDD1603E3 for ; Fri, 14 Oct 2022 19:27:38 +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 15.1.2507.12; Fri, 14 Oct 2022 19:27:38 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-macrophage. Date: Fri, 14 Oct 2022 19:27:28 +0200 Message-ID: <20221014172728.3982-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-AS-Result: No-10--7.995100-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiKaVzGETDUtnArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFDnl0XDEnyb7ruNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtII8At8YCVVsfqbs +nJ/tFJER2mYLPjXkrmZw9r+P6lFy3SWdjqTh/wrGL//8mlodA27/cF+aeNZMU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8gVPU8Gz4xVjfJT+hf62k2Yw16aQE3Vo3KQDSPaIxCrZHRJq eoBGlaoLhGCx+H8KTXmgf/twp+vCOulxyHOcPoH X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.995100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.001 X-TM-SNTS-SMTP: DA85BDBEC03E439E0385DAA56B1469839738E3205E97C5FB8BC9F5C7190C663D2002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@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 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 (--) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioconductor.scm (r-macrophage): 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 ecb60f2e24..3692bb94af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1384,6 +1384,29 @@ (define-public r-genomationdata downloaded from Encode.") (license license:gpl3+))) +(define-public r-macrophage + (package + (name "r-macrophage") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "macrophage" version + 'experiment)) + (sha256 + (base32 + "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms")))) + (properties `((upstream-name . "macrophage"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/macrophage") + (synopsis "Human macrophage immune response data") + (description + "This package provides the output of running @code{Salmon} on a set of 24 +RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and +gene expression indicate a role for enhancer priming in immune response\", published +in Nature Genetics, January 2018.") + (license license:gpl2+))) + (define-public r-msdata (package (name "r-msdata") base-commit: 10d429f2fce321d8285684503094694ec3979865 -- 2.37.3 ------------=_1665869042-30240-1--